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5-HTTLPR
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Coriell Personalized Medicine Collaborative
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Doi:10.1186/1471-2156-10-88
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(hide) 5-HTTLPR
long form of 5-HTTLPR. less sensitive to pain 23andMe reports that this genotype is not reliable on their platform. 23andMe users should ignore this result. happier, less sensitive to pain You consider perpetrating unintentional harm as more acceptable The genotype of this SNP is not meaningful on 23andme v3. *https://www.23andme.com/you/community/thread/6192/
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According to David Hinds of 23andMe on community forums, 'nearly everyone (99.97%) is getting called as CC, and there is no clear heterozygote cluster' ... 'the genotype calls for rs25531 on our platform are not meaningful.' Looking at OpenSNP frequency data, this seems to be universal for direct to consumer genotyping services at this stage. The minor allele (G) of rs25531 is almost always in phase with the long (L) allele of the 5-HTTLPR, which is the most commonly studied variation in this region. The (L) long allele may be associated with lower levels of serotonin. The article and video from 'The Atlantic' suggests that children with the short allele (A), may need and benefit greatly from more maternal support *http://www.theatlantic.com/doc/200912/dobbs-orchid-gene In contrast to earl...
Magnitude: 2
You have two long form 5-HTTLPR.
You likely have two long-form 5-HTTLPR (serotonin-transporter-linked polymorphic region). Variations in the region have been extensively investigated in connection with neuropsychiatric disorders. Identification of tag haplotypes for 5HTTLPR for different genome-wide SNP platforms
maybe: higher scores on anxiety-related personality traits; greater placebo response One study of (only) 25 people shows this genotype was a significant predictor of clinical placebo response, being associated with greater improvement in anxiety symptoms. A criticism of this study has also been published, and it has not been replicated since the original publication years ago. This SNP has been linked to several psychiatric and/or behavioral phenomena, including: *higher scores on anxiety-related personality traits *obsessive compulsive disorder *panic disorder with a possible gender-dependent effect
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rs4570625, also known as G-703T, is a SNP in the tryptophan hydroxylase 2 TPH2 gene. This SNP has been linked to several psychiatric and/or behavioural phenomena, including: * rs4570625 and rs4565946 linked to the pathogenesis of early-onset obsessive compulsive disorder * rs4570625 and rs11178997 in TPH2's regulatory region display preferential transmission * rs4570625(G;G) homozygosity was a significant predictor of clinical placebo response, being associated with greater improvement in anxiety symptoms. g2b2mh is rs4570625(G;G) is a significant predictor of clinical placebo response? maybe not panic disorder with a possible gender-dependent effect Transmission disequilibrium of polymorphic variants in the tryptophan hydroxylase-2 gene in attention-deficit/hyperactivity disorder. Associa...
Frequency: 17.9%
References:1
References:1
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Based on with 2823 samples a haplotype of A+A in rs2129785+rs11867581 predicts short allele of 5-HTTLPR with good accuracy. Haplotype G+G has not been generally observed, so phase can always be determined. The only possible haplotypes are thus A+A short 91% of the time, A+G long 96% of the time and G+A always long. uses regression model over eight SNP's available on Illumina microarray with higher expected accuracy.
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Based on with 2823 samples a haplotype of A+A in rs2129785+rs11867581 predicts short allele of 5-HTTLPR with good accuracy. Haplotype G+G has not been generally observed, so phase can always be determined. The only possible haplotypes are thus A+A short 91% of the time, A+G long 96% of the time and G+A always long. uses regression model over eight SNP's available on Illumina microarray with higher expected accuracy.
may be part of a haplotype associated with OCD
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rs25532 is a SNP in a regulatory region upstream of the serotonin transporter SLC6A4 gene. The more common allele, rs25532(C), is the higher-expressing allele. A study of patients with obsessive compulsive disorder (OCD) concluded that the major allele of rs25532 was a major contributor to the association of a corresponding haplotype with this disorder. [PharmGKB:Curated This study found that the minor allele of the functional C > T single nucleotide polymorphism, rs25532, located less than 150 nucleotides centromeric of the serotonin transporter-linked polymorphic region indel (known as 5-HTTLPR) significantly decreased luciferase reporter gene expression levels by 15-80%, depending on 5-HTTLPR allele background and cell type.]
1 genoset 5 snps
(hide) African American
Normal (lower) risk of Type 2 Diabetes and Gestational Diabetes. Normal insulin secretion in the pancreas. This has been confirmed in most races.
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This SNP in TCF7L2 influences the risk of Type-2 diabetes (T2D). This SNP is also known as IVS3C>T. rs7903146(C;T) rs7903146(T;T) strongly predicted future type-2 diabetes. Considered in context with rs7903146 rs12255372 rs10885406. Note: this is one of two SNPs within the TCF7L2 gene that have been reported to be associated with type-2 diabetes, the other being rs4506565. They have approximately equal power to estimate risk for type-2 diabetes, and the results from one correlate 92% of the time with the other. Full text of the paper is available from from Plos Medicine. Or from NCBI as . TCF7L2 polymorphisms and progression to diabetes in the Diabetes Prevention Program. reconfirmed in a diverse population Associated in a study of ~1000 Hispanic-Americans with reduced insulin secretion...
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In 'Association of the ADRA2A polymorphisms with the risk of type 2 diabetes: a meta-analysis.' a meta-analysis of publications prior to September 2012 showed no overall association between rs553668 and T2D risk, but did find an association with very high (poor) P-value for Europeans under recessive gene model (GT=AA, OR=1.36, p=0.02, 95% CI: 1.05, 1.76). In 'Genetic association of adrenergic receptor alpha 2A with obesity and type 2 diabetes.' rs553668 was found to correlate with obesity in Swedish population, but not significantly for BMI-corrected T2D risk. ADRA2A is involved in sympathetic nervous system's inhibition of insulin secretion and lipolysis, so direct effect on T2D is usually sought, but the Swedish study suggest it could work through body mass. It also mentions that rs55366...
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A study of 10572 African American and Hispanic American subjects linking genetics, magnesium intake and ethnicity Genetic Variations in Magnesium-Related Ion Channels May Affect Diabetes Risk among African American and Hispanic American Women suggests a link (OR = 0.84, false discovery rate (FDR)-adjusted P = 0.02) between rs6584273 in CNNM1 and T2D risk in African American women. Association between in vivo alcohol metabolism and genetic variation in pathways that metabolize the carbon skeleton of ethanol and NADH reoxidation in the Alcohol Challenge Twin Study
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This is a triallelic SNP - note that the sidebar (currently) only shows 3 of the 6 possible genotypes. ====CRP==== claims that this SNP does not affect the serum concentration of CRP, while older resources seem to disagree. However, they do report an association between CRP levels and risk of abdominal aortic aneurysm (AAA). rs3091244 serum CRP level and cardiovascular risk in the NHLBI Family Heart Study. the AA genotype of the triallelic SNP rs3091244 in the gene C-reactive protein was associated with prevalent coronary heart disease in the non-Hispanic white population Association study of CRP gene polymorphisms with serum CRP level and cardiovascular risk in the NHLBI Family Heart Study. rs3093059 rs3091244 Weaker linkage disequilibrium in this region in African Americans allows the co...
common one paper reports increased risk of alcoholism for African-Americans with this genotype.
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This paper found significant association with rs2066702, the SNP that defines ADH1B*3, in African American families. Association was strongest with the ICD-10 definitions of alcoholism, with P=0.046 for PDTsum and 0.029 for PDTaverage; it was also significant for DSM-IV for PDTaverage (P=0.039). The high-risk allele was the C that encodes ADH1B*1, and the low-risk allele encodes ADH1B*3. A review of the (at times conflicting) findings regarding ADH1B genotypes and maternal and fetal alcohol syndromes is available.In some African American] and Native American populations, the ADH1B*3 allele (Arg369Cys in exon 9) is correlated with protection against alcoholism. [PharmGKB:In-Depth This allele has been found in some African American and Native American populations to be correlated with prote...
5 snps
(hide) Ageing
common but 10x higher glaucoma risk in most (but not all) populations This genotype is found in 2 out of 3 people, but has been repeatedly linked to a much higher risk of glaucoma. However a 2010 paper in a south african population reports reduced risk, casting some doubts.
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rs3825942, also known as G153D, a SNP causing an amino acid change in the lysyl oxidase 1 LOXL1 gene, has been linked to exfoliation glaucoma (also known as exfoliation syndrome). This form of glaucoma causes up to 10% of the cases of blindness in many countries, including the US. From the abstract of this study: 'Approximately 25% of the general population is homozygous for the highest risk haplotype [C;C here combined with other risk SNPs] and their risk of suffering XFG (exfoliation glaucoma) is over 100 times that of those only carrying low-risk haplotypes.' The risk allele for this SNP is rs3825942(C), as oriented with respect to the dbSNP entry, and it confers a estimated relative risk (by itself) of 27 compared to the (T) allele. The odds ratio is 20.10 (CI 10.80-37.41). [Note that ...
Avg. fasting Plasma Glucose 5.18 mmol/L (93 mg/dl). Slightly higher blood glucose. Fasting Plasma Glucose is the amount of sugar in your blood when you wake up. It's required to power your body, but too much is very bad for you. Fasting plasma glucose between 5.6 mmol/L and 6.9 mmol/L (101 – 125 mg/dl) is considered pre-diabetes. Fasting plasma glucose higher than 7 mmol/L (126 mg/dl) is considered diabetes.
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rs560887, p = 4 x 10(-7)) *654 normoglycemic subjects, replicated in 9,353 subjects *fasting plasma glucose (FPG) (beta = -0.06 mmol/l per A-allele, combined p = 4 x 10(-23)) and with pancreatic beta-cell function (Homa-B model, combined p = 3 x 10(-13)) in three populations; however it was not associated with type 2 diabetes risk. (ageing) Blood Glucose [PharmGKB:Non-Curated Phenotype 1: In a meta-analysis of 21 GWAS cohorts followed by analysis in additional individuals, this SNP was found to be associated with fasting glucose level. Study size: 119,169. Significance metric(s): p = 8.7 x 10(-218). Phenotype 2: In the same study, this SNP was found to be associated with HOMA-B (homeostasis model assessment of beta-cell function). Study size: 94,839. Significance metric(s): p = 1.5 x 10(-...
Slightly increased lifespan?
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This SNP, a variant in the TP53 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the G allele encodes an arginine at position 72 of the protein (where there's normally a proline), and the SNP is commonly called the Arg72 variant, although P72R and Arg72Pro are also common in the literature. Minor allele homozygotes, i.e. rs1042522(C;C) genotypes, live on average 3 years longer than major allele (G;G) homozygotes, based on a study of 9,200+ Danish individuals. The increased longevity is speculated to be related to the i...
Less mental decline with age. One copy of the good version of the SIRT1 longevity gene. This is believed to slow the aging of the brain, and perhaps to increase longevity.
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rs3758391, a SNP in the SIRT1 gene, has been reported to potentially have some role in either longevity, or with higher statistical significance, better cognitive function in older individuals. SIRT1 is thought to regulate neuronal metabolism and survival in response to stress, and the equivalent gene in other species influences maximal life span. The study reporting improved cognition for carriers of rs3758391(T) alleles was based on over 1,000 Finnish adults over the age of 85, and a weak trend towards lower cardiovascular disease was also reported for this allele.
Faster aging. Increased risk for Dementia. Less good cholesterol. This reduces HDL ('good') cholesterol. HDL cholesterol removes cholesterol from artery walls and improves health. This SNP seems to be associated with higher blood pressure, less longevity, and more diseases of aging, in particular memory decline and dementia, and lower odds of living to 100, especially in Ashkenazi Jews. Attempting to raise HDL cholesterol may (or may not) be useful to mitigate the effects of this SNP.
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This SNP rs5882 in the CETP gene referred to as ILE405VAL and RSAI405V has been related to ageing and exceptional long life. A study in Ashkenazi Jews showed that individuals homozygotic for the G allele have significantly longer lifespans. New research also indicates that G homozygotes have an average of 70% less risk of dementia and Alzheimer's disease. The study also found that heterozygotes have a lower risk of dementia and Alzheimer's disease but more study is needed to determine the risk reduction for heterozygotes. See Association of a Functional Polymorphism in the Cholesteryl Ester Transfer Protein (CETP) Gene With Memory Decline and Incidence of Dementia and CETP Variant Linked to Slower Cognitive Decline and Reduced Dementia Risk . [PharmGKB:Curated Risk or phenotype-associated...
Women have lower risk of Endometriosis but normal risk for Endometrial Cancer, and more cognitive impairment with age. Men have zero risk, but can pass this on to their daughters. This is the normal version of Estrogen Receptor 1 (alpha). It has more cognitive decline than the rare version, with old women only remembering half as much details on the East Boston Memory Test immediate recall test.
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rs9340799 is a SNP in the estrogen alpha receptor ESR1 gene, and it is also known as the -351A>G variant. Among women, rs8179176, rs9340799, rs1256065, and rs1256030 were associated with likelihood of developing cognitive impairment with ageing. In men, rs728524, rs1255998, and rs1256030 were associated with cognitive impairment. A study of 6,200+ Dutch individuals did not replicate previously reported associations between this SNP (rs9340799) and risk of ischemic stroke. A study of 702 cases with invasive endometrial cancer concluded that the less common alleles of SNP rs9340799 lowered risk for the disease. The odds ratio was 0.75 (CI: 0.60-0.93) for (A;G) and 0.53 (CI: 0.37-0.77) for (G;G) compared to rs9340799(A;A) individuals. Endometriosis Uterine Fibroids [PharmGKB:Curated SNP i...
Normal (lower) risk of Type 2 Diabetes and Gestational Diabetes. Normal insulin secretion in the pancreas. This has been confirmed in most races.
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This SNP in TCF7L2 influences the risk of Type-2 diabetes (T2D). This SNP is also known as IVS3C>T. rs7903146(C;T) rs7903146(T;T) strongly predicted future type-2 diabetes. Considered in context with rs7903146 rs12255372 rs10885406. Note: this is one of two SNPs within the TCF7L2 gene that have been reported to be associated with type-2 diabetes, the other being rs4506565. They have approximately equal power to estimate risk for type-2 diabetes, and the results from one correlate 92% of the time with the other. Full text of the paper is available from from Plos Medicine. Or from NCBI as . TCF7L2 polymorphisms and progression to diabetes in the Diabetes Prevention Program. reconfirmed in a diverse population Associated in a study of ~1000 Hispanic-Americans with reduced insulin secretion...
Magnitude: 1.1
Repute:Bad
References:1
Repute:Bad
References:1
Less longevity for Ashkenazi Jewish women.
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rs34516635 is one of a small number of (rare) SNPs in the IGF1R gene found in a study of 384 Ashkenazi centenarians to potentially be associated with longevity and ageing. The rs34516635(A) allele was found somewhat more frequently (p=0.02) in female centenarians than in controls. No association was found for males. Higher IGF1 levels and an average decrease in maximal lifetime height of 2.5cm were also reported to be associated with (female Ashkenazi) centenarians.
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[PharmGKB:Non-Curated GWAS results: Common variants at 30 loci contribute to polygenic dyslipidemia. (Initial Sample Size: 19,840 individuals; Replication Sample Size: Up to 20,623 individuals); (Region: 2p24.1; Reported Gene(s): APOB; Risk Allele: rs7557067-G); (p-value= 0.000000000009).This variant is associated with Triglycerides.] [GWAS:Triglycerides]
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Polymorphisms of the DNMT3B gene and risk of squamous cell carcinoma of the head and neck: a case-control study. Haplotypes of DNMT1 and DNMT3B are associated with mutagen sensitivity induced by benzo[a]pyrene diol epoxide among smokers. Human intelligence and polymorphisms in the DNA methyltransferase genes involved in epigenetic marking. Dietary methyl donors, methyl metabolizing enzymes, and epigenetic regulators: diet-gene interactions and promoter CpG island hypermethylation in colorectal cancer. Genetic variation in the promoter of DNMT3B is associated with the risk of colorectal cancer. DNMT3B promoter polymorphisms and risk of late onset Alzheimer's disease. Low-level environmental cadmium exposure is associated with DNA hypomethylation in Argentinean women.
Frequency: 39.8%
References:1
References:1
higher blood pressure if <50
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rs8192678 encodes a SNP also known as Gly482Ser; the (A) allele encodes the Ser. Some reports have linked this SNP to risk for hypertension and systolic blood pressure (SBP). However, a meta-analysis of 13,000+ individuals did not find any such association. However, gene-age interaction was apparent. For diastolic blood pressure (DBP), p(interaction)<0.0001; for systolic BP, p(interaction)=0.026. In younger individuals (<50yrs; n=2511) the rs8192678(A) allele was associated with higher DBP (p=4.2 x 10<sup>-12</sup>) and SBP (p=7.2 x 10<sup>-12</sup>), but no association was evident for individuals over 50yrs (n=5088). Analysis of PGC-1alpha variants Gly482Ser and Thr612Met concerning their PPARgamma2-coactivation function. PPARGC1A coding variation may initiat...
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Data-mining analysis suggests an epigenetic pathogenesis for type 2 diabetes. Genetic prediction of future type 2 diabetes. Interaction between the UCP2-866G/A, mtDNA 10398G/A and PGC1alpha p.Thr394Thr and p.Gly482Ser polymorphisms in type 2 diabetes susceptibility in North Indian population. Association between obesity and insulin resistance with UCP2-UCP3 gene variants in Spanish children and adolescents. Association of genetic variants with chronic kidney disease in Japanese individuals. Polymorphisms of the UCP2 gene are associated with proliferative diabetic retinopathy in patients with diabetes mellitus. Interaction between the UCP2 -866 G>A polymorphism, diabetes, and beta-blocker use among patients with acute coronary syndromes. Effect of the common -866G/A polymorphism of the u...
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rs1367117 (C711T/711C>T) is a SNP within APOB (Apolipoprotein B). among 97 hypertensive subjects, C allele carriers responded to irbesartan with an average blood pressure reduction of 19 mmHg, however, they did not respond to atenolol associated with apoB levels [PharmGKB:Curated The APOB:711C>T, C allele was associated with reduction of blood pressure in response to irbesartan treatment but not atenolol treatment.] [OMIM:?] [GWAS:None]
Normal 0.97x risk for Age Related Macular Degeneration. When the retina cells in the eye get damaged with age, it is known as Age Related Macular Degeneration. This SNP has about the average risk. The SENS Research Foundation is working on a promising cure for Age Related Macular Degeneration: http://www.sens.org/outreach/conferences/lysosens-synthetic-biology-approach-treat-age-related-macular-degeneration
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may influence age related macular degeneration (damage to the eye with ageing) when part of the haplotype of rs1061170 rs3753394 rs800292 rs1329428 (TGTC), but does not appear to do so alone. age related macular degeneration [GWAS:Age-related macular degeneration]
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Synergistic association of mitochondrial uncoupling protein (UCP) genes with schizophrenia. A genetic association analysis of cognitive ability and cognitive ageing using 325 markers for 109 genes associated with oxidative stress or cognition. Ala55Val polymorphism on UCP2 gene predicts greater weight loss in morbidly obese patients undergoing gastric banding. Lack of association between uncoupling protein-2 Ala55Val polymorphism and incident diabetes in the atherosclerosis risk in communities study. Ser1369Ala variant in sulfonylurea receptor gene ABCC8 is associated with antidiabetic efficacy of gliclazide in Chinese type 2 diabetic patients. Human uncoupling protein 2 and 3 genes are associated with obesity in Japanese. Physiogenomic comparison of edema and BMI in patients receiving ros...
elevated lipids
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rs693 increases susceptibility to Elevated Apolipoprotein B and LDL-Cholesterol for carriers of the T allele [PharmGKB:Non-Curated GWAS results: Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. (Initial Sample Size: 17,797 individuals; Replication Sample Size: NR); (Region: 2p24.1; Reported Gene(s): APOB; Risk Allele: rs693-G); (p-value= 0.00000000000000004).This variant is associated with LDL cholesterol.] [OMIM:APOLIPOPROTEIN B; APOB] [GWAS:Cholesterol, total]
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rs2229765(A;A) associated with ischemic stroke (OR = 1.641, P = 0.022) in a Chinese population
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[OMIM:UNCOUPLING PROTEIN 3; UCP3]
Frequency: 58.4%
References:1
References:1
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Associated with risk of lung cancer in a Chinese population Effects of the type 2 diabetes-associated PPARG P12A polymorphism on progression to diabetes and response to troglitazone.
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[GWAS:Attention deficit hyperactivity disorder (combined symptoms)]
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[GWAS:Attention deficit hyperactivity disorder (combined symptoms)]
References:17
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* rs2279744, rs1042522, rs17878362 and rs1625895 associated with high grade endometrial cancer
References:3
References:0
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[GWAS:None]
normal fat metabolism; common in clinvar
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rs1801282, also known as Pro12Ala, is a common SNP in the peroxisome proliferator-activated receptor PPARG gene. The more common (C) allele (in dbSNP orientation) encodes the 'Pro' amino acid at this SNP position. rs1801282 has been reported to be associated with metabolic syndrome, but other studies have not been able to replicate any strong or significant effect. The association between type-2 diabetes and SNP rs1801282 is mentioned as being replicated in rs1801282 and risk of cognitive decline in elders? Maybe with diabetes. A ten-year study of 679 male patients with symptomatic coronary artery disease found that rs1801282(G) carriers had a much lower (10 year) cardiovascular risk, with the hazard ratio estimated to be 0.10 (CI: 0.01-0.70, p = 0.02) for ischemic heart disease and 0.24 f...
most common in all populations but having one copy of the rarer (C) allele is linked to increased executive function
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Variation in longevity gene KLOTHO is associated with greater cortical volumes
common in clinvar
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Variations in the peroxisome proliferator-activated receptor-gamma gene and melanoma risk. PPAR-gamma gene polymorphisms and psoriatic arthritis. The Genetics of PPARG and the Skeleton. The association of Pro12Ala polymorphism of peroxisome proliferator-activated receptor-gamma gene with serum osteoprotegerin levels in healthy Korean women. Association of stearoyl-CoA desaturase 1 activity with familial combined hyperlipidemia. Polymorphism of genes related to insulin sensitivity and the risk of biliary tract cancer and biliary stone: a population-based case-control study in Shanghai, China. PPAR Genomics and Pharmacogenomics: Implications for Cardiovascular Disease. Association of FTO with obesity-related traits in the Cebu Longitudinal Health and Nutrition Survey (CLHNS) Cohort. Differen...
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[GWAS:Attention deficit hyperactivity disorder (combined symptoms)]
Magnitude: 0
Frequency: 99.1%
Repute:Good
References:2
Frequency: 99.1%
Repute:Good
References:2
Normal risk of drug induced liver injury with diclofenac
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[GWAS:Drug-induced liver injury]
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[GWAS:None]
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
common in complete genomics
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rs17887200 and rs12951053 associated with ER negative breast cancer tumors (1.48 (1.11-1.93) p-trend = 0.01 and 1.29 (1.06-1.58) p-trend = 0.009, respectively)
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[GWAS:Lipoprotein-associated phospholipase A2 activity and mass]
72 snps
(hide) Anger
Frequency: 14.3%
References:1
References:1
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[GWAS:Anger]
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[GWAS:Anger]
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[GWAS:Anger]
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[GWAS:Anger]
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[GWAS:Anger]
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[GWAS:Anger]
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[GWAS:Anger]
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[GWAS:Anger]
9 snps
(hide) APOE
2x risk of Alzheimer's disease
You carry one APOE-ε3 allele and one APOE-ε4 allele. This results in 2x increased relative risk of Alzheimer's disease. For non-caucasians the risk is increased, but SNPedia has not yet seen any reliable estimates. This is based on *rs429358(C;T) *rs7412(C;C)
lower levels of ApoE
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Significant Alzheimer's disease associations with were found for rs449647(A;A) and rs405509(G;G) genotypes (positive), and rs449647(A;T) and rs405509(T;T)
more likely to gain weight if taking olanzapine
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The ancestral allele is C. The rs7412(T) allele, also known as Arg176Cys, generally indicates the presence of an Apoε2 allele; see the ApoE page for a full discussion of the ApoE alleles and their association with Alzheimer's disease. Another SNP related to ApoE is rs429358. In a study of 67 mostly Caucasian patients prescribed the atypical antipsychotic olanzapine, carriers of a rs7412(C) allele were more likely to gain significant weight compared to rs7412(T;T) carriers, as assessed by physiogenomic analysis of corresponding weight profiles. Two other SNPs, rs5092 and rs4765623, were also significantly associated with weight profiles in these patients. Current limitations of SNP data from the public domain for studies of complex disorders: a test for ten candidate genes for obesity ...
normal
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Conflicting reports of possible small increase in Alzheimer's risk. Currently dubious at best. rs2373115 is one of several SNPs in the GAB2 gene indicating an increased risk (OR 4.1) of late-onset Alzheimer's disease, but apparently only in individuals also carrying ApoE4 alleles, i.e. rs429358(C) alleles rs2373115 marker does not modify the risk of Alzheimer's disease in Spanish APOE e4 carriers. rs2373115(G) is the risk allele. (p = 9 x 10(-11)) was associated with an odds ratio of 4.06 (confidence interval 2.81-14.69) However, a separate study of 1,749 Alzheimer patients concluded that this GAB2 SNP is 'at best a minor genetic determinant' since the authors of this study observed only a slight tendency for an increase of the (G;G) genotype (odds ratio of 1.3 vs (G;T) and (T;T), CI:1.0-1...
increased risk for Alzheimer's
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rs1050283, a SNP also known as +1073, is located in the 3' untranslated region of the oxidized low density lipoprotein (lectin-like) receptor 1 OLR1 gene, which is also known as the LOX-1 gene. The rs1050283(C) allele has been associated with increased risk for Alzheimer's disease in several studies of ~200 Southern Italian Alzheimer patients. The risk is independent of ApoE status, and may also be defined by haplotypes including one or both of neighboring SNPs rs12316150 and rs669.
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This appears to be the snp on the Illumina Human 550 which is closest to rs4420638 [PharmGKB:Non-Curated GWAS results: Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. (Initial Sample Size: 17,815 individuals; Replication Sample Size: NR); (Region: 19q13.32; Reported Gene(s): TOMM40, APOE; Risk Allele: rs439401-G); (p-value= 0.000000002).This variant is associated with Triglycerides.] [GWAS:Triglycerides]
more likely to gain weight if taking olanzapine
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rs4765623 is a SNP in the scavenger receptor class B, member 1 SCARB1 gene. In a study of 67 mostly Caucasian patients prescribed the atypical antipsychotic olanzapine, carriers of a rs4765623(C) allele were more likely to gain significant weight compared to rs4765623(T;T) carriers, as assessed by physiogenomic analysis of corresponding weight profiles. Two other SNPs, rs5092 and rs7412, were also significantly associated with weight profiles in these patients. Combining fMRI and SNP data to investigate connections between brain function and genetics using parallel ICA. [GWAS:None]
possibly increased risk for Alzheimers
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rs669 is a SNP in the alpha-2-macroglobulin A2M gene. In dbSNP orientation, the rs669(A) allele encodes an isoleucine, and the rs669(G) allele encodes a valine; the SNP is also known as the Ile/Val variant. On its own, rs669 was not seen to reproducibly and independently increase risk for Alzheimer's disease in several studies of ~200 Italian patients. However, the T-C-A haplotype of rs12316150-rs1050283-rs669 was associated with both early- and late-onset Alzheimer's disease. The majority of the disease risk from this haplotype was based on rs1050283. The original 2004 study of 148 Italian sporadic AD patients yielded an odds ratio for the rs669(G;G) genotype (as oriented in dbSNP orientation) of 3.81 (CI: 1.66-8.75). The presence of rs2333227(C;C), in addition to rs669(G;G), appears to s...
References:2
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rs12316150, a SNP also known as +1071, is located in the 3' untranslated region of the oxidized low density lipoprotein (lectin-like) receptor 1 OLR1 gene, which is also known as the LOX-1 gene. The rs12316150 risk allele has been associated with increased risk for Alzheimer's disease in several studies of ~200 Southern Italian Alzheimer patients, but only within the context of a haplotype including one or both of neighboring SNPs rs1050283 and rs669.
normal
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rs3025786 is a SNP in the presenilin 1 PSEN1 gene. A study of a Spanish case-control sample of 1,183 individuals showed rs3025786 was associated with Alzheimer's disease in an ApoE-specific manner: more specifically rs3025786(C) allele carriers have a decreased AD risk among carriers of the ApoE4 allele.
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obstructive sleep apnea rs405509 Significant Alzheimer's disease associations with were found for rs449647(A;A) and rs405509(G;G) genotypes (positive), and rs449647(A;T) and rs405509(T;T) [PharmGKB:Curated A study in 2150 Japanese individuals with metabolic syndrome, including 411 subjects with chronic kidney disease (CKD) and 1739 controls found that the -219G-->T SNP in APOE (rs405509) was most significantly associated with CKD in Japanese individuals with metabolic syndrome.]
>3x increased risk for Alzheimer's; 1.4x increased risk for heart disease
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This SNP, located in the fourth exon of the ApoE gene, affects the amino acid at position 130 of the resulting protein. The more common rs429358 allele is (T). If the allele is (C) and the same chromosome also harbors the rs7412(C) allele, the combination is known as an APOE-ε4 allele. The APOE-ε4 allele has a strong influence on the risk of Alzheimer's disease. Both deCODEme and 23andMe (v3 chip) test for this SNP. Many studies have estimated the level of risk, and it varies depending on age, sex, ethnicity, and other factors. One meta-analysis estimated the odds ratios for homozygous rs429358(C;C) individuals compared to the more common ApoE3/ApoE3 homozygotes to be 12x for late-onset Alzheimer's and 61x for early-onset disease. Meta-analyses have also supported the association between t...
more likely to gain weight if taking olanzapine
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rs5092 is a SNP in the apolipoprotein A4 APOA4 gene. In a study of 67 mostly Caucasian patients prescribed the atypical antipsychotic olanzapine, carriers of a rs5092(G) allele were less likely to gain significant weight compared to rs5092(A;A) carriers, as assessed by physiogenomic analysis of corresponding weight profiles. Two other SNPs, rs4765623 and rs7412, were also significantly associated with weight profiles in these patients.
1.19x increased risk for Alzheimer's disease
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rs5963409 is a SNP in the ornithine carbamoyltransferase OTC gene; this SNP is also known as the -389 G/A SNP. Previous association studies were extended to a population of 2113 Alzheimer's disease cases and 1580 controls from northern France, western France, the United Kingdom and Italy. The rs5963409(A) minor allele was weakly but significantly associated with an increased risk of developing Alzheimer's disease (odds ratio 1.19, p = 0.004). This association was independent of age and ApoE status.
normal risk
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RNA made containing the rs688(T) SNP, a variant near exon 12 of the low-density lipoprotein receptor (LDLR) that is a receptor for ApoE proteins, is spliced at lower efficiency in males. Presumably due to this, the rs688(T;T) genotype was associated with increased risk for Alzheimer's disease odds in males (odds ratio 1.49, CI: 1.13-1.97, uncorrected p=0.005), but not in females. The presence of the rs688(T) allele associates with increased total and LDL-cholesterol in female members of the Framingham Offspring Study; rs688 was not associated with significant differences in HDL-cholesterol. The largest rs688-associated cholesterol differences were observed in pre-menopausal women. Taken together, rs688, a SNP present in approximately 60% of Caucasians, is associated with significant 10% in...
Magnitude: 0
Frequency: 98.2%
Repute:Bad
References:19
Frequency: 98.2%
Repute:Bad
References:19
normal Since the rare geno is good, this can be considered slightly bad
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rs11591147, also known as R46L, is a SNP in the PCSK9 gene. As early as 2006, the minor rs11591147(T) allele was reported to be associated with lower LDL cholesterol levels, and most studies since have found that this also correlates to a two to three fold reduced risk for both early- and late-onset cardiovascular events and disease. As part of a 9 SNP set studied in a meta-analysis totaling over 300,000 patients, rs11591147 was the SNP with the greatest effect on LDL-C and therefore cardiovascular risk reduction. The set of SNPs was as follows, ordered from strongest to least effect on coronary risk, and the allele shown is the one associated with reduced LDL-C levels along with the associated (or nearby) lipid metabolism gene: * rs11591147(T), PCSK9 * rs4420638(A), APOE * rs6511720(T), L...
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
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[PharmGKB:Curated In a GWAS of apparently healthy women, seven loci were found to be significantly associated with C-Reactive protein levels. Two SNPs in APOE were significantly associated with CRP, and of these, this SNP showed the most significant association.] [GWAS:C-reactive protein]
common in clinvar
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The ancestral allele is C. Association of ApoE genetic variants with obstructive sleep apnea in children. Subarachnoid hemorrhage: tests of association with apolipoprotein E and elastin genes. [OMIM:HYPERLIPOPROTEINEMIA, TYPE III, ASSOCIATED WITH APOE2]
increased risk in men for biliary conditions
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rs440446 is a SNP in an intron of the apolipoprotein E APOE gene; it is also known as the IVS1+69 variant. In a study of ~1,000 Chinese patients with various biliary tract conditions, including cancer and gallstones, men carrying a rs440446(C) allele (in dbSNP orientation) had a 1.7x risk of gallstone disease [CI: 1.2-2.4], a 1.8x risk of gallbladder cancer (CI: 1.0-3.3), a 3.7x risk of bile duct cancer (CI: 2.0-7.0), and a 4x risk of ampullary cancer (CI: 1.4-12.4). Note: orientation relative to dbSNP entry is reversed as published. Current limitations of SNP data from the public domain for studies of complex disorders: a test for ten candidate genes for obesity and osteoporosis. Patterns of linkage disequilibrium and haplotype distribution in disease candidate genes. Subarachnoid hemorrh...
1 genoset 23 snps
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probably light-skinned, European ancestry This SNP influences skin pigmentation and indicates indicates light-skinned European ancestry. estimates that the rs1426654(A) allele (light skin pigmentation) spread through the European population around 6,000 - 12,000 years ago. Prior to that, 'European ancestors' were most likely relatively brown-skinned.
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This SNP influences skin pigmentation. The allele, A111T, rs1426654(A), indicates light-skinned european ancestry. It appears as if this SNP is a relatively new one in human evolution; one estimate is that the rs1426654(A) allele, in other words, light skin pigmentation, spread through the European population around 6,000 - 12,000 years ago. Prior to that, 'European ancestors' were most likely relatively brown-skinned. Another study () has concluded that almost individuals carrying the A111T variant can trace ancestry back to a single person who most likely lived at least 10,000 years ago. This SNP is one of three from the SLC24A5 gene that can be analyzed to categorize the ancestry of a person as either European, African, or Asian, based on a 2009 study. The 3 SNPs are: * rs1426654 * rs25...
6x increased risk for cleft lip
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A genome-wide association study involving 224 cases and 383 controls of Central European origin found that significant association between rs987525 and risk for nonsyndromic cleft lip with or without cleft palate (NSCL/P). The odds ratio for rs987525(A;G) individuals was 2.57 (CI: 2.02-3.26), and for rs987525(A;A), 6.05 (CI: 3.88-9.43). The calculated population attributable fraction for this marker is 0.41, suggesting that this study has identified a major genetic cause for NSCL/P. 23andMe blog article Associated with European Facial Appearance *rs7590268 *rs16903544 *rs987525 *rs9574565 *rs227731 *rs642961 *rs1258763 Family-based study shows heterogeneity of a susceptibility locus on chromosome 8q24 for nonsyndromic cleft lip and palate. Association between genetic variants of reported c...
0.78x reduced risk of Male Pattern Baldness. Discovered by 23andWe based on customer surveys, and considered preliminary research.
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This is the 23andWe discovery: 'Male Pattern Baldness: Preliminary Research'. It affects appearance.
2-4x higher risk of sun sensitivity if part of risk haplotype. Increased risk of sunburns and freckles instead of tanning.
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rs1015362 is a SNP near the ASIP (agouti signaling protein) gene on chromosome 20. This SNP is one of a tightly-linked pair that increases the likelihood of an individual being prone to sun sensitivity, in other words, freckles and sunburn, based on a study of 6,000+ Caucasians (5,000+ Icelanders + 1,000+ Dutch). The odds ratios, presumably on a dominant basis, and at least in the largest population (Icelanders) for 'freckles and burns vs. no freckles and tans' for the haplotype pair rs1015362(G) - rs4911414(T) is 3.91 (CI: 2.54-6.03) for males and 2.42 (CI: 1.52-3.86) for females, with an overall p=0.051. Based on a study by the same authors of 4,000+ skin cancer patients, this haplotype was seen to confer significant increased risk for cutaneous malignant melanoma (odds ratio 1.45, p = 1...
Normal (higher) risk of Male Pattern Baldness. Discovered by 23andWe based on customer surveys, and considered preliminary research.
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This is the 23andWe discovery: 'Male Pattern Baldness: Preliminary Research'. It affects appearance.
Magnitude: 1.1
Repute:Bad
References:1
Repute:Bad
References:1
Less longevity for Ashkenazi Jewish women.
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rs34516635 is one of a small number of (rare) SNPs in the IGF1R gene found in a study of 384 Ashkenazi centenarians to potentially be associated with longevity and ageing. The rs34516635(A) allele was found somewhat more frequently (p=0.02) in female centenarians than in controls. No association was found for males. Higher IGF1 levels and an average decrease in maximal lifetime height of 2.5cm were also reported to be associated with (female Ashkenazi) centenarians.
Generally European; Light skin; Possibly an increased risk of melanoma This SNP is associated with skin, hair, and eye colour, and risk of melanoma. Individuals with the G;G genotype are generally of European descent and have fair skin. In a population-based case-control study investigating a number of pigmentation-related SNPs and their correlation with cutaneous malignant melanoma (CMM) in a Caucasian Australian population, rs16891982 (variant F374L) was found to be associated with odds ratios of 3.44, 2.86, 1.68, and 1.68 for all study subjects (1,738 CMM cases and 4,517 controls); subjects with northern European ancestry (1,438 cases and 3,098 controls); northern European subjects adjusted for hair, eye, and skin colour; and northern European subjects adjusted for the MC1R genotype, r...
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This snp influences skin pigmentation. The allele p.L374F indicates light-skinned european ancestry c.1122C>G, p.Phe374Leu (NCBI dbSNP rs16891982) in SLC45A2 was associated with protection from malignant melanoma (OR, 0.41; 95% CI, 0.24-0.70; P=0.008 after adjustment for multiple testing) An association study conducted on a population of European origin concluded that the rare (in Europeans, at least) allele L374, i.e. rs16891982(C) in dbSNP orientation, significantly increases the possibility of having black hair color, with an odds ratio of around 7. This population-based case-control study investigated a number of pigmentation-related SNPs and their correlation with cutaneous malignant melanoma (CMM) in an Australian population. rs16891982 (variant F374L) was found to be associated w...
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[PharmGKB:Non-Curated GWAS Results: Two newly identified genetic determinants of pigmentation in Europeans (Initial Sample Size: 5,130 individuals; Replication Sample Size: 3,330 individuals; Risk/trait Allele: rs1408799-C). This variant is associated with Blue vs. green eyes.] [OMIM:TYROSINASE-RELATED PROTEIN 1; TYRP1] [GWAS:Eye color] [GWAS:Blue vs. green eyes]
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Influences appearance gnxp A genomewide association study of skin pigmentation in a South Asian population. Complex signatures of selection for the melanogenic loci TYR, TYRP1 and DCT in humans.
associated with the absence of freckles
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Influences appearance The A allele of rs1042602 is associated with the absence of freckles [PharmGKB:Non-Curated GWAS Results: A genomewide association study of skin pigmentation in a South Asian population (Initial Sample Size: 363 with maxL* < 56 and 374 with maxL* > 63; 20% tails of distribution; Replication Sample Size: 116 low maxL*, 115 high maxL* individuals). This variant is associated with skin pigmentation by reflectance spectroscopy.] [OMIM:SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 3; SHEP3] [GWAS:Freckles] [GWAS:Skin pigmentation by reflectance spectroscopy]
Frequency: 40.7%
References:0
References:0
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Influences appearance gnxp
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This SNP influences appearance and is located in the TPCN2 gene. A study of 5130 Icelanders (with further followup in another 2116 Icelanders and 1214 Dutch individuals) found significant association between a group of SNPs within the TPCN2 gene.All of the discovered difference between blonde and brown hair could be explained by genotypes with rs3829241 and Rs35264875. The A allele was significantly associated with blonde versus brown hair with a P-value 6.2e-16 Summaried in gnxp [OMIM:TWO-PORE SEGMENT CHANNEL 2; TPCN2]
Frequency: 52.2%
References:10
References:10
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associated with hair color rs12896399 rs12203592 [OMIM:SOLUTE CARRIER FAMILY 24 (SODIUM/POTASSIUM/CALCIUM EXCHANGER), MEMBER] [GWAS:Black vs. blond hair color]
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Associated with European Facial Appearance *rs7590268 *rs16903544 *rs987525 *rs9574565 *rs227731 *rs642961 *rs1258763 [GWAS:Nonsyndromic cleft lip with or without cleft palate]
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Associated with European Facial Appearance *rs7590268 *rs16903544 *rs987525 *rs9574565 *rs227731 *rs642961 *rs1258763 [GWAS:Nonsyndromic cleft lip with or without cleft palate]
Normal risk of cleft lip
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risk of cleft lip 23andMe considers rs861020 a proxy Associated with European Facial Appearance *rs7590268 *rs16903544 *rs987525 *rs9574565 *rs227731 *rs642961 *rs1258763 Genome scan, fine-mapping, and candidate gene analysis of non-syndromic cleft lip with or without cleft palate reveals phenotype-specific differences in linkage and association results. Lack of association between IRF6 polymorphisms (rs2235371 and rs642961) and non-syndromic cleft lip and/or palate in a Brazilian population. Current concepts in genetics of nonsyndromic clefts. Studies of palatine rugae and interferon regulatory factor 6 variations in a group of families with sporadic hypodontia. IRF6 gene variants in Central European patients with non-syndromic cleft lip with or without cleft palate. Family-based study sh...
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Associated with European Facial Appearance *rs7590268 *rs16903544 *rs987525 *rs9574565 *rs227731 *rs642961 *rs1258763 [GWAS:Nonsyndromic cleft lip with or without cleft palate]
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Influences appearance gnxp For the rs642742 SNP (184745.0002), located 326 kb upstream of the KITLG transcription start site, the frequency of the ancestral A allele is at least 92% in West Africans, whereas the frequency of the derived G allele is at least 86% in Europeans and East Asians. Admixture mapping suggested that replacement of AA with GG in the rs642742 SNP may account for a lightening of a person's skin by 6 to 7 melanin units. In comparison, the overall skin reflectance difference between West Africans and Europeans is 30 melanin units. [OMIM:KIT LIGAND; KITLG]
straighter hair; common
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hair curl rs17646946 and rs7349332. source genetic future Appearance [GWAS:Common traits (Other)]
Frequency: 81.5%
References:0
References:0
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Associated with European Facial Appearance *rs7590268 *rs16903544 *rs987525 *rs9574565 *rs227731 *rs642961 *rs1258763
blue/gray eyes more possible
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rs1800407 is located in exon 13 of the OCA2 gene at amino acid position 419, and it is therefore also known as the R419Q variant. The (A) allele encodes the amino acid glutamine (instead of arginine), and it is associated with increased odds of having green/hazel eye color in some Caucasian populations. One copy of of rs1800407(A) is sufficient for this effect. [PMID 12163334, PMID 15889046; OMIM 203200.0012] According to tree scanning analysis, the proportion of eye colour variation explained by this nucleotide position is merely 4%. Thus, additional variation present in the OCA2 gene and perhaps some other pigment related genes must be taken into account in order to explain the high phenotypic variation in iris colour. Among rs12913832(A;A) individuals, the penetrance for green/hazel eye...
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blog The two most significant associations found were between nose width and SNP rs1258763 near the GREM1 gene in the German cohort (P=6 × 10?4), and between bizygomatic distance and SNP rs987525 at 8q24.21 near the CCDC26 gene (P=0.017) Genetic determination of human facial morphology: links between cleft-lips and normal variation. Associated with European Facial Appearance *rs7590268 *rs16903544 *rs987525 *rs9574565 *rs227731 *rs642961 *rs1258763 [GWAS:Nonsyndromic cleft lip with or without cleft palate]
blue/gray eyes possible
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rs1800401 is located in exon 7 of the OCA2 gene at amino acid position 305. The (T) allele encodes the amino acid tryptophan (instead of arginine), and it is one of several SNPs associated with increased odds of having brown or black eye color in Caucasians. One copy of of rs1800401(T) is sufficient for this effect. [PMID 12163334, PMID 15889046; OMIM 203200.0011] [OMIM:?]
common in complete genomics
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plos the association between rs12203592 and hair color was independent of rs1540771, a SNP between the IRF4 and EXOC2 genes previously found to be associated with hair color. [PharmGKB:Non-Curated GWAS Results: Genetic determinants of hair, eye and skin pigmentation in Europeans (Initial Sample Size: 2,986 individuals; Replication Sample Size: 3,932 individuals). This variant is associated with freckles.] [OMIM:SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 8; SHEP8] [GWAS:Freckles]
slight increase in skin cancer risk
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rs1126809 is a SNP in the TYR tyrosinase gene. This SNP is also known as R402Q (or, 1205G>A) based on the amino acid change at position 402 from an arginine (R) to a glutamine (Q). The rs1126809(G) allele encodes the more common (R)/arginine, while the variant rs1126809(A) allele encodes the (Q)/glutamine. rs1126809(A) has previously been shown to affect eye color and sun sensitivity. Based on a study of 4,000+ skin cancer patients, it also conferred increased risk of cutaneous malignant melanoma (odds ratio 1.21, p = 2.8 x 10<sup>-7</sup>) and basal cell carcinoma (odds ratio 1.14, p = 6.1 x 10<sup>-4</sup>). rs1126809 is not associated with albinism. [PharmGKB:Curated This variant is associated with the risk of cutaneous melanoma and basal cell carcinoma. It i...
normal
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rs4911414 is a SNP near the ASIP (agouti signaling protein) gene on chromosome 20. This SNP is one of a tightly-linked pair that increases the likelihood of an individual being prone to sun sensitivity, in other words, freckles and sunburn, based on a study of 6,000+ Caucasians (5,000+ Icelanders + 1,000+ Dutch). The odds ratios, presumably on a dominant basis, and at least in the largest population (Icelanders) for 'freckles and burns vs. no freckles and tans' for the haplotype pair rs1015362(G) - rs4911414(T) is 3.91 (CI: 2.54-6.03) for males and 2.42 (CI: 1.52-3.86) for females, with an overall p=0.051. Based on a study by the same authors of 4,000+ skin cancer patients, this haplotype was seen to confer significant increased risk for cutaneous malignant melanoma (odds ratio 1.45, p = 1...
Magnitude: 0
Frequency: 70.8%
Repute:Good
References:20
Frequency: 70.8%
Repute:Good
References:20
common on affy axiom data
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plos rs12203592 showed the largest allele frequency difference between the Irish individuals and those individuals of Northern, Central European and Eastern European descent associated with hair color rs12896399 rs12203592 rs12203592 for freckling was previously associated with hair color, eye color, and tanning response to sunlight Squamous Cell Carcinoma [PharmGKB:Non-Curated GWAS Results: A Genome-Wide Association Study Identifies Novel Alleles Associated with Hair Color and Skin Pigmentation (Initial Sample Size: 2,287 women; Replication Sample Size: up to 8,465 individuals; Risk/trait Allele: rs12203592-T). This variant is associated with Black vs. red hair color.] [GWAS:Eye color] [GWAS:Black vs. red hair color]
Magnitude: 0
Frequency: 71.7%
Repute:Good
References:8
Frequency: 71.7%
Repute:Good
References:8
normal
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A 2007 study based on the Icelanders and Dutch concluded that individuals with an rs12821256(C) allele were ~2x fold more likely to have blond than brown hair color. The specific odds ratio claimed is 2.32, p = 5.5 x 10<sup>-14</sup>. [PharmGKB:Non-Curated GWAS Results: Genetic determinants of hair, eye and skin pigmentation in Europeans (Initial Sample Size: 2,986 individuals; Replication Sample Size: 3,932 individuals). This variant is associated with blond vs. brown hair.] [OMIM:KIT LIGAND; KITLG] [GWAS:Hair color] [GWAS:Blond vs. brown hair]
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Influences appearance gnxp Digital Quantification of Human Eye Color Highlights Genetic Association of Three New Loci[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2865509/] Common sequence variants on 20q11.22 confer melanoma susceptibility. Genome-wide association study identifies three loci associated with melanoma risk. Web-based, participant-driven studies yield novel genetic associations for common traits.
normal
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Although the rs26722(T) alllele is relatively rare, at least statistically it seems to be associated with darker eye, hair, and skin color, all other things being equal. A genomewide association study of skin pigmentation in a South Asian population. A genome-wide association study identifies novel alleles associated with hair color and skin pigmentation. Association of the SLC45A2 gene with physiological human hair colour variation. Genome-wide association study of tanning phenotype in a population of European ancestry. Genetic variants in pigmentation genes, pigmentary phenotypes, and risk of skin cancer in Caucasians. Genetic determinants of hair and eye colours in the Scottish and Danish populations. [OMIM:PIGMENTATION OF HAIR, SKIN, AND EYES, VARIATION IN]
common in complete genomics
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Influences appearance gnxp associated with skin pigmentation in two samples of East Asian ancestry and it confirms previous evidence indicating that evolution towards light skin occurred, at least in part, independently in Europe and East Asia. The OCA2 gene has been under positive selection in Europe and East Asia, but different alleles have been selected in each region. 23andMe blog each rs1800414(C) was associated with a 1.3 melanin unit reduction in skin pigmentation. This SNP accounts for 9% of the variation in skin color seen in the study population.
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Influences appearance gnxp
common in clinvar
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[PharmGKB:Non-Curated GWAS Results: Two newly identified genetic determinants of pigmentation in Europeans (Initial Sample Size: 5,130 individuals; Replication Sample Size: 3,330 individuals; Risk/trait Allele: rs35264875-T). This variant is associated with Blond vs. brown hair.] [OMIM:TWO-PORE SEGMENT CHANNEL 2; TPCN2] [GWAS:Blond vs. brown hair]
34 snps
(hide) Appearance/Eye color
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[PharmGKB:Non-Curated GWAS Results: Two newly identified genetic determinants of pigmentation in Europeans (Initial Sample Size: 5,130 individuals; Replication Sample Size: 3,330 individuals; Risk/trait Allele: rs1408799-C). This variant is associated with Blue vs. green eyes.] [OMIM:TYROSINASE-RELATED PROTEIN 1; TYRP1] [GWAS:Eye color] [GWAS:Blue vs. green eyes]
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Influences appearance gnxp A genomewide association study of skin pigmentation in a South Asian population. Complex signatures of selection for the melanogenic loci TYR, TYRP1 and DCT in humans.
Frequency: 40.7%
References:0
References:0
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Influences appearance gnxp
blue/gray eyes more possible
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rs1800407 is located in exon 13 of the OCA2 gene at amino acid position 419, and it is therefore also known as the R419Q variant. The (A) allele encodes the amino acid glutamine (instead of arginine), and it is associated with increased odds of having green/hazel eye color in some Caucasian populations. One copy of of rs1800407(A) is sufficient for this effect. [PMID 12163334, PMID 15889046; OMIM 203200.0012] According to tree scanning analysis, the proportion of eye colour variation explained by this nucleotide position is merely 4%. Thus, additional variation present in the OCA2 gene and perhaps some other pigment related genes must be taken into account in order to explain the high phenotypic variation in iris colour. Among rs12913832(A;A) individuals, the penetrance for green/hazel eye...
blue/gray eyes possible
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rs1800401 is located in exon 7 of the OCA2 gene at amino acid position 305. The (T) allele encodes the amino acid tryptophan (instead of arginine), and it is one of several SNPs associated with increased odds of having brown or black eye color in Caucasians. One copy of of rs1800401(T) is sufficient for this effect. [PMID 12163334, PMID 15889046; OMIM 203200.0011] [OMIM:?]
normal
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rs4911414 is a SNP near the ASIP (agouti signaling protein) gene on chromosome 20. This SNP is one of a tightly-linked pair that increases the likelihood of an individual being prone to sun sensitivity, in other words, freckles and sunburn, based on a study of 6,000+ Caucasians (5,000+ Icelanders + 1,000+ Dutch). The odds ratios, presumably on a dominant basis, and at least in the largest population (Icelanders) for 'freckles and burns vs. no freckles and tans' for the haplotype pair rs1015362(G) - rs4911414(T) is 3.91 (CI: 2.54-6.03) for males and 2.42 (CI: 1.52-3.86) for females, with an overall p=0.051. Based on a study by the same authors of 4,000+ skin cancer patients, this haplotype was seen to confer significant increased risk for cutaneous malignant melanoma (odds ratio 1.45, p = 1...
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Influences appearance gnxp Digital Quantification of Human Eye Color Highlights Genetic Association of Three New Loci[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2865509/] Common sequence variants on 20q11.22 confer melanoma susceptibility. Genome-wide association study identifies three loci associated with melanoma risk. Web-based, participant-driven studies yield novel genetic associations for common traits.
common in complete genomics
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Influences appearance gnxp associated with skin pigmentation in two samples of East Asian ancestry and it confirms previous evidence indicating that evolution towards light skin occurred, at least in part, independently in Europe and East Asia. The OCA2 gene has been under positive selection in Europe and East Asia, but different alleles have been selected in each region. 23andMe blog each rs1800414(C) was associated with a 1.3 melanin unit reduction in skin pigmentation. This SNP accounts for 9% of the variation in skin color seen in the study population.
8 snps
(hide) Ashkenazi Jews
Faster aging. Increased risk for Dementia. Less good cholesterol. This reduces HDL ('good') cholesterol. HDL cholesterol removes cholesterol from artery walls and improves health. This SNP seems to be associated with higher blood pressure, less longevity, and more diseases of aging, in particular memory decline and dementia, and lower odds of living to 100, especially in Ashkenazi Jews. Attempting to raise HDL cholesterol may (or may not) be useful to mitigate the effects of this SNP.
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This SNP rs5882 in the CETP gene referred to as ILE405VAL and RSAI405V has been related to ageing and exceptional long life. A study in Ashkenazi Jews showed that individuals homozygotic for the G allele have significantly longer lifespans. New research also indicates that G homozygotes have an average of 70% less risk of dementia and Alzheimer's disease. The study also found that heterozygotes have a lower risk of dementia and Alzheimer's disease but more study is needed to determine the risk reduction for heterozygotes. See Association of a Functional Polymorphism in the Cholesteryl Ester Transfer Protein (CETP) Gene With Memory Decline and Incidence of Dementia and CETP Variant Linked to Slower Cognitive Decline and Reduced Dementia Risk . [PharmGKB:Curated Risk or phenotype-associated...
Magnitude: 1.1
Repute:Bad
References:1
Repute:Bad
References:1
Less longevity for Ashkenazi Jewish women.
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rs34516635 is one of a small number of (rare) SNPs in the IGF1R gene found in a study of 384 Ashkenazi centenarians to potentially be associated with longevity and ageing. The rs34516635(A) allele was found somewhat more frequently (p=0.02) in female centenarians than in controls. No association was found for males. Higher IGF1 levels and an average decrease in maximal lifetime height of 2.5cm were also reported to be associated with (female Ashkenazi) centenarians.
Frequency: 54.0%
References:3
References:3
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rs11098403 is an intergenic SNP on chromosome 4 located ~300kb upstream of the 5' end of the NDST3 gene. Although in one publication the rs11098403(G) allele is said to be associated with increased risk for schizophrenia (odds ratio of 1.4, at least in Ashkenazi Jews), in another report this same allele is associated with decreased risk (odds ratio 0.6, in Han Chinese).,
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rs6584400 is a SNP in the neuregulin 3 NRG3 gene. Based on a study of 1515 Ashkenazi Jewish individuals, including 285 parent-child trios, 173 unrelated cases, and 487 unrelated controls, three SNPs (rs10883866, rs10748842, and rs6584400) were found to be associated with the 'delusion' factor as a quantitative trait in schizophrenia, even though no SNP in this study withstood multiple test correction for association with the binary schizophrenia phenotype itself. After replication in an independent set of 153 Ashkenazi Jewish samples, the empirical study-wide significance across all 9 factors studied was estimated to be p = 2.7x10e-3. [PharmGKB:Curated In a study of Ashkenazi Jewish SZ (schizophrenia and schizoaffective disorder),the minor allele (A) of rs6584400 was found to be associate...
Frequency: 82.3%
References:3
References:3
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rs10748842 is a SNP in the neuregulin 3 NRG3 gene. Based on a study of 1515 Ashkenazi Jewish individuals, including 285 parent-child trios, 173 unrelated cases, and 487 unrelated controls, three SNPs (rs10883866, rs10748842, and rs6584400) were found to be associated with the 'delusion' factor as a quantitative trait in schizophrenia, even though no SNP in this study withstood multiple test correction for association with the binary schizophrenia phenotype itself. After replication in an independent set of 153 Ashkenazi Jewish samples, the empirical study-wide significance across all 9 factors studied was estimated to be p = 2.7x10e-3. [PharmGKB:Curated In a study of Ashkenazi Jewish SZ (schizophrenia and schizoaffective disorder),the minor allele (C) of rs10748842 was found to be associa...
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Familial hypercholesterolemia; aka FH Lithuania, the most common FH mutation in Ashkenazi Jews see rs121908027
Duffy-positive This genotype is associated with European populations and southwestern Native American populations.
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rs2814778 is within the DARC gene, which encodes the Duffy blood group antigen . This SNP shows an almost perfectly fixed difference in frequency between Europeans and those with African ancestry. (One exception appears to be a certain population of Czech gypsies, and certain non-Ashkenazi Jewish populations.) Additionally the Namibian San samples of the CEPH-HGDP are, uncharacteristically for Africans, all AA homozygotes for this SNP. The rs2814778 (G) allele is associated with African populations, while rs2814778 (A) is associated with European populations and southwestern Native American populations. rs2814778(G;G) protect against Plasmodium vivax malaria and predicts of white blood cell and neutrophil count 23andMe blog discussion Malaria Resistance (Duffy Antigen) [PharmGKB:Curated A...
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rs10883866 is a SNP in the neuregulin 3 NRG3 gene. Based on a study of 1515 Ashkenazi Jewish individuals, including 285 parent-child trios, 173 unrelated cases, and 487 unrelated controls, three SNPs (rs10883866, rs10748842, and rs6584400) were found to be associated with the 'delusion' factor as a quantitative trait in schizophrenia, even though no SNP in this study withstood multiple test correction for association with the binary schizophrenia phenotype itself. After replication in an independent set of 153 Ashkenazi Jewish samples, the empirical study-wide significance across all 9 factors studied was estimated to be p = 2.7x10e-3. [PharmGKB:Curated In a study of Ashkenazi Jewish SZ (schizophrenia and schizoaffective disorder),the minor allele (G) of rs10883866 was found to be associa...
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Based on a study of ~2500 female patients of European ancestry with sporadic postmenopausal breast cancer, this SNP in the FGFR2 showed the greatest risk. The risk allele is rs1219648(G), with a pooled odds ratio of 1.64 (CI:1.42-1.90) for rs1219648(G;G) homozygotes, and an odds ratio of 1.20 (CI: 1.07-1.42) for rs1219648(A;G) heterozygotes, compared with rs1219648(A;A) homozygotes. rs1219648 represents the SNP in the FGFR2 gene with the strongest association with breast cancer. However, nearby SNPs are almost as predictive. In particular, the following SNP alleles all have linkage values of 0.96 or greater with the rs1219648(G) allele in European populations: *rs2981579(A) *rs2420946(T) *rs11200014(A) An experimental rationale is presented indicating that this SNP is part of a haplotype t...
normal
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i400415, also known as N370S (risk genotype CC) Possibly associated with Gaucher's disease. * Type I (N370S homozygote), the most common, also called the 'non-neuropathic' type occurs mainly in Ashkenazi Jews, at 100 times the occurrence in the general populace. The median age at diagnosis is 28 years of age, and life expectancy is mildly decreased. There are no neurological symptoms. rs76763715 Parkinson's disease Gaucher Disease
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
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rs12948217, also known as Y231X or Tyr231Ter, is a SNP in the ASPA gene. According to 23andMe, only the A allele at rs12948217 confers risk to Canavan disease. A person with the CC, CT, or TT alleles is not a carrier; someone with the AC or AT alleles is a carrier; and people with two AA alleles are affected with the disease. [OMIM:[[Canavan disease]]]
Magnitude: 0
Repute:Good
References:4
Repute:Good
References:4
common in clinvar
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rs28940279, also known as E285A or Glu285Ala, is a SNP in the ASPA gene. rs28940279 is one of several known causal SNPs of Canavan disease. Canavan disease is a degenerative disease of the nervous system. It is a childhood onset disease which begins in early infancy. It is characterized by disordered muscular behavior (e.g., hypotonia, hyperextension) and neurological symptoms, such as blindness, developmental and cognitive delays. The neurological findings appear to be due to demyelination and leukodystrophy. Histology indicates the presence of spongy degeneration; cytology confirms astrocytic swelling of normal neurons and abnormality of astrocyte mitochondria. Ultimately, sufferers become extremely ill and die on average at 18 months of age. rs28940279 is a SNP in the aspartoacylase ASP...
Magnitude: 0
Repute:Good
References:7
Repute:Good
References:7
normal
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First discovered in 2004, rs34637584 is a SNP indicating a position within the LRRK2 that encodes a variant protein. This SNP is commonly referred to as the G2019S variant (or, mutation) based on the potential change from glycine (encoded by rs34637584(G) allele) to serine (encoded by the rs34637584(A) allele) at position 2019 of the LRRK2 protein. One copy of a rs34637584(A) allele is sufficient to greatly increase one's risk for Parkinson's disease. It is considered a disease causing mutation because it is rarely found in healthy, elderly people without Parkinson's disease, and it has been found in both familial and sporadic types of the disease. While there are many different SNPs that can influence one's risk for Parkinson's disease, rs34637584 is an especially common cause of the dise...
normal
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The accuracy of claims about this snp are called into question by table 1 of discusses the process of including this snp into Coriell and raises some doubt about the value of its inclusion. rs7754840 replicated as significant for type-2 diabetes risk in 1,900 Japanese patients, with odds ratio of 1.28 (CI: 1.17-1.41, p = 4.5 x 10e-7) type-2 diabetes Carriers of the (C;G) and (C;C) genotypes of rs7754840 had 11% and 24% lower first-phase insulin release in an IVGTT compared to that in carriers of the (G;G) genotype (P=0.002). The C allele was also associated with higher glucose area under the curve in an OGTT (P=0.016). rs7754840 type-2 diabetes Ashkenazi Jewish population shows an even stronger effect for rs7754840 than the general Caucasian population, based on 1,131 cases versus 1,147 co...
common in complete genomics common for Caucasians on the 23andme platform
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also known as rs28933380 related to colorectal cancer, FAMILIAL, Ashkenazi The APC I1307K mutation is primarily found in people of Ashkenazi Jewish heritage (Jews of Eastern European or Russian ancestry). Researchers believe that 6% of Ashkenazi Jews carry this gene mutation, making them at a significantly higher risk for developing colorectal cancer. It is also found among Sephardi and Mizrahi Jews and Muslim and Christian Palestinian Arabs, as well as Negev Bedouin. Many patients with colorectal cancer experience no symptoms in the early stages. In fact, symptoms may not appear until the disease is in advanced stage. Routine colorectal screening is very important. Even children from 11 years of age should be screened if there is a family history of colorectal cancer. * APC I1307K and Col...
common in clinvar
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rs63750875 is a SNP in the MSH2 gene on chromosome 2, associated with Lynch syndrome (HNPCC). The origin of this mutation appears to be in a population of Ashkenazi Jews. This variant meets the criteria published in 2013 by the ACMG regarding incidental findings in exome or genome sequencing, as a variant that they do recommend informing a patient about. See also OMIM 609309.0012 Characterization of chicken liver dihydrofolate reductase after purification by affinity chromatography and isoelectric focusing. Single-amplicon MSH2 A636P mutation testing in Ashkenazi Jewish patients with colorectal cancer: role in presurgical management. Homozygosity of MSH2 c.1906G-->C germline mutation is associated with childhood colon cancer, astrocytoma and signs of Neurofibromatosis type I. Classifyin...
16 snps
(hide) BCHE
possible increased Alzheimer's risk
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The rs1803274(A) allele encodes a version of the butyrylcholinesterase enzyme known as the K variant; it may also be known as CHE*539T or BCHE*539T. The allele produces a 30% reduction in serum butyrylcholinesterase activity, and it is often co-inherited with the SNP encoding the so-called 'atypical' butyrylcholinesterase, rs1799807. Although not replicated by other studies, some studies have found, at least in certain populations, a possible association between this SNP and risk for Alzheimer's disease (independent of ApoE4 status): * reports ~2x increased Alzheimer's risk for carriers of one or more rs1803274(A) alleles, based on a study of 135 Canadian patients * reports ~3.5x increased Alzheimer's risk for carriers of one or more rs1803274(A) alleles, based on a study of 175 patients f...
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This SNP, on chromosome 3 upstream of BCHE (butyrylcholinesterase), is associated with higher cerebral amyloid deposition. The risk allele is G. [http://www.nature.com/mp/journal/vaop/ncurrent/fig_tab/mp201319f4.html]
Typical BuChE
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rs1799807, also known as D70G, is a SNP in the BCHE gene. This SNP affects the structure, activity, and substrate specificity of the BuChE (butyrylcholinesterase) enzyme. [Cholinesterases and cholinesterase inhibitors, p. 48] The variant form, rs1799807(G), replaces aspartate with glycine at the secondary substrate/inhibitor binding site. This single base substitution yields the 'atypical' version of BChE. This version has a lower affinity for many substrates, including many Cholinesterase Inhibitors (CIs). A different cholinesterase (acetylcholinesterase, AChE) is an important component of neurotransmission by acetylcholine (ACh), terminating the action of ACh after it has been released during neurotransmission. BChE is found widely in the plasma and normally binds to CIs, protecting AChE...
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar common
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(T;T) has a moderate change in BCHE activity according to annerwright Pseudocholinesterase Deficiency [PharmGKB:Curated This variant is associated with prolonged apnea is response to succinyldicholine (also known as succinylcholine).] [OMIM:BCHE, FLUORIDE 1]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
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(T;T) abolishes catalytic activity in BCHE according to annerwright Pseudocholinesterase Deficiency [PharmGKB:Curated This variant is associated with prolonged apnea is response to succinyldicholine (also known as succinylcholine).] [OMIM:BCHE, FLUORIDE 2]
6 snps
(hide) Breast size
Frequency: 31.0%
References:1
References:1
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breast size
Frequency: 38.9%
References:3
References:3
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[GWAS:Breast size]
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[GWAS:Breast size]
Frequency: 49.6%
References:1
References:1
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[GWAS:Breast size]
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[GWAS:Breast size]
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[GWAS:Breast size]
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[GWAS:Breast size]
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[GWAS:None]
9 snps
(hide) Cannabis
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[GWAS:None]
Frequency: 27.7%
References:1
References:1
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[GWAS:None]
Frequency: 29.5%
References:1
References:1
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
more resistant to treatment for depression
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Based on a study of 256 Caucasian patients being treated for depression, carriers of a rs1049353(G) allele were less likely to respond favorably, particularly if they were females with comorbid anxiety. rs806368(C) together with rs1049353(A) or rs1049353(G) make up a haplotype associated with PTSD, with the C-A haplotype somewhat associated (p=0.04) with higher risk of PTSD and the C-G haplotype associated (p=0.01) with a lower risk of PTSD. Cannabis receptor haplotype associated with fewer cannabis dependence symptoms in adolescents. No evidence for an involvement of variants in the cannabinoid receptor gene (CNR1) in obesity in German children and adolescents. The G1422A variant of the cannabinoid receptor gene (CNR1) is associated with abdominal adiposity in obese men. No association of...
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risk of the development of substance dependence significantly increased with the number of 'G' alleles at rs6454674 and SNP8 (rs806368);T/T genotypes had significant interaction effects (p = .0003 for comorbid drug dependence (DD) and alcohol dependence (AD), .0002 for DD, and .007 for AD). SNP3 and SNP8 together exerted stronger genetic effects on SD (substance dependence) than either did individually. The peak delta values among all the markers were seen for SNP3 and SNP8 (rs806368) rs806368(C) together with rs1049353(A) or rs1049353(G) make up a haplotype associated with PTSD, with the C-A haplotype somewhat associated (p=0.04) with higher risk of PTSD and the C-G haplotype associated (p=0.01) with a lower risk of PTSD. Alcoholic patients with TGT haplotype (corresponding to rs6454674-r...
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This snp, located in intron 2 of the central cannabinoid receptor CNR1 gene, has been linked to cannabis dependence. The (G) allele is reported to have a protective effect, and is a defining part of a haplotype that is associated with lower odds of developing cannabis dependence. The (A) allele is more common in all populations studied. Variation in the human cannabinoid receptor CNR1 gene modulates gaze duration for happy faces. (G;G) is also associated with the longest gaze duration for happy faces.
None
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This SNP in the GABRA2 gene has been linked to Alcoholism. The effect of this SNP, a synonymous change at amino acid residue 132, is unknown, but it does not change the GABRA2 protein sequence. Carriers of at least one rs279858(G) allele respond slower to the effects of alcohol and are thereby apparently more prone to alcoholism than carriers of two rs279858(A) alleles. Finasteride, an FDA approved drug for the treatment of benign prostatic hypertrophy and a modulator of GABRA2, was shown to have more of a blocking effect on rs279858(A) homozygotes. Note that nearby SNPs have been grouped into a haplotype that shows statistically stronger association with alcohol dependence, namely the haplotype consisting of the rs279871(A) + rs279845(T) + rs279836(A) alleles . 1050 nicotine-dependent cas...
multiple associations, see details
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rs4680 (Val158Met) is a well studied SNP in the COMT gene. 23andMe blog summarizes them as *rs4680(A) = Worrier. Met, more exploratory, lower COMT enzymatic activity, therefore higher dopamine levels; lower pain threshold, enhanced vulnerability to stress, yet also more efficient at processing information under most conditions *rs4680(G) = Warrior. Val, less exploratory, higher COMT enzymatic activity, therefore lower dopamine levels; higher pain threshold, better stress resiliency, albeit with a modest reduction in executive cognition performance under most conditions Roughly speaking, the predominant wisdom (known colloquially as the warrior/worrier hypothesis; summary at ) posits that people with Val alleles have increased COMT activity and lower prefrontal extracellular dopamine compar...
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risk of the development of substance dependence significantly increased with the number of 'G' alleles at rs6454674 and SNP8;T/T genotypes had significant interaction effects (p = .0003 for comorbid DD and AD, .0002 for DD, and .007 for AD). SNP3 and SNP8 together exerted stronger genetic effects on SD than either did individually. The peak delta values among all the markers were seen for SNP3 and SNP8 (rs806368) rs806377(C) together with rs6454674(G) make up a haplotype associated (p=0.008) with higher risk of ADHD. In addition, the haplotype was more associated (p=0.03) with ADHD in males than in females with the risk haplotype. Cannabis receptor haplotype associated with fewer cannabis dependence symptoms in adolescents. No association of CNR1 gene variations with susceptibility to schi...
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rs806377(C) together with rs6454674(G) make up a haplotype associated (p=0.008) with higher risk of ADHD. In addition, the haplotype was more associated (p=0.03) with ADHD in males than in females with the risk haplotype. Cannabis receptor haplotype associated with fewer cannabis dependence symptoms in adolescents. Evidence for association between polymorphisms in the cannabinoid receptor 1 (CNR1) gene and cannabis dependence. Interaction between two independent CNR1 variants increases risk for cocaine dependence in European Americans: a replication study in family-based sample and population-based sample. Candidate genes for cannabis use disorders: findings, challenges and directions. The association between cannabinoid receptor 1 gene (CNR1) and cannabis dependence symptoms in adolescent...
1.4x higher schizophrenia risk
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rs6277 (957C>T, Pro319Pro) is one of several SNPs in the dopamine receptor DRD2 gene. In a study of 300+ Russian patients with schizophrenia, the rs6277(C) allele was associated with higher risk. From a pooled meta-study (total of 4 other reports plus this one) the allelic odds ratio is 1.42 (CI: 1.26-1.61, p<0.00005), and the genotypic odds ratio for the (C;C) genotype was 1.6 (CI: 1.32-1.95, p<0.00005). Note that rs6275 and rs6277 are only 18bp apart, hence their very tight linkage (r<sup>2</sup>=1). gs278 reflects a gene-gene interaction between this SNP and a NR3A SNP, rs10989591, in which older adults with a particular combination of genotypes at these two (independent) loci are reported to exhibit better episodic memory. C allele associated significantly (p = 0.0...
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[GWAS:None]
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rs2494732 is a SNP in the AKT1 gene, encoding one of three serine/threonine-protein kinases regulating numerous processes such as cell survival, growth and angiogenesis. Medical conditions that may be linked to the rarer (minor) rs2494732(C) allele include drug response, schizophrenia, and drug-related psychoses, in particuler, cannabis-related psychosis. A case-control study of 489 first-episode psychosis patients concluded that while rs2494732 was not associated with an increased risk of a psychotic disorder, with lifetime cannabis use, or with frequency of use, there was a significant association between psychosis and cannabis use. rs2494732(C;C) individuals with a history of cannabis use had an increased likelihood of a psychotic disorder (odds ratio 2.18, CI: 1.1 - 4.3) when compared ...
normal
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rs324420 is a SNP, also known as Pro129Thr, in the fatty acid amide hydrolase FAAH gene, which has shown associations with some substance use disorders. rs324420(C) encodes the more common Pro, while the (A) allele encodes the Thr. Among 80 individuals with drug abuse or alcoholism and over 1,000 controls, the odds ratio for risk of problem drug or alcohol use among rs324420(A;A) individuals was 4.5 (CI: 2.2 - 8.4); the odds ratio for risk of street drug use was 2.2 (CI: 1.3–3.7); and the odds ratio for risk of combined street drug use and problem drug/alcohol use was 4.9 (CI: 2.5–9.7) When this study was pooled with the results of another study of 249 subjects with documented multiple different drug addictions compared to drug free individuals of the same ethnic backgrounds, t...
common/normal Val/val (normal) variant of the Val66Met snp in the BDNF gene that codes for brain-derived neurotrophic factor. Met/met is associated with susceptibility to neuropsychiatric disorders.
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rs6265, also known as Val66Met, is a SNP in brain-derived neurotrophic factor BDNF gene. The more common G allele encodes the Val, while the A allele encodes Met. Met/A allele associated with introversion The A allele may also be protective against depression when subjected to repeated defeat g2b2mh blog On a driving-based motor learning task subjects with this genotype showed greater error during short-term learning and poorer retention over 4 days, relative to subjects without the polymorphism. The presence of this BDNF polymorphism is associated with differences in brain motor system function, altered short-term plasticity, and greater error in short-term motor learning. Wired discusses the research as does 23andMe blog. Alzheimer's disease risk for non ApoE4 carriers is affected by the...
normal
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The rs1799971(G) allele in exon 1 of the mu opioid receptor OPRM1 gene causes the normal amino acid at residue 40, asparagine (Asn), to be replaced by aspartic acid (Asp). In the literature this SNP is also known as A118G, N40D, or Asn40Asp. Carriers of at least one rs1799971(G) allele appear to have stronger cravings for alcohol than carriers of two rs1799971(A) alleles, and are thus hypothesized to be more at higher risk for alcoholism. However, subsequent research results are mixed, and there are other studies both agreeing or disagreeing with this finding Among 200+ alcoholics treated with naltrexone, rs1799971(G) carriers receiving the drug (even without behavioral intervention) had an increased percentage of days abstinent (p = .07) and a decreased percentage of heavy drinking days (...
normal
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rs1076560 is located in intron 6 of the dopamine receptor D2 gene. In one study of Japanese males, rs1076560(A) alleles were 1.3 fold more associated with Alcoholism than the rs1076560(C) alleles. The DRD2 risk allele A was more prevalent in the alcoholic patients than in the healthy controls. These data identify rs1076560 as a potentially important variable in the development of alcoholism. rs1076560 and the DAT 3'-VNTR variant influences memory Genetic variants altering dopamine D2 receptor expression or function modulate the risk of opiate addiction and the dosage requirements of methadone substitution [PharmGKB:Curated This variant is a potential marker for alcoholism. A allele was more prevalent in the alcoholic patients than in the healthy controls in a study consists of 248 alcohol...
Magnitude: 0
Frequency: 81.0%
Repute:Good
References:5
Frequency: 81.0%
Repute:Good
References:5
common in complete genomics
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Association of the cannabinoid receptor gene (CNR1) with ADHD and post-traumatic stress disorder. Cannabinoid receptor 1 (CNR1) gene: impact on antidepressant treatment response and emotion processing in major depression. Cannabinoid receptor 1 gene association with nicotine dependence. Cannabinoid type-1 receptor gene polymorphisms are associated with central obesity in a Southern Brazilian population. Evidence for association between polymorphisms in the cannabinoid receptor 1 (CNR1) gene and cannabis dependence. Genetic variation in cannabinoid receptor 1 (CNR1) is associated with derangements in lipid homeostasis, independent of body mass index. Candidate genes for cannabis use disorders: findings, challenges and directions. The implication of CNR1 gene's polymorphisms in the modulatio...
Magnitude: 0
Frequency: 88.5%
Repute:Good
References:1
Frequency: 88.5%
Repute:Good
References:1
24 snps
(hide) Cholinesterase Inhibitors
higher risk of of coronary heart disease coronary heart disease
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rs662, also known as Q192R, is a SNP in the PON1 gene. It codes for amino acid 192 of the paraoxonase (PON) protein. Variants of this SNP affect PON catalytic efficiency and are correlated with Heart disease and trait-anxiety scores. The normal form, rs662(A), encodes a glutamine (Q), while the variant, rs662(G)), encodes an arginine (R). . While some populations show an association between this SNP and Heart disease, not all do. Perhaps the most striking finding was reported in Japanese patients with non-insulin dependent diabetes mellitus (NIDDM). NIDDM patients with either one or two rs662(G) alleles had a 9 fold higher risk of coronary heart disease compared with rs662(A;A) NIDDM patients. table of odds for cardiovascular disease outcomes 274 ovarian epithelial carcinoma cases and 452 ...
Smokes normal (lower) number of cigarettes if a smoker. Less nicotine dependence. Also smokes each cigarette less deeply. Therefore there is a reduced risk of lung cancer and a reduced (0.8x) risk of Peripheral Artery Disease. This doesn't affect whether people start smoking though.
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rs1051730, also known as D398N, is a SNP in the nicotinic acetylcholine receptor alpha 3 subunit CHRNA3 gene. In two recent (2008) studies, together comprising over 6,000 lung cancer patients of European ancestry, the rs1051730(T) allele was very significantly associated with increased risk. Having one copy (i.e. being a rs1051730(C;T) genotype) increased risk for lung cancer about 1.3x, and having two copies (rs1051730(T;T) individuals) represented 1.8x increased risk. Up to 14% of lung cancer incidence may be attributable to this allele. An independent study published at the same time concluded that (T) allele carriers for SNP rs1051730 are not at higher risk of becoming smokers compared to (C) carriers. However, if they do smoke, (T) carriers are quite likely to smoke more cigarettes th...
normal
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rs705381, also known as -161C/T and -162A/G, is a SNP in the upstream promoter region of the PON1 gene. (The assumption of equivalence between these names is based on the results of searching for rs705381 in the Variant Name Mapper.) In a study of 101 mostly Caucasian patients prescribed the atypical antipsychotic risperidone, carriers of a rs705381(C) allele were less likely to gain significant weight compared to rs705381(T;T) carriers, as assessed by physiogenomic analysis of corresponding weight profiles. Two other SNPs, rs8179183 and rs6837793, were also significantly associated with weight profiles in these patients. In a study of 461 participants in the HERITAGE cohort (172 African-American, 289 Caucasian), the combination of rs705381 with 'PON-126' (RS ID unknown) were found to sign...
possible increased Alzheimer's risk
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The rs1803274(A) allele encodes a version of the butyrylcholinesterase enzyme known as the K variant; it may also be known as CHE*539T or BCHE*539T. The allele produces a 30% reduction in serum butyrylcholinesterase activity, and it is often co-inherited with the SNP encoding the so-called 'atypical' butyrylcholinesterase, rs1799807. Although not replicated by other studies, some studies have found, at least in certain populations, a possible association between this SNP and risk for Alzheimer's disease (independent of ApoE4 status): * reports ~2x increased Alzheimer's risk for carriers of one or more rs1803274(A) alleles, based on a study of 135 Canadian patients * reports ~3.5x increased Alzheimer's risk for carriers of one or more rs1803274(A) alleles, based on a study of 175 patients f...
some positive effect of AChE inhibitors for Alzheimer's patients
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rs733722, also known as -5293C>T, is a SNP near the choline acetyltransferase CHAT gene. A study of 121 Alzheimer's disease patients treated primarily with the acetylcholinesterase (AChE) inhibitors donepezil or galantamine found different rates of mental decline depending on rs733722 genotypes. Individuals of rs733722(C;C) genotype effectively showed declines in cognition over time equivalent to untreated patients, whereas rs733722(C;T) individuals showed less decline, and rs733722(T;T) patients had a negligible decline over the course of the study (~15 months). An earlier study by these authors found no association between SNPs in this gene and actual risk for Alzheimer's.
Magnitude: 0
Frequency: 38.9%
References:103
Frequency: 38.9%
References:103
normal
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Associated with smoking phenotype (p=0.007) based on association study of 2,000+ individuals, and functional studies demonstrated that the risk allele decreased response to a nicotine agonist, therefore the rs16969968(A) allele is likely to be involved in nicotine dependence. In a study 500+ individuals with cocaine dependence, the same rs16969968(A) allele was associated with a 0.67x decreased risk (p = 0.0045). A study of 200 individuals replicated the association between this SNP and nicotine dependence, and also concluded that the rs16969968(A) allele was significantly associated with 'enhanced pleasurable responses' to a person's first cigarette. 23andMe blog 23andMe considers rs1051730 equivalent The association between rs16969968 and lung cancer may, in part, be confounded by chroni...
Typical BuChE
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rs1799807, also known as D70G, is a SNP in the BCHE gene. This SNP affects the structure, activity, and substrate specificity of the BuChE (butyrylcholinesterase) enzyme. [Cholinesterases and cholinesterase inhibitors, p. 48] The variant form, rs1799807(G), replaces aspartate with glycine at the secondary substrate/inhibitor binding site. This single base substitution yields the 'atypical' version of BChE. This version has a lower affinity for many substrates, including many Cholinesterase Inhibitors (CIs). A different cholinesterase (acetylcholinesterase, AChE) is an important component of neurotransmission by acetylcholine (ACh), terminating the action of ACh after it has been released during neurotransmission. BChE is found widely in the plasma and normally binds to CIs, protecting AChE...
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar common
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(T;T) has a moderate change in BCHE activity according to annerwright Pseudocholinesterase Deficiency [PharmGKB:Curated This variant is associated with prolonged apnea is response to succinyldicholine (also known as succinylcholine).] [OMIM:BCHE, FLUORIDE 1]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
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(T;T) abolishes catalytic activity in BCHE according to annerwright Pseudocholinesterase Deficiency [PharmGKB:Curated This variant is associated with prolonged apnea is response to succinyldicholine (also known as succinylcholine).] [OMIM:BCHE, FLUORIDE 2]
9 snps
(hide) Coffee
Magnitude: 2.5
more stimulated by coffee
You appear to have a common genotype in the gene CYP1A2 which metabolizes coffee more slowly than some other forms. The same amount of caffeine will tend to have more stimulating effect on slow metabolizers than on fast metabolizers. Ciprofloxacin is also metabolized by CYP1A2, but is unclear if your genotype should influence its effect.
Carrier of one CYP1A2*1F allele; Slow Caffeine Metabolizer. One copy of the slow caffeine metaboliser SNP, and one copy of the fast version. This makes you more strongly affected by drinking coffee, as caffeine is broken down slower in the liver. Supposedly this increases the risk of heart attacks, although other studies show caffeine is generally good for the heart. It also makes caffeine more effective at preventing Breast Cancer, Alzheimer's Disease, and Parkinson's disease. Too much caffeine will shrink your breasts.
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rs762551, also known as -164A>C or -163C>A, is a SNP encoding the CYP1A2*1F allele of the CYP1A2 gene. For historic reasons, the rs762551(C) allele is considered the wild-type, even though it is the rarer allele in most populations. The rs762551(A) allele is the 'fast metabolizer' allele known as CYP1A2*1F; the (C) allele is by comparison a slower metabolizer of certain substrates (including caffeine). In terms of genotypes, only rs762551(A;A) individuals are considered fast metabolizers. Individuals who are rs762551(A;C) heterozygotes or rs762551(C;C) homozygotes are both considered slow metabolizers. The CYP1A2 gene encodes a member of the cytochrome p450 family of proteins, which metabolize nutrients and drugs. One well known substrate of CYP1A2 is caffeine; individuals who are ca...
significantly higher anxiety levels after moderate caffeine consumption
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Variation at this SNP, rs5751876, also referred to as 1976C>T or 1976T>C, appears to influence how an individual responds to moderate levels (150mg) of caffeine. T/T carriers displaying significantly increased subjective levels of anxiety after consumption. However a PharmGKB variant annotation suggests it is (C;C) genotypes who are more sensitive to caffeine. rs5751876 is not associated with how much coffee one drinks, though, nor with risk for Parkinson's disease, based on a study of 1,200 subjects. 'rs2298383 shows functional potential based on in silico analyses and might therefore represent the true underlying causal variant'
Able to taste bitterness.
Normal tasting ability for bitterness. This makes turnip, cabbage, brussels sprouts, broccoli, and other cruciferous vegetables taste more interesting and less horribly bland. Coffee and dark beers also tastes more bitter. You can taste propylthiouracil (PROP), PTC, and related chemicals. On the other hand, you can't taste the unpleasant bitterness of the tropical fruit from the Bignay tree, it will taste sweet to you. You probably eat healthier.
Can taste bitter. Normal tasting ability for bitterness. This makes turnip, cabbage, brussels sprouts, broccoli, and other cruciferous vegetables taste more interesting and less horribly bland. Coffee and dark beers also tastes more bitter. You can taste propylthiouracil (PROP), PTC, and related chemicals. On the other hand, you can't taste the unpleasant bitterness of the tropical fruit from the Bignay tree, it will taste sweet to you. You probably eat healthier.
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rs713598 is one of three SNPs that form the main haplotypes behind the ability to perceive as bitter the taste of the compound phenylthiocarbamide (PTC) and similar molecules in foods (like cabbage and raw broccoli) or drinks (like coffee and dark beers). The rs713598(G) allele, in the orientation shown in dbSNP, is the 'tasting' allele, and it is dominant to the 'non-tasting' allele rs713598(C), so having one copy is enough to have the bitter tasting ability. If you are a 'taster', you're also likely to carry at least one rs10246939(C) and one rs1726866(C) allele since, along with rs713598(G), these three SNPs form the most common tasting haplotype. If you lack these alleles, you're quite likely (~80%) to be a non-taster of bitterness, meaning that foods that may taste bitter to others ta...
can taste bitter
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rs1726866 is one of three SNPs that form the main haplotypes behind the ability to perceive as bitter the taste of the compound phenylthiocarbamide (PTC) and similar molecules in foods (like cabbage and raw broccoli) or drinks (like coffee and dark beers). The rs1726866(C) allele is the 'tasting' allele, and it is dominant to the 'non-tasting' allele rs1726866(T), so having one copy is enough to have the bitter tasting ability. If you are a 'taster', you're also likely to carry at least one rs713598(G) and one rs10246939(C) allele since, along with rs1726866(C), these three SNPs form the most common tasting haplotype. If you lack these alleles, you're quite likely (~80%) to be a non-taster of bitterness, meaning that foods that may taste bitter to others taste far less bitter to you. (C;C)...
Magnitude: 0.1
Frequency: 47.8%
References:10
Frequency: 47.8%
References:10
can taste bitter
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rs10246939 is one of three SNPs that form the main haplotypes behind the ability to perceive as bitter the taste of the compound phenylthiocarbamide (PTC) and similar molecules in foods (like cabbage and raw broccoli) or drinks (like coffee and dark beers). The rs10246939(C) allele, in the orientation shown in dbSNP, is the 'tasting' allele, and it is dominant to the 'non-tasting' allele rs10246939(T), so having one copy is enough to have the bitter tasting ability. If you are a 'taster', you're also likely to carry at least one rs713598(G) and one rs1726866(C) allele since, along with rs10246939(C), these three SNPs form the most common tasting haplotype. If you lack these alleles, you're quite likely (~80%) to be a non-taster of bitterness, meaning that foods that may taste bitter to oth...
common on affy axiom data
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rs2472297 is a SNP located between the CYP1A1 and CYP1A2 genes on ch 15q24. A meta-analysis of four GWAS studies of coffee consumption among a total of ~8,000 coffee drinkers of European ancestry found that the rs2472297(T) was strongly associated with increased consumption (p = 5.4 x 10e-14). The estimated effect was an increase of 0.2 cups a day per allele for both this SNP and one other (rs6968865).
2 genosets 6 snps
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1.6x increased risk for prostate cancer; also other cancers 1.4 times as likely to develop colorectal cancer
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rs6983267 is a SNP on chromosome 8q24, associated with increased risk for several cancers, particularly prostate cancer. In studies dividing the 8q24 region, this SNP falls in region 3. This SNP has also been reported to influence the cancer-risk-decreasing effect of aspirin. In a study of over 3,600 Caucasians with prostate cancer, rs6983267 is one of five SNPs used (with family history as a sixth factor) to cumulatively predict overall risk. On their own, the rs6983267(G;G) and (G;T) risk genotypes yield an odds ratio for developing prostate cancer of 1.37 (CI: 1.18-1.59, p=3.4-10e-5) and may account for 22.2% of population attributable risk. The increased risk of developing prostate cancer associated with rs6983267 now appears to be independent of the risk associated with its close neig...
1.2x risk Rheumatoid Arthritis
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rs6920220 has been reported in a large study to be associated with rheumatoid arthritis. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.20 (CI 1.06-1.36), and for homozygotes, 1.72 (CI 1.33-2.22). rheumatoid arthritis *rs6920220 [P= 2.6 x 10(-6), OR 1.22 (1.13-1.33)]. *rs5029937 *rs13207033 protective [P= 0.0001, OR 0.86 (0.8-0.93)] perfectly correlated with rs10499194 The combination of the carriage of both risk alleles of rs6920220 and rs5029937 together with the absence of the protective allele of rs13207033 was strongly associated with RA when compared to carriage of none [OR of 1.86 (95% CI) (1.51-2.29)]. This equates to an effect size of 1.50 (95% CI 1.21-1.85) Lack of association or interactions between the IL-4, IL-4Ralpha an...
Magnitude: 2.5
Frequency: 8.2%
Repute:Good
References:102
Frequency: 8.2%
Repute:Good
References:102
0.26x lower risk for certain autoimmune diseases. Substantially decreased risk of Ankylosing Spondylitis (0.6x), Chron's Disease (0.37x), Psoriasis (0.6x), and Ulcerative Colitis (0.59x). This is the rare version of the interleukin-23 (IL-23) receptor.
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A relatively rare allele at SNP rs11209026, in the IL23R gene, appears to provide a fairly strong protective effect against the development of Crohn's disease in both Jewish and non-Jewish populations. Note that in this study the (A;A) and (A;G) genotypes were combined for statistical reasons (there were too few (A;A) individuals to study by themselves), so the risk is shown as equal for both. associated With Inflammatory Bowel Diseases but Not With Celiac Disease rs11209026 had a protective effect for IBD in the case-control analysis (odds ratio [OR] 0.19, 95% confidence interval [CI] 0.10-0.37, P= 6.6E-09). Both CD (OR 0.14, CI 0.06-0.37, P= 3.9E-07) and UC (OR 0.33, CI 0.15-0.73, P= 1.4E-03) were associated with IL23R. rs2241880 was associated with CD susceptibility (OR 1.36, CI 1.12-1....
reduced risk (0.84x) for late-onset (adult) asthma Found in 38% of all Caucasions, this genotype is associated with a reduced risk (relative risk = 0.84) for late-onset (adult) asthma.
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rs1837253 is a SNP found a bit upstream of the thymic stromal lymphopoietin TSLP gene on chromosome 5. The TSLP protein plays a role in inflammation of cells in the trachea and alveoli therefore may have a causative role in certain types of asthma. The rs1837253(T) allele has been found to reduce the risk of developing late-onset (adult) asthma in several studies, and it is recognized by the CPMC Study as one they report to their participants. [GWAS:None]
reduced risk (0.59x) of pancreatic cancer
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23andMe reports that the G allele of this SNP appears to lower the risk of pancreatic cancer. Genome-wide association study of pancreatic cancer in Japanese population. [OMIM:?] [GWAS:Pancreatic cancer]
1.4x higher risk of lupus increased risk of Systemic lupus erythematosus.
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CPMC uses this to indicate increased risk of Systemic lupus erythematosus. [GWAS:Systemic lupus erythematosus]
Magnitude: 2
Frequency: 43.1%
References:13
Frequency: 43.1%
References:13
CYP2C19*17 ultra fast metabolizer; drug metabolism effects; also 0.77x decreased breast cancer risk
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rs12248560(T) defines the CYP2C19*17 allele, an ultra fast metabolizer phenotype of the CYP2C19 gene. CYP2C19*17 is likely to lead to less effective drug treatment by, for example, proton pump inhibitors (such as omeprazole) and antidepressants. On the other hand, cancer patients who are CYP2C19*17 carriers are more likely to benefit from tamoxifen treatment, presumably because they break it down more rapidly into the antiestrogenic metabolites endoxifen and 4-hydroxytamoxifen. A study of 1,000+ breast cancer patients showed a 0.77x decreased risk of breast cancer for carriers of a CYP2C19*17 allele (CI: 0.65-0.93, p = 0.005). Analysis of a subgroup of such carriers who were using hormone therapy for ten years or longer showed an even stronger effect (odds ratio 0.57, CI: 0.39-0.83, p = 0....
lower warfarin dosing
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rs2108622 is a SNP in the cytochrome P450, family 4, subfamily F, polypeptide 2 CYP4F2 gene. In the males rs2108622(G) was significantly higher in cerebral infarction patients (P = 0.025) A study of Italian patients concluded that rs2108622(T;T) patients require 5.49 mg/day of warfarin versus 2.93 mg/day for (C;C) patients. Analysis of variance indicates that about 7% of mean weekly warfarin dose variance is explained by CYP4F2 genotype. A study of 370 Brazilian ('admixed') patients concludes that prospective CYP4F2 genotyping is of little value to these patients, presumably due to ethnic-based differences. [PharmGKB:Curated Risk or phenotype-associated allele: no allelic association. Phenotype: Improved pharmacogenetic algorithm-based warfarin dosing. Study size: 370. Study population/et...
1.2x increased bladder cancer risk
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rs9642880 is a SNP located in chromosome region 8q24, a region that has been linked to prostate, breast, and colon cancer. A study ultimately totaling over 4,000 bladder cancer patients of European ancestry (and 40,000 controls) concluded that individuals carrying two copies of rs9642880(T) were at 1.49x increased risk (allele-specific odds ratio = 1.22, p = 9 x 10e-12) for the disease. This SNP was not associated, however, with risk for prostate, breast, or colon cancer. Another study in Chinese populations found similar results in regard to bladder cancer. rs9642880(T;T) estimated risk of developing 1.49 times that of noncarriers. 1,803 urinary bladder cancer cases and 34,336 controls. No association with prostate, colorectal and breast cancers. In contrast to GSTM1 SNPs, the rs9642880(T...
non-protective against testicular cancer
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23andMe blog each rs4624820(G) increases the odds of testicular cancer by 2.5x. <p><br> As reported by the CPMC, relative to men who are rs995030(A;A), men who are rs995030(A;G) have a 0.38 relative risk, and those who are (G;G) have a 0.15 relative risk. Association of genetic markers within the KIT and KITLG genes with human male infertility. Common variation in KITLG and at 5q31.3 predisposes to testicular germ cell cancer. [OMIM:?] [GWAS:Testicular germ cell tumor]
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A genome-wide association study of pulmonary function measures in the Framingham Heart Study. Hedgehog-interacting protein is a COPD susceptibility gene: the Rotterdam Study. [PharmGKB:Non-Curated GWAS results: A Genome-Wide Association Study in Pulmonary Disease, Chronic Obstructive (COPD): Identification of Two Major Susceptibility Loci. (Initial Sample Size: 823 cases, 810 controls; Replication Sample Size: 2,840 family members, 389 cases, 472 controls); (Region: 4q31.22; Reported Gene(s): HHIP; Risk Allele: rs1828591-?); (p-value= 0.0000001).This variant is associated with Pulmonary Disease, Chronic Obstructive.] [GWAS:Chronic Obstructive Pulmonary Disease]
normal
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rs401681 is a SNP in the CLPTM1-like CLPTM1 gene. The following studies span several types of cancer, and over 30,000 cases and 45,000 controls. deCODE press release reports rs401681 linked to basal cell carcinoma and many cancers for individuals with shorter telomeres, whereas those with long telomeres are at greater risk of melanoma. Neighboring rs2736098 also increases risk of cancer by affecting telomerase reverse transcriptase. The risk of these different cancers conferred by these two SNPs appears to be independent. 23andMe blog rs2736098 and rs401681 linked to many cancers, including susceptibility to pancreatic cancer However, a very large study (encompassing thousands of cases and controls) found no association between rs401681 and either (1) mean telomere length, or, (2) breast c...
complex; see details
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rs1143634, also known as +3954, is a SNP in the IL-1 beta IL1B gene. A study of 556 adults in the Western Australian coronary heart disease (CHD) population concluded that rs1143634(T;T) homozygotes had larger waist circumference, by 1.8cm on average, compared to major allele (C;C) homozygotes. This association was even more pronounced in patients with higher levels of obesity or inflammatory markers. rs1143634 increases susceptibility to Alopecia Areata 2.67 times for heterozygotes (CT) and 1.13 times for homozygotes (TT) rs1143634 increases susceptibility to Alzheimer's disease 2.33 times for homozygotes (TT) rs1143634 increases susceptibility to Cervical lesions, low-grade squamous intraepithelial lesions 4.29 times for heterozygotes (CT) and 3.57 times for homozygotes (TT) rs1143634 in...
References:0
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influences statin response *rs72559745 (SLCO1B1*1) AA AA *rs56061388 (SLCO1B1*3) TT TT *rs4149056 (SLCO1B1*5) TT TT *rs55901008 (SLCO1B1*6) TT TT
normal
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rs9332131, also known as 818delA, 10601delA or 273Frame shift, is a SNP in the CYP2C9 gene. The rs9332131(-) allele defines the CYP2C9*6 variant, which is inactive. [PharmGKB:Curated Phenotype: In African Americans patients, weekly warfarin dose requirements were lower in those with the CYP2C9*8 allele (34 (30-47) mg; P = 0.023) and the CYP2C9 *2, *3, *5, *6, or *11 allele (33(28-40 mg); P < 0.001) as compared with those with the CYP2C9*1/*1 genotype (43 (35-56) mg). Adding the *5,*6,*8 and *11 alleles to a model containing the *2 and *3 alleles plus the VKORC1 -1639 G>A allele (along with clinical variables) explained 36% vs. 30% of the variability in dose requirements. Study size: 226 . Study population/ethnicity: African-American . Type of association: PD;GN;CO]
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influences statin response *rs72559745 (SLCO1B1*1) AA AA *rs56061388 (SLCO1B1*3) TT TT *rs4149056 (SLCO1B1*5) TT TT *rs55901008 (SLCO1B1*6) TT TT
normal; no change in warfarin metabolism
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rs1799853 is a SNP in the CYP2C9 gene and is linked to poor warfarin metabolism. Advanced knowledge of this may influence initial warfarin dosing by physicians. Warfarin is monitored through INR (international normalized ratio) and proper dosing is influenced by a variety of factors including warfarin metabolism and diet. rs1799853 is a SNP in the CYP2C9 gene. The rs1799853(T) allele encodes a variant amino acid, cysteine, which has been linked to poor metabolism of warfarin and thus sensitivity . The common nomenclature for this polymorphism is CYP2C9*2 (Cys amino acid, T allele; the SNP is also known as C430T or Cys144Arg). The CYP2C9*2 allele is also associated with higher sensitivity to the anti-epileptic drug phenytoin. The effect of CYP2C9 variants on drug metabolism should not be pr...
normal; no effect on warfarin metabolism
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SNP rs1057910(A), located in the cytochrome p450 CYP2C9 gene, most commonly encodes the amino acid isoleucine at position 359, and the resulting allele is also known as CYP2C9*1. rs1057910(C) encodes a leucine at this same position, and the resulting allele is called CYP2C9*3. This SNP is also known as Ile359Leu or A1075C. The effect of CYP2C9 variants on drug metabolism should not be predicted without also considering CYP2C9*2, defined as the common loss of function variant rs1799853(T) (NM_000771:c.430C>T, NP_000762:p.144R>C) Studies of the effects of these alleles include: * rs1057910(C;C)] genotypes may clear drugs like celecoxib (trade name Celebrex) twice as slowly as rs1057910(A;A) genotypes; the rs1057910(A;C) genotypes are in-between clearance rates. Lower clearance rates wi...
normal
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rs9272346 has been reported in a large study to be associated with type-1 diabetes. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 5.49 (CI 4.83-6.24), and for homozygotes, 18.52 (CI 12.69-27.03). Note that the (A) allele is the most common in various human populations; instead of labeling (A) as a risk allele, we could consider the (G) allele protective. Risk alleles for multiple sclerosis identified by a genomewide study. Pharmacogenetics: data, concepts and tools to improve drug discovery and drug treatment. Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations. A study of CNVs as trait-associated polymorphisms and as expression quantitative trait loci. [PharmGKB:Curated GWAS ...
normal
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rs2981582 in the FGFR2 gene was one of the four strongest associations found in a genome-wide association study (GWAS) of over 4,000 breast cancer samples. The T allele was more strongly related to ER-positive (per-allele odds ratio 1.31 (CI: 1.27-1.36)) than ER-negative (odds ratio 1.08 (CI:1.03-1.14)) disease (p for heterogeneity = 10(-13)). While on its own still of fairly small effect, this was the most significant of 7 SNPs to help estimate risk of breast cancer. Family history and/or BRCA1 or BRCA2 testing status are more significant factors, which were not part of this panel. Based on a study of 1,049 Chinese breast cancer patients, carriers of risk alleles at three SNPs (rs2981582, rs1219648 and rs2420946) were at 1.36x increased risk for breast cancer (CI: 1.13-1.62, p = 0.001). A...
normal
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Several SNPs in the VKORC1 gene have been linked to warfarin sensitivity, with perhaps the most common being this SNP rs9923231. Note that the orientation as published in scientific articles is often on the opposite strand compared to the orientation in dbSNP, so you will sometimes see it as a G>T snp. It is also known as *-1639G>A with the minus indicating that this is in an upstream promoter *3673 based on its position in GenBank accession number AY587020. *VKORC1*2. The main findings related to the treatment of venous thromboembolism (aka VTE; from hypercoagulability) with the blood thinner warfarin for this SNP are that carriers of the rs9923231(T) allele require significantly reduced doses of warfarin, and are (otherwise) at a higher risk of serious bleeding. Clinical studies de...
Magnitude: 0
Frequency: 61.1%
Repute:Good
References:58
Frequency: 61.1%
Repute:Good
References:58
normal
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rs10490924 was identified as a risk factor from chromosome 10 related to age related macular degeneration. The risk allele is (T). Odds ratios for heterozygotes and homozygotes are, respectively, 2.69 (CI: 2.22-3.27) and 8.21 (CI: 5.79-11.65). Disease risk in combination with the rs1061170 SNP in the CFH gene is dramatically increased. Homozygotes for both the rare/risk alleles at both loci are estimated to be at 57 fold higher risk for age related macular degeneration than individuals homozygous for the common alleles at both loci. A subsequent study indicated that the risk based on solely the ARMS2 SNP rs10490924 is significantly higher in smokers than in non-smokers. Based on a study of ~750 patients, rs10490924 is significantly higher in participants with choroidal neovascularization t...
normal
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influences statin response *rs72559745 (SLCO1B1*1) AA AA *rs56061388 (SLCO1B1*3) TT TT *rs4149056 (SLCO1B1*5) TT TT *rs55901008 (SLCO1B1*6) TT TT rs4149056, also known as 37041T>C or V174A, is a SNP in the SLCO1B1 gene, which encodes the 'organic anion transporting polypeptide 1B1' (OATP1B1) protein. This protein, found primarily in the liver, regulates the uptake of numerous drugs and natural compounds. The rs4149056(C) SNP defines the SLCO1B1*5 allele. The rs4149056(C) allele gives rise to an amino acid change (from valine to alanine at residue 174) which has reduced uptake/transport activity. Therefore, drugs metabolized by OATP1B1 tend to build up to higher circulating concentrations than they would otherwise.. The drugs known (or in some cases, thought) to be transported less well ...
normal
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rs3736228 is a SNP in the LRP5 gene that is also known as Ala1330Val or A1330V; the more common (C) allele encodes the Ala (alanine), while the rarer (T) allele encodes the Val (valine), which is the risk allele. rs3736228(T) is associated with vertebral fractures and reduced bone mineral density (BMD), with an overall odds ratio for fractures of 1.06 per allele (CI: 1.01-1.12; 7802 fractures among 31,199 individuals studied). More specifically, the rs3736228(T) allele was associated with reduced lumbar spine BMD (p = 2.6 x 10<sup>-9</sup>), and femoral neck BMD (p = 5.0 x 10<sup>-6</sup>). Note that rs4988321, another LRP5 SNP (also known as Val667Met), was independently associated with BMD in this same study. news rs3736228 was associated with a 30% increase in th...
normal
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rs4244285 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*2 variant. This variant is the most common reason for poor metabolism of compounds like mephenytoin (an anti-convulsant), some antidepressants, the anti-platelet drug Plavix, and some drugs used for ulcer conditions of various types. The risk allele is rs4244285(A). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (trade name Prevacid). In Caucasians, SNPs in CYP2C19 are relatively rare (in contrast to SNPs in CYP2D6), but SNPs in this gene are common in Asians. Ulcer treatment with omeprazole to reduce Helicobacter pyl...
normal
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A total of 2,019 cutaneous melanoma cases and 2,105 controls (Australians of European descent) were included in this genome-wide pooling association study. Using pooling, a new melanoma risk locus was identified on chromosome 20 (rs910873 and rs1885120; combined P < 1E-15. The per allele odds ratio was 1.75 (95% CI, 1.53-2.01), with evidence for stronger association in early-onset cases (age ≤40 OR, 1.83 (95% CI, 1.39-2.41); age >40 OR, 1.30 (95% CI, 1.00-1.69)). This study, which was conducted within the Nurses' Health Study, included 492 cases of non-melanoma skin cancer (NMSC; basal cell and squamous cell carcinomas) and 619 controls. The subjects were all Caucasian women, and the follow-up period was 28 years. rs910873, an ASIP gene-related SNP, was found to be associated w...
Not a C282Y hemochromatosis carrier.
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rs1800562 represents a SNP that accounts for ~85% of all cases of hemochromatosis, a disorder whose symptoms include cirrhosis of the liver, diabetes, hypermelanotic pigmentation of the skin, and heart failure. OMIM indicates that liver cancer is responsible for about one-third of deaths of rs1800562(A;A) homozygotes, and since hemochromatosis is a relatively easily treated disorder if diagnosed, this is a form of preventable cancer. The rs1800562(A) allele is known as the C282Y or Cys282Tyr mutation, and it is found at a frequency of around 5-10% in many Caucasian populations, leading to an incidence of (A;A) homozygotes around 1 in 200. Early identification of rs1800562(A;A) homozygotes can prevent complications of hemochromatosis; however, the percentage of all (A;A) homozygotes who act...
Magnitude: 0
Frequency: 93.8%
Repute:Good
References:52
Frequency: 93.8%
Repute:Good
References:52
normal risk
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rs16901979 is a SNP on chromosome 8q24, associated with increased risk for prostate cancer in several studies. In some studies, the regions have been divided, and this SNP falls in region 2. In a study of over 3,600 Caucasians with prostate cancer, rs16901979 is one of five SNPs used (with family history as a sixth factor) to cumulatively predict overall risk. On their own, the rs16901979(A;A) and (A;C) risk genotypes yield an odds ratio for developing prostate cancer of 1.53 (CI: 1.22-1.92, p=1.8x10e-4) and may account for 3.6% of population attributable risk. cancer related according to this blog Two genetic markers in the 8q24 region of chromosome 8 rs7008482 and rs16901979 have been linked to an increased risk of prostate cancer in African Americans. abstract In follow-up studies looki...
common in clinvar
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rs1142345 is a SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The risk allele for this SNP is rs1142345(G), and when it is the only variant in the TPMT gene, it encodes the TPMT*3C allele. While still rare, it is more common in African-Americans (2.4% of all alleles) than in Caucasians. Note that if the same allele also carries the rs1800460(A) SNP, the allele is actually a TPMT*3A allele (OMIM). The medicine 6-Mercaptopurine is metabolized by TPMT. Individual differences in TPMT activity associated with this SNP are now used to determine appropriate dosage range and interval for treatment. 23an...
common in complete genomics
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rs1800584 is a rare SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The rs1800584(A) SNP defines the TPMT*4A allele (OMIM). wikipedia thiopurine drugs metabolized by TPMT include azathioprine, mercaptopurine, and thioguanine [PharmGKB:In-Depth This splicing variant results in very low TPMT activity and risk for hematologic toxicity as a result of treatment with thiopurines.]
normal
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rs1800460 is a SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The risk allele for this SNP is rs1800460(A), and when it is the only variation in the TPMT gene, it encodes the TPMT*3B allele. While still rare, it is more common in Caucasians (4.5% of all alleles) than in African-Americans (0.8%). Note that if the same allele also carries the rs1142345(G) SNP, the allele is actually a TPMT*3A allele (OMIM). The medicine 6-Mercaptopurine is metabolized by TPMT. Individual differences in TPMT activity associated with this SNP are now used to determine appropriate dosage range and interval for treatm...
Magnitude: 0
Repute:Good
References:5
Repute:Good
References:5
normal
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rs28371685, also known as 1003C>T, 42542C>T or R335W is a SNP in the CYP2C9 gene. The rs28371685(T) allele defines the CYP2C9*11 variant, which has decreased activity. According to a 23andMe discussion This is one of the SNPs which were re-analyzed April 2009. Customers with older data may wish to redownload. SNPs effected rs4420638, rs34276300, rs3091244, rs34601266, rs2033003, rs7900194, rs9332239, rs28371685, rs1229984, and rs28399504. [PharmGKB:Curated Phenotype: In African Americans patients, weekly warfarin dose requirements were lower in those with the CYP2C9*8 allele (34 (30-47) mg; P = 0.023) and the CYP2C9 *2, *3, *5, *6, or *11 allele (33(28-40 mg); P < 0.001) as compared with those with the CYP2C9*1/*1 genotype (43 (35-56) mg). Adding the *5,*6,*8 and *11 alleles to a...
Magnitude: 0
Repute:Good
References:7
Repute:Good
References:7
normal
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rs28399504 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*4 variant. This variant has been linked to poor metabolism of compounds like mephenytoin. It is also known as M1V or Met1Val. The risk allele is rs28399504(G). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (Prevacid). According to a 23andMe discussion This is one of the SNPs which were re-analyzed April 2009. Customers with older data may wish to redownload. SNPs effected rs4420638, rs34276300, rs3091244, rs34601266, rs2033003, rs7900194, rs9332239, rs28371685, rs1229984, and rs28399504. Clopidogrel Efficacy [Pharm...
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
normal
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Defines the CYP2C19 variant known as CYP2C19*8. Carriers of the rs41291556(C) allele may have decreased activity and poor metabolizer (PM) phenotype. This variant is associated with a dramatic (approximately 90% and 70%) reduction in the metabolism of S-mephenytoin and tolbutamide in vitro. Clopidogrel Efficacy [PharmGKB:Curated This variant is the defining SNP for CYP2C19*8 and leads to decreased activity and poor metabolizer (PM) phenotype.This variant is associated with a dramatic (approximately 90% and 70%) reduction in the metabolism of S-mephenytoin and tolbutamide in vitro.]
normal
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rs4986893 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*3 variant. This variant has been linked to poor metabolism of compounds like mephenytoin as well as proguanil, and it therefore has implications for malaria prophylaxis. The risk allele is rs4986893(A). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (Prevacid). Clopidogrel Efficacy [PharmGKB:Curated In contrast to other PPIs, esomeprazole-induced healing of GERD appears to be unrelated to the CYP2C19*3 variant.] [OMIM:MEPHENYTOIN, POOR METABOLISM OF]
normal
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rs1333049 has been reported in a large study to be associated with heart disease, in particular, coronary artery disease. The risk allele (oriented to the dbSNP entry) is most likely (C); the odds ratio associated with heterozygotes is 1.47 (CI 1.27-1.70), and for homozygotes, 1.9 (CI 1.61-2.24). This SNP has also been reported to have the highest association of any SNP studied in a subsequent experiment conducted with the resources of the German MI [Myocardial Infarction] Family Study. The initial studies were conducted on Caucasian populations. A subsequent study of Japanese and Korean patients has also found rs1333049 to be associated with increased coronary artery disease risk, with roughly similar odds ratios. '''Further reading (with comments)''' - A long-term study of a cohort of 76...
normal
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The accuracy of claims about this snp are called into question by table 1 of discusses the process of including this snp into Coriell and raises some doubt about the value of its inclusion. rs7754840 replicated as significant for type-2 diabetes risk in 1,900 Japanese patients, with odds ratio of 1.28 (CI: 1.17-1.41, p = 4.5 x 10e-7) type-2 diabetes Carriers of the (C;G) and (C;C) genotypes of rs7754840 had 11% and 24% lower first-phase insulin release in an IVGTT compared to that in carriers of the (G;G) genotype (P=0.002). The C allele was also associated with higher glucose area under the curve in an OGTT (P=0.016). rs7754840 type-2 diabetes Ashkenazi Jewish population shows an even stronger effect for rs7754840 than the general Caucasian population, based on 1,131 cases versus 1,147 co...
normal for 23andMe appears common for 23andMe users
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rs1800462, also known as A80P, is a rare SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The risk allele for this SNP (in orientation to the dbSNP entry) is rs1800462(C), and it encodes the TPMT*2 allele. It may occur at a frequency of 1 in 200 alleles among Caucasians. wikipedia thiopurine drugs metabolized by TPMT include azathioprine, mercaptopurine, and thioguanine [PharmGKB:In-Depth The TPMT:238G>C SNP was cloned from a patient with severe mercaptopurine toxicity. It results in a non-synonymous protein change TPMT:Ala80Pro that has a 100-fold reduction in catalytic activity compared to w...
normal common for Caucasians on the 23andme platform
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rs28371686, also known as 1080C>G, 42619C>G or D360E, is a SNP in the CYP2C9 gene. The rs28371686(G) allele defines the CYP2C9*5 variant, which appears to have decreased activity. [PharmGKB:Curated Phenotype: In African Americans patients, weekly warfarin dose requirements were lower in those with the CYP2C9*8 allele (34 (30-47) mg; P = 0.023) and the CYP2C9 *2, *3, *5, *6, or *11 allele (33(28-40 mg); P < 0.001) as compared with those with the CYP2C9*1/*1 genotype (43 (35-56) mg). Adding the *5,*6,*8 and *11 alleles to a model containing the *2 and *3 alleles plus the VKORC1 -1639 G>A allele (along with clinical variables) explained 36% vs. 30% of the variability in dose requirements. Study size: 226 . Study population/ethnicity: African-American . Type of association: PD;GN;...
normal
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The rs72558186(A) SNP represents a CYP2C19 allele known as CYP2C19*7; it reflects a splice donor mutation that leads to a poor metabolizer phenotype. This SNP is also known as CYP2C19_19294T>A, and in the Affymetrix DMET panel, as DMET3B10072. Note: absence of allele frequency data leaves this as a possible ambiguous flip.
41 snps
(hide) CYP1A2
Magnitude: 2.5
more stimulated by coffee
You appear to have a common genotype in the gene CYP1A2 which metabolizes coffee more slowly than some other forms. The same amount of caffeine will tend to have more stimulating effect on slow metabolizers than on fast metabolizers. Ciprofloxacin is also metabolized by CYP1A2, but is unclear if your genotype should influence its effect.
Carrier of one CYP1A2*1F allele; Slow Caffeine Metabolizer. One copy of the slow caffeine metaboliser SNP, and one copy of the fast version. This makes you more strongly affected by drinking coffee, as caffeine is broken down slower in the liver. Supposedly this increases the risk of heart attacks, although other studies show caffeine is generally good for the heart. It also makes caffeine more effective at preventing Breast Cancer, Alzheimer's Disease, and Parkinson's disease. Too much caffeine will shrink your breasts.
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rs762551, also known as -164A>C or -163C>A, is a SNP encoding the CYP1A2*1F allele of the CYP1A2 gene. For historic reasons, the rs762551(C) allele is considered the wild-type, even though it is the rarer allele in most populations. The rs762551(A) allele is the 'fast metabolizer' allele known as CYP1A2*1F; the (C) allele is by comparison a slower metabolizer of certain substrates (including caffeine). In terms of genotypes, only rs762551(A;A) individuals are considered fast metabolizers. Individuals who are rs762551(A;C) heterozygotes or rs762551(C;C) homozygotes are both considered slow metabolizers. The CYP1A2 gene encodes a member of the cytochrome p450 family of proteins, which metabolize nutrients and drugs. One well known substrate of CYP1A2 is caffeine; individuals who are ca...
carrier of one CYP1A2*1K_-739T>G allele
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rs2069526 is a SNP in the CYP1A2 gene. The rs2069526(T) allele defines the CYP1A2*1K_-739T>G variant. [PharmGKB:Curated Present in reduced function haplotype, unlikely to be causative.]
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[GWAS:None]
CYP1A2_1545T>C homozygote
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rs2470890 is a SNP in the CYP1A2 gene. The rs2470890(C) allele defines the CYP1A2_1545T>C variant. Low-penetrance alleles predisposing to sporadic colorectal cancers: a French case-controlled genetic association study. [PharmGKB:Curated Weakly associated with tardive dyskinesia and schizophrenia.]
References:1
also known as F186L, Phe186Leu, c.558C>A, g.32755C>A, g.45833194C>A According to the literature, this is the cause of the CYP1A2*11 homozygote which produces 5% Vmax of the normal enzyme level. However 23andMe data shows that A is more common. in allele CYP1A2*11; drastic reduction in O-deethylation of phenacetin and 7-ethoxyresorufin; has a Vmax of approximately 5% of that of the wild-type and 5-fold lower Km value.
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rs72547513, also known as 558C>A or F186L, is a SNP in the CYP1A2 gene. In a CYP database, it is listed as defining the CYP1A2*11 allele. 23andMe and opensnp show A as more common. dbSNP shows C as the reference, and A as the variant, but no population frequency information is provided. This SNP was originally observed in a Japanese population at a frequency of 0.3%; in an Italian study of 500 healthy individuals, it was not observed. claims that A is the variant, and that it defined the CYP1A2*11 allele with a Vmax approximately 5% of that of the CYP1A2 wild type, and reduced enzymatic activity. Two subsequent theoretical studies provide hypotheses for why this change results in lowered activity.,
common on affy axiom data
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rs2472297 is a SNP located between the CYP1A1 and CYP1A2 genes on ch 15q24. A meta-analysis of four GWAS studies of coffee consumption among a total of ~8,000 coffee drinkers of European ancestry found that the rs2472297(T) was strongly associated with increased consumption (p = 5.4 x 10e-14). The estimated effect was an increase of 0.2 cups a day per allele for both this SNP and one other (rs6968865).
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:2
Frequency: 100.0%
Repute:Good
References:2
normal
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rs12720461 is a SNP in the CYP1A2 gene. The rs12720461(T) allele defines the CYP1A2*1K_-729C>T variant. [PharmGKB:Curated Likely disrupts transcription factor binding, leading to reduced function.]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
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rs28399424, also known as 5090C>T or R431W, is a SNP in the CYP1A2 gene. The rs28399424(T) allele defines the CYP1A2*6 decreased activity variant. [PharmGKB:Curated Reduced expression.]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
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rs55889066, also known as 3497G>A or C406Y, is a SNP in the CYP1A2 gene. The rs55889066(A) allele defines the CYP1A2*5 variant. [PharmGKB:Curated Risk or phenotype-associated allele: A Phenotype: In an in vitro system, this variant showed no catalytic activity against the carcinogen NNK. The wild type protein bioactivates this carcinogen. The variant also produced extra metabolites of phenacetin that were not observed with the wild type protein. Type of association: FA]
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
normal
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rs56276455, also known as 2385G>A, 5347T>C or D348N is a SNP in the CYP1A2 gene. The rs56276455(A) allele defines the CYP1A2*3 variant.
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
normal
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rs72547515, also known as 2473G>A, 5347T>C or R377Q, is a SNP in the CYP1A2 gene. The rs72547515(T) allele defines the CYP1A2*16 variant.
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
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rs72547517, also known as 5166G>A, 5347T>C or R456H, is a SNP in the CYP1A2 gene. The rs72547517(A) allele defines the CYP1A2*8 variant. [PharmGKB:Curated Risk or phenotype-associated allele: A Phenotype: In an in vitro system, this variant showed no activity for the drug substrates clozapine or phenacetin even at the highest substrate and double membrane concentrations, it also showed reduced expression of holoprotein in bacterial cells. Type of association: FA]
normal
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rs72547516, also known as 2499A>T or I386F, is a SNP in the CYP1A2 gene. The rs72547516(T) allele defines the CYP1A2*4 variant. [PharmGKB:Curated Risk or phenotype-associated allele: T Phenotype: In an in vitro system, this variant showed no activity for the drug substrates clozapine or phenacetin even at the highest substrate and double membrane concentrations, it also showed reduced expression of holoprotein in bacterial cells. Type of association: FA]
1 genoset 13 snps
(hide) CYP2A6
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
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rs28399444 is a truncated non-functioning variant of CYP2A6 known as CYP2A6*20 [PharmGKB:In-Depth This variant results in a truncated protein and no enzyme activity; part of the CYP2A6*20 haplotype.]
Magnitude: 0
Frequency: 99.1%
Repute:Good
References:1
Frequency: 99.1%
Repute:Good
References:1
common in complete genomics
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CYP2B6 (c.516G-->T) and CYP2A6 (*9B and/or *17) polymorphisms are independent predictors of efavirenz plasma concentrations in HIV-infected patients. [PharmGKB:In-Depth This variant decreases enzyme activity and affects metabolism of coumarin and nicotine; part of the CYP2A6*17 haplotype.]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
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[PharmGKB:In-Depth This variant is part of the *10 haplotype and affects nicotine metabolism.]
common in complete genomics
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[PharmGKB:In-Depth This variant affects heat stability and affects nicotine metabolism; part of the CYP2A6*7 and CYP2A6*10 haplotypes.]
common in clinvar
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minor form is a slow metaboliser according to pharmgkb [PharmGKB:In-Depth This variant results in enzyme inactivity and is considered to be part of the %22slow metabolizer%22 group; part of the CYP2A6*2 haplotype.] [OMIM:?] [GWAS:Smoking behavior]
5 snps
(hide) CYP2C19
Magnitude: 2
Frequency: 43.1%
References:13
Frequency: 43.1%
References:13
CYP2C19*17 ultra fast metabolizer; drug metabolism effects; also 0.77x decreased breast cancer risk
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rs12248560(T) defines the CYP2C19*17 allele, an ultra fast metabolizer phenotype of the CYP2C19 gene. CYP2C19*17 is likely to lead to less effective drug treatment by, for example, proton pump inhibitors (such as omeprazole) and antidepressants. On the other hand, cancer patients who are CYP2C19*17 carriers are more likely to benefit from tamoxifen treatment, presumably because they break it down more rapidly into the antiestrogenic metabolites endoxifen and 4-hydroxytamoxifen. A study of 1,000+ breast cancer patients showed a 0.77x decreased risk of breast cancer for carriers of a CYP2C19*17 allele (CI: 0.65-0.93, p = 0.005). Analysis of a subgroup of such carriers who were using hormone therapy for ten years or longer showed an even stronger effect (odds ratio 0.57, CI: 0.39-0.83, p = 0....
Slower metaboliser for some drugs
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rs1045642, also known as C3435T, is a SNP located in the ABCB1 gene. It is often studied in conjunction with rs2032582. C3435T has been mentioned by: * A 'Silent' Polymorphism in the MDR1 Gene Changes Substrate Specificity (for example, to verapamil) * (R)-lansoprazole (Prevacid) concentrations are significantly increased in CYP2C19 extensive metabolizers with ABCB1 C3435T C allele. * In a Korean population, plasma concentrations of fexofenadine (Allegra) were 17% lower in 2677AA/3435CC subjects and 47% higher in the 2677TT/3435TT subjects compared to 2677GG/3435CC subjects. * In contrast, in this study no association was observed between the C3435T polymorphism and fexofenadine plasma or urine concentrations in a German Caucasian population. * A meta-analysis including 9 case-control stud...
Frequency: 75.5%
References:1
References:1
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[GWAS:Acenocoumarol maintenance dosage]
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[GWAS:Blood metabolite levels]
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[GWAS:Migraine]
References:1
normal
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The rs5787121(-) (i.e. deletion) SNP defines the CYP2C19 allele known as G439- or 90052delG.
References:0
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The rs72558185(G) SNP is an insertion variant in the CYP2C19 gene; it is also known as hCV34328665, and is in the Affymetrix DMET panel.
normal
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rs4244285 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*2 variant. This variant is the most common reason for poor metabolism of compounds like mephenytoin (an anti-convulsant), some antidepressants, the anti-platelet drug Plavix, and some drugs used for ulcer conditions of various types. The risk allele is rs4244285(A). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (trade name Prevacid). In Caucasians, SNPs in CYP2C19 are relatively rare (in contrast to SNPs in CYP2D6), but SNPs in this gene are common in Asians. Ulcer treatment with omeprazole to reduce Helicobacter pyl...
normal
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The rs3758581(A) SNP defines a CYP2C19 allele known as V331I. Analysis of 50 SNPs in CYP2D6, CYP2C19, CYP2C9, CYP3A4 and CYP1A2 by MALDI-TOF mass spectrometry in Chinese Han population.
normal
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The rs6413438(T) allele defines the CYP2C19 allele known as CYP2C19*10. This allele may lead to reduced metabolism of S-mephenytoin at least in vitro. [PharmGKB:Curated This variant is the defining SNP for CYP2C19*10. This variant is associated with reduction in the metabolism of S-mephenytoin in vitro.]
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
normal
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The rs17882687(C) SNP defines the CYP2C19 allele known as CYP2C19*15, and also known as CYP2C19_55A>C or I19L.
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
normal
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The rs17884712(A) allele defines the CYP2C19 variant known as CYP2C19*9, which is associated with a slight decrease in the metabolism of S-mephenytoin (at least in vitro). [PharmGKB:Curated This variant is the defining SNP for CYP2C19*9 and associated with a modest decrease in the V(max) for 4'-hydroxylation of S-mephenytoin in vitro.]
Magnitude: 0
Repute:Good
References:7
Repute:Good
References:7
normal
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rs28399504 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*4 variant. This variant has been linked to poor metabolism of compounds like mephenytoin. It is also known as M1V or Met1Val. The risk allele is rs28399504(G). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (Prevacid). According to a 23andMe discussion This is one of the SNPs which were re-analyzed April 2009. Customers with older data may wish to redownload. SNPs effected rs4420638, rs34276300, rs3091244, rs34601266, rs2033003, rs7900194, rs9332239, rs28371685, rs1229984, and rs28399504. Clopidogrel Efficacy [Pharm...
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Association of warfarin dose with genes involved in its action and metabolism. The largest prospective warfarin-treated cohort supports genetic forecasting.
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
normal
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Defines the CYP2C19 variant known as CYP2C19*8. Carriers of the rs41291556(C) allele may have decreased activity and poor metabolizer (PM) phenotype. This variant is associated with a dramatic (approximately 90% and 70%) reduction in the metabolism of S-mephenytoin and tolbutamide in vitro. Clopidogrel Efficacy [PharmGKB:Curated This variant is the defining SNP for CYP2C19*8 and leads to decreased activity and poor metabolizer (PM) phenotype.This variant is associated with a dramatic (approximately 90% and 70%) reduction in the metabolism of S-mephenytoin and tolbutamide in vitro.]
normal
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rs4986893 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*3 variant. This variant has been linked to poor metabolism of compounds like mephenytoin as well as proguanil, and it therefore has implications for malaria prophylaxis. The risk allele is rs4986893(A). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (Prevacid). Clopidogrel Efficacy [PharmGKB:Curated In contrast to other PPIs, esomeprazole-induced healing of GERD appears to be unrelated to the CYP2C19*3 variant.] [OMIM:MEPHENYTOIN, POOR METABOLISM OF]
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
normal
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The rs55640102(C) SNP defines the CYP2C19 allele known as CYP2C19*12, also known as X491C.
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
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The rs55752064(C) SNP defines the CYP2C19 allele known as CYP2C19*14, also known as L17P.
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
normal
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The rs72552267(A) SNP defines the CYP2C19 allele known as CYP2C19*6, also known as R132Q.
normal
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The rs17878459(C) SNP defines the CYP2C19 allele known as CYP2C19*2B, or as E92D.
normal
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The rs72558186(A) SNP represents a CYP2C19 allele known as CYP2C19*7; it reflects a splice donor mutation that leads to a poor metabolizer phenotype. This SNP is also known as CYP2C19_19294T>A, and in the Affymetrix DMET panel, as DMET3B10072. Note: absence of allele frequency data leaves this as a possible ambiguous flip.
24 snps
(hide) CYP2C9
warfarin sensitivity (~2.5 mg/day)
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rs8050894, is located on chromosome 16 in the gene VKORC1. VKORC1 is the primary target of the drug warfarin (Coumadin), a commonly used oral anticoagulant. rs8050894 is one of several polymorphisms found in VKORC1 that is associated with specific warfarin doses (). Other polymorphisms in VKORC1 (rs7196161, rs9923231, rs9934438, rs2359612) are equally predictive of warfarin dose requirement in both European and Asian-descent individuals. Other polymorphisms found in the gene cytochrome P450 2C9 (CYP2C9) influence the metabolism of warfarin and have a smaller effect on warfarin dose. These polymorphisms are rs1799853 (CYP2C9*2) and rs1057910 (CYP2C9*3). In several hundred Europeans, no association was found between rs8050894 and risk for ischemic stroke. Genetic-based dosing in orthopedic p...
Frequency: 27.4%
References:2
References:2
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[Distribution of variant alleles association with warfarin pharmacokinetics and pharmacodynamics in the Han population in China].
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[PharmGKB:Curated In a GWAS study, this SNP was modestly associated with warfarin dose, and was in perfect linkage disequilibrium with rs4086116.]
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[GWAS:Blood metabolite levels]
normal
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rs9332131, also known as 818delA, 10601delA or 273Frame shift, is a SNP in the CYP2C9 gene. The rs9332131(-) allele defines the CYP2C9*6 variant, which is inactive. [PharmGKB:Curated Phenotype: In African Americans patients, weekly warfarin dose requirements were lower in those with the CYP2C9*8 allele (34 (30-47) mg; P = 0.023) and the CYP2C9 *2, *3, *5, *6, or *11 allele (33(28-40 mg); P < 0.001) as compared with those with the CYP2C9*1/*1 genotype (43 (35-56) mg). Adding the *5,*6,*8 and *11 alleles to a model containing the *2 and *3 alleles plus the VKORC1 -1639 G>A allele (along with clinical variables) explained 36% vs. 30% of the variability in dose requirements. Study size: 226 . Study population/ethnicity: African-American . Type of association: PD;GN;CO]
normal; no change in warfarin metabolism
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rs1799853 is a SNP in the CYP2C9 gene and is linked to poor warfarin metabolism. Advanced knowledge of this may influence initial warfarin dosing by physicians. Warfarin is monitored through INR (international normalized ratio) and proper dosing is influenced by a variety of factors including warfarin metabolism and diet. rs1799853 is a SNP in the CYP2C9 gene. The rs1799853(T) allele encodes a variant amino acid, cysteine, which has been linked to poor metabolism of warfarin and thus sensitivity . The common nomenclature for this polymorphism is CYP2C9*2 (Cys amino acid, T allele; the SNP is also known as C430T or Cys144Arg). The CYP2C9*2 allele is also associated with higher sensitivity to the anti-epileptic drug phenytoin. The effect of CYP2C9 variants on drug metabolism should not be pr...
normal; no effect on warfarin metabolism
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SNP rs1057910(A), located in the cytochrome p450 CYP2C9 gene, most commonly encodes the amino acid isoleucine at position 359, and the resulting allele is also known as CYP2C9*1. rs1057910(C) encodes a leucine at this same position, and the resulting allele is called CYP2C9*3. This SNP is also known as Ile359Leu or A1075C. The effect of CYP2C9 variants on drug metabolism should not be predicted without also considering CYP2C9*2, defined as the common loss of function variant rs1799853(T) (NM_000771:c.430C>T, NP_000762:p.144R>C) Studies of the effects of these alleles include: * rs1057910(C;C)] genotypes may clear drugs like celecoxib (trade name Celebrex) twice as slowly as rs1057910(A;A) genotypes; the rs1057910(A;C) genotypes are in-between clearance rates. Lower clearance rates wi...
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A genome-wide association study of acenocoumarol maintenance dosage. [PharmGKB:Curated In a GWAS study, this SNP was modestly associated with warfarin dose, accounting for ~9% of the variance in dose. This SNP was in perfect linkage disequilibrium with rs4917639.] [GWAS:Warfarin maintenance dose]
Magnitude: 0
Frequency: 86.6%
Repute:Good
References:3
Frequency: 86.6%
Repute:Good
References:3
normal
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rs9332130, also known as 815A>G, 10598A>G or E272G, is a SNP in the CYP2C9 gene. The rs9332130(G) allele defines the CYP2C9*10 variant.
normal
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rs2256871, also known as 752A>G, 10535A>G or H251R, is a SNP in the CYP2C9 gene. The rs2256871(C) allele defines the CYP2C9*9 variant.
normal
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rs1057909 is a SNP in the CYP2C9 gene. The rs1057909(G) allele defines the CYP2C9_42612A>G variant, about which little is known.
normal
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rs9332239, also known as 1465C>T, 50338C>T or P489S, is a SNP in the CYP2C9 gene. The rs9332239(T) allele defines the CYP2C9*12 variant. According to a 23andMe discussion This is one of the SNPs which were re-analyzed April 2009. Customers with older data may wish to redownload. SNPs effected rs4420638, rs34276300, rs3091244, rs34601266, rs2033003, rs7900194, rs9332239, rs28371685, rs1229984, and rs28399504.
Magnitude: 0
Repute:Good
References:5
Repute:Good
References:5
normal
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rs28371685, also known as 1003C>T, 42542C>T or R335W is a SNP in the CYP2C9 gene. The rs28371685(T) allele defines the CYP2C9*11 variant, which has decreased activity. According to a 23andMe discussion This is one of the SNPs which were re-analyzed April 2009. Customers with older data may wish to redownload. SNPs effected rs4420638, rs34276300, rs3091244, rs34601266, rs2033003, rs7900194, rs9332239, rs28371685, rs1229984, and rs28399504. [PharmGKB:Curated Phenotype: In African Americans patients, weekly warfarin dose requirements were lower in those with the CYP2C9*8 allele (34 (30-47) mg; P = 0.023) and the CYP2C9 *2, *3, *5, *6, or *11 allele (33(28-40 mg); P < 0.001) as compared with those with the CYP2C9*1/*1 genotype (43 (35-56) mg). Adding the *5,*6,*8 and *11 alleles to a...
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
normal
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rs72558190, also known as 485C>A or S162X, is a SNP in the CYP2C9 gene. The rs72558190(A) allele defines the CYP2C9*15 variant, which is inactive.
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
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rs7900194, also known as 449G>A, 3627G>A or R150H, is a SNP in the CYP2C9 gene. The rs7900194(A) allele defines the CYP2C9*8 variant, which has decreased activity. According to a 23andMe discussion This is one of the SNPs which were re-analyzed April 2009. Customers with older data may wish to redownload. SNPs effected rs4420638, rs34276300, rs3091244, rs34601266, rs2033003, rs7900194, rs9332239, rs28371685, rs1229984, and rs28399504. [PharmGKB:Curated Phenotype: In African Americans patients, weekly warfarin dose requirements were lower in those with the CYP2C9*8 allele (34 (30-47) mg; P = 0.023) and the CYP2C9 *2, *3, *5, *6, or *11 allele (33(28-40 mg); P < 0.001) as compared with those with the CYP2C9*1/*1 genotype (43 (35-56) mg). Adding the *5,*6,*8 and *11 alleles to a mod...
normal
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rs1057911 is a SNP in the CYP2C9 gene. The rs1057911(T) allele defines the CYP2C9_50298A>T variant, about which little is known. Warfarin
normal common for Caucasians on the 23andme platform
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rs28371686, also known as 1080C>G, 42619C>G or D360E, is a SNP in the CYP2C9 gene. The rs28371686(G) allele defines the CYP2C9*5 variant, which appears to have decreased activity. [PharmGKB:Curated Phenotype: In African Americans patients, weekly warfarin dose requirements were lower in those with the CYP2C9*8 allele (34 (30-47) mg; P = 0.023) and the CYP2C9 *2, *3, *5, *6, or *11 allele (33(28-40 mg); P < 0.001) as compared with those with the CYP2C9*1/*1 genotype (43 (35-56) mg). Adding the *5,*6,*8 and *11 alleles to a model containing the *2 and *3 alleles plus the VKORC1 -1639 G>A allele (along with clinical variables) explained 36% vs. 30% of the variability in dose requirements. Study size: 226 . Study population/ethnicity: African-American . Type of association: PD;GN;...
23 snps
(hide) CYP2D6
Magnitude: 2
CYP2D6*10
CYP2D6*10 reduced metabolism
Carrier of one CYP2D6 decreased or non-functioning variant. Your body may have a reduced ability to process some medicines. You are a carrier for rs1065852(T;T)
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The wild type (normal) allele at this SNP is (C). The (T) variant indicates the presence of a non-wild type CYP2D6 variant, but it appears in many different variants so it can not be used to determine the presence of any particular variant. The most common variants it appears in are CYP2D6*10 and CYP2D6*4, but these are not the only ones. While this is the defining mutation for CYP2D6*10, it is not possible by itself for this mutation to determine a particular variant. In addition, the CYP2D6*4 variant includes this mutation, but the defining mutation 1846G>A SNP is not available in the common direct to consumer testing services. While it is not possible for this mutation to identify one particular variant, all the variants in which it appears have reduced or no CYP2D6 activity. If two ...
Homozygous for CYP2D6 variants (non-CYP2D6*1)
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rs1135840, also known as 4180G>C or S486T, is a SNP in the CYP2D6 gene. The wild type (normal) allele at this SNP is (G). The (C) variant indicates the presence of a non-wild type CYP2D6 variant, but it appears in many different variants so it can not be used to determine the presence of any particular variant. Please be careful when interpreting results for this SNP as it is in dbSNP and SNPedia in minus orientation where the risk allele is C, but test results are usually in plus orientation where the risk allele is G. This SNP has an ambiguous flip which can make this very confusing. Polymorphisms affecting gene transcription and mRNA processing in pharmacogenetic candidate genes: detection through allelic expression imbalance in human target tissues. [PharmGKB:Curated Risk or phenot...
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a variation in CYP2D6
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a variation in CYP2D6
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a variation in CYP2D6
References:3
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rs28360521 is a SNP in the vicinity of the CYP2D6 gene. Little is known of the significance of either allele.
References:0
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a variation in CYP2D6
References:1
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[PharmGKB:In-Depth Causes deletion of amino acid, K281. Contrary to in vitro results, in vivo study has cast doubt on whether or not this variant leads to reduced function.]
References:0
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a variation in CYP2D6
References:0
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a variation in CYP2D6
normal
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The (-) form of this SNP, representing a deletion of one nucleotide, causes a frameshift such that the resulting CYP2D6 protein is nonfunctional. The associated allele is also known as CYP2D6*6, and there are several subtypes but they are all nonfunctional. If two copies of this (or similar) changes are inherited, CYP2D6 poor metabolism ('PM') is observed. CYP2D6 poor metabolism may affect the efficacy or degree of side effects of drugs metabolized by CYP2D6, such as dextromorphan, sparteine, nortriptyline, venlafaxine and codeine. Response to serotonin reuptake inhibitors in OCD is not influenced by common CYP2D6 polymorphisms. [PharmGKB:Curated This variant is part of the CYP2D6*6 PM haplotype. Plasma concentrations of metoprolol were shown to be were 4.9-fold higher in the PMs, with gr...
References:1
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[PharmGKB:In-Depth This variant is part of the reduced functioning haplotype CYP2D6*29, which is found at an estimated allele frequency of 20% in African Tanzanians.]
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a variation in CYP2D6
References:0
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a variation in CYP2D6
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a variation in CYP2D6
a common variant
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The wild type (normal) allele at this SNP is (G). The (A) variant indicates the presence of a non-wild type CYP2D6 variant, but it appears in many different variants so it can not be used to determine the presence of any particular variant. Inheriting a normal number of copies of this allele results in CYP2D6 function that is indistinguishable from wild-type (normal) activity. However, this variant has been seen present in higher copy numbers, and in these cases, can result in the ultrafast metabolizer phenotype . [PharmGKB:In-Depth Risk or phenotype-associated allele: T. Phenotype: The CYP2D6*2A haplotype was associated with lower incidence of breast cancer on tamoxifen compared to placebo in a prevention study. The CYP2D6*2A allele may be associated with increased efficacy of tamoxifen....
common
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rs1080983 is a SNP near the 5' end of the CYP2D6 gene. Little is known of the significance of either allele.
common/normal
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The public name for this SNP is rs72549354, a CYP2D6 variant representing a single nucleotide insertion and defining the allele encoding the CYP2D6*20 non-functioning protein.
normal normal
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rs5030656, also known as 2615_2617delAAG or K281del, is a SNP in the CYP2D6 gene. The rs5030656(-) allele defines the CYP2D6*9 variant, which has decreased activity.
normal
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rs4244285 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*2 variant. This variant is the most common reason for poor metabolism of compounds like mephenytoin (an anti-convulsant), some antidepressants, the anti-platelet drug Plavix, and some drugs used for ulcer conditions of various types. The risk allele is rs4244285(A). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (trade name Prevacid). In Caucasians, SNPs in CYP2C19 are relatively rare (in contrast to SNPs in CYP2D6), but SNPs in this gene are common in Asians. Ulcer treatment with omeprazole to reduce Helicobacter pyl...
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a variation in CYP2D6
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a variation in CYP2D6
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a variation in CYP2D6
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a variation in CYP2D6
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a variation in CYP2D6
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a variation in CYP2D6
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a variation in CYP2D6
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a variation in CYP2D6
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a variation in CYP2D6
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a variation in CYP2D6
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a variation in CYP2D6
normal
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Also known as 1858C>T, the (A) allele is a marker for CYP2D6*4F non-functioning variant.
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a variation in CYP2D6
normal
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2938C>T marker. The (A) allele indicates non-functioning CYP2D6*4G variant.
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a variation in CYP2D6
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a variation in CYP2D6
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a variation in CYP2D6
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a variation in CYP2D6
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a variation in CYP2D6
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a variation in CYP2D6
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a variation in CYP2D6
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
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a variation in CYP2D6
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
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a variation in CYP2D6
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
normal
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rs28371706, also known as 1023C>T or T107I, is a SNP in the CYP2D6 gene. The rs28371706(T) allele is found in several CYP2D6 variants: * CYP2D6*17 decreased activity variant * CYP2D6*40 non-functioning variant * CYP2D6*58 variant * CYP2D6*64 variant [PharmGKB:In-Depth Variant was identified as being part of the reduced function haplotype CYP2D6*17.]
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
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a variation in CYP2D6
Magnitude: 0
Repute:Good
References:5
Repute:Good
References:5
normal
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rs28371725, also known as 2988G>A, is a SNP in the CYP2D6 gene. The rs28371725(A) allele defines the CYP2D6*41 variant, which has decreased activity. 23andMe also has SNP i4001476 at the same position. [PharmGKB:In-Depth This variant is part of the CYP2D6*41 IM haplotype. Plasma concentrations of metoprolol were shown to be were 4.9-fold higher in the PMs, with greater reductions in heart rate, diastolic blood pressure, and mean arterial pressure in PMs than in non-PMs.]
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
normal
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rs5030862, also known as 124G>A or G42R, is a SNP in the CYP2D6 gene. The rs5030862(A) allele defines the CYP2D6*12 variant, which is inactive.
normal
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rs5030867, also known as 2935A>C or H324P, is a SNP in the CYP2D6 gene. The rs5030867(C) allele defines the CYP2D6*7 variant, which is inactive.
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in complete genomics
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[PharmGKB:In-Depth This variant is part of the reduced functioning haplotype CYP2D6*29, which is found at an estimated allele frequency of 20% in African Tanzanians.]
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
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a variation in CYP2D6
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a variation in CYP2D6
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a variation in CYP2D6
1 genoset 95 snps
(hide) CYP2E1
carrier of one CYP2E1*7_-71G>T allele
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rs6413420 is a SNP in the CYP2E1 gene. The rs6413420(T) allele defines the CYP2E1*7_-71G>T variant.
carrier of one CYP2E1*1B allele
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rs2070676, also known as 9896C>G, is a SNP in the CYP2E1 gene. The rs2070676(G) allele defines the CYP2E1*1B variant.
carrier of one CYP2E1_10463T>C(F421F) allele
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rs2515641 is a SNP in the CYP2E1 gene. The rs2515641(T) allele defines the CYP2E1_10463T>C(F421F) variant.
carrier of one CYP2E1*7_-333T>A allele
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rs2070673 is a SNP in the CYP2E1 gene. The rs2070673(A) allele defines the CYP2E1*7_-333T>A variant.
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[GWAS:Obesity-related traits]
normal
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rs2031920 is a SNP in the CYP2E1 gene. The rs2031920(T) allele defines the CYP2E1_-1055C>T variant. [OMIM:CYTOCHROME P450, SUBFAMILY IIE; CYP2E1]
normal
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rs2070672 is a SNP in the CYP2E1 gene. The rs2070672(G) allele defines the CYP2E1*7_-352A>G variant.
normal
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rs4646976 is a SNP in the CYP2E1 gene. The rs4646976(G) allele defines the CYP2E1_marker8 variant, as used in the 2008 study determining the 16 most common CYP2E1 haplotypes world-wide.(see CYP2E1 for details)
normal
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rs6413419, also known as 4768G>A or V179I, is a SNP in the CYP2E1 gene. The rs6413419(A) allele defines the CYP2E1*4 variant.
normal
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rs915909 is a SNP in the CYP2E1 gene. The rs915909(T) allele defines the CYP2E1_6498C>T(I321I) variant.
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
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rs55897648, also known as 10023G>A or V389I, is a SNP in the CYP2E1 gene. The rs55897648(A) allele defines the CYP2E1*3 variant.
normal
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Also known as CYP2E1_-1295G>C, this SNP is reported to mark the c2 allele of CYP2E1. The rs3813867(C) allele defines the CYP2E1_-1295G>C variant allele. [OMIM:CYTOCHROME P450, SUBFAMILY IIE; CYP2E1]
23 snps
(hide) CYP3A5
CYP3A5 non-expressor
This is common for Caucasians, but rare for African populations. As a CYP3A5 non-expressor you are unable to metabolize some common medications. This influences the synthesis of cholesterol, steroids and other lipids. The enzyme metabolizes drugs such as olanzapine, tacrolimus, nifedipine and cyclosporine as well as the steroid hormones testosterone, progesterone and androstenedione.
CYP3A5*3 homozygote; CYP3A5 non-expressor Impacts metabolism of tacrolimus, an immunosuppressive drug used in organ transplantation. This is the most common phenotype in caucasian and many other populations. Only in africans is expressing the gene common.
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rs776746, also known as 6986A>G, is a SNP encoding the (nonfunctional) CYP3A5*3 allele of the CYP3A5 gene. CYP3A5*3 has been studied especially in connection with the metabolism of tacrolimus, an immunosuppressive drug used in organ transplantation. The optimal therapeutic dose is in a relatively narrow window, so blood concentration monitoring is recommended. CYP3A5*3 carriers tend to build up higher levels of tacrolimus than CYP3A5*1 carriers, unless their tacrolimus intake is reduced. Risk of testicular germ cell cancer in relation to variation in maternal and offspring cytochrome p450 genes involved in catechol estrogen metabolism. Polymorphisms in the cytochrome P450 genes CYP1A2, CYP1B1, CYP3A4, CYP3A5, CYP11A1, CYP17A1, CYP19A1 and colorectal cancer risk. Prevalence of common dis...
Magnitude: 2.5
Repute:Bad
References:2
Repute:Bad
References:2
CYP3A5*7 homozygote; nonexpressor for CYP3A5
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rs41303343, also known as 27131_27132insT, is a SNP in the CYP3A5 gene. The rs41303343(T) allele defines the CYP3A5*7 variant, which is nonfunctional.
normal
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rs1057868, also known as A503V, is a relatively common variant defining the POR*28 allele of the P450 (cytochrome) oxidoreductase POR gene. The POR gene encodes a protein involved in electron transport of cytochrome p450 enzymes such as CYP3A4, CYP3A5 and CYP3A7. A study of 251 individuals from two independent studies (182 patients treated with methadone and 69 patients with clozapine) for CYP3A activity found that CYP3A SNPs themselves did not predict particularly well inter-individual variability in overall CYP3A activity. However, rs1057868(T;T) individuals had a 1.6x increased CYP3A activity compared to rs1057868(C) carriers (n=182, p=0.004), and the finding was replicated in a second independent dataset. The authors conclude that this POR gene SNP is a better predictor of overall CYP3...
Magnitude: 0
Frequency: 98.2%
Repute:Good
References:0
Frequency: 98.2%
Repute:Good
References:0
normal
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rs28365083, also known as 27289C>A, is a SNP in the CYP3A5 gene. The rs28365083(A) allele defines the CYP3A5*2 variant, which is nonfunctional. Polymorphisms in the cytochrome P450 genes CYP1A2, CYP1B1, CYP3A4, CYP3A5, CYP11A1, CYP17A1, CYP19A1 and colorectal cancer risk. Genotyping panel for assessing response to cancer chemotherapy. Polymorphisms of drug-metabolizing enzymes (GST, CYP2B6 and CYP3A) affect the pharmacokinetics of thiotepa and tepa. Pazopanib-induced hyperbilirubinemia is associated with Gilbert's syndrome UGT1A1 polymorphism.
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:9
Frequency: 100.0%
Repute:Good
References:9
normal
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rs10264272, also known as 14690G>A, is a SNP in the CYP3A5 gene. indicates that this corresponds with CYP3A5*6, however, this seems doubtful. CYP3A5 allele nomenclature found at http://www.cypalleles.ki.se/cyp3a5.htm indicates that CYP3A5*6 (also known as 14690G>A) is a splicing defect resulting in essentially no activity in the gene. This does not correspond with dbSNP, which indicates that is a nucleotide substition (624G-A) which only results in a 'silent' substitution of AAG (Lysine) to AAA (Lysine). [PharmGKB:In-Depth Nonfunctional allele present predominantly in the African American population.]
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
normal
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rs28383468, also known as 3705C>T or H30Y, is a SNP in the CYP3A5 gene. The rs28383468(T) allele defines the CYP3A5*H30Y variant, which is nonfunctional.
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
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rs28383479, also known as 19386G>A, is a SNP in the CYP3A5 gene. The rs28383479(A) allele defines the CYP3A5*9 variant, which is nonfunctional.
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
normal
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rs41279854, also known as 29748T>C or F446S, is a SNP in the CYP3A5 gene. The rs41279854(G) allele defines the CYP3A5*10 variant, which is nonfunctional.
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
normal
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rs41279857, also known as 7298C>A or S100Y, is a SNP in the CYP3A5 gene. The rs41279857(T) allele defines the CYP3A5*S100Y variant, which is nonfunctional.
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
normal
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should this be an A/G or a C/T? rs55817950, also known as 3699C>T, is a SNP in the CYP3A5 gene. The rs55817950(A) allele defines the CYP3A5*8 variant, which is nonfunctional.
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
normal
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should this be an A/C or a G/T? rs56244447, also known as L82R, is a SNP in the CYP3A5 gene. The rs56244447(C) allele defines the CYP3A5*3D variant, which is nonfunctional.
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
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Cytochrome P450 3A (CYP3A) family of isoenzymes are responsible for metabolizing over half of prescribed drugs, thus determining absence of CYP3A expression is important for optimizing medical treatments. CYP3A5*4 is a rare variant in Chinese, Caucasians and Indians which may therefore not warrant screening for. At least one CYP3A5*1 allele is needed for expressing CYP3A5 protein, with normal levels up to half of CYP3A present in the liver. Allele variant *4 is identified by rs56411402 (14665A > G, p.Gln200Arg or Q200R) in exon 8. Note the reverse orientation; the most common form of this SNP is rs56411402(T), which is the same as '14665A' in publications. The rs56411402(C) allele defines the CYP3A5*4 variant, which is nonfunctional. Differential expression of cytochrome p450 enzymes in...
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
normal
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rs72552791, also known as 3775A>G or Y53C, is a SNP in the CYP3A5 gene. The rs72552791(G) allele defines the CYP3A5*11 variant, which is nonfunctional.
1 genoset 13 snps
(hide) DCDC2
2-5x increased dyslexia risk higher risk of dyslexia
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Rs807701, a SNP in the DCDC2 gene, is in a region that crops up in several independent studies as likely to associated with dyslexia. The risk allele in the Caucasian populations studied is (C). One study reports that the odds ratio for rs807701 genotypes increases if calculated from subsets of more severely dyslexic individuals as compared to more heterogenous, larger groups of dyslexic individuals. The genotype relative risk (GRR) for rs807701(C;C) increased from 1.88 (95% CI 0.89-3.97; P=.058) for the larger group up to 5.04 (95% CI 1.35-18.88; P=.002) for the most severely affected group. Combined with another SNP marker in the DCDC2 gene, rs793862, the (haplotype) GRR also increased for the homozygous haplotype rs793862(A)-rs807701(C), from 4.11 (95% CI 2.77-6.08; P<.0001) for the ...
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Strong genetic evidence of DCDC2 as a susceptibility gene for dyslexia.
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[OMIM:?]
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[OMIM:?]
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[GWAS:None]
increased dyslexia risk
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Rs793862, a SNP in the DCDC2 gene, is in a region that crops up in several independent studies as likely to associated with dyslexia. The risk allele in the Caucasian populations studied is (A). One study reports that the odds ratio for rs793862 genotypes increases if calculated from subsets of more severely dyslexic individuals as compared to more heterogenous, larger groups of dyslexic individuals. The genotype relative risk (GRR) for rs793862(A;A) increased from 3.15 (95% CI 1.30-7.66; P=.011) for the larger group up to 5.40 (95% CI 1.27-23.01; P=.002) for the most severely affected group. Combined with another SNP marker in the DCDC2 gene, rs807701, the (haplotype) GRR also increased for the homozygous haplotype A-C, from 4.11 (95% CI 2.77-6.08; P<.0001) for the larger group, up to ...
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[OMIM:?]
8 snps
(hide) Doi:10.1186/1471-2156-10-88
Carrier of one CYP1A2*1F allele; Slow Caffeine Metabolizer. One copy of the slow caffeine metaboliser SNP, and one copy of the fast version. This makes you more strongly affected by drinking coffee, as caffeine is broken down slower in the liver. Supposedly this increases the risk of heart attacks, although other studies show caffeine is generally good for the heart. It also makes caffeine more effective at preventing Breast Cancer, Alzheimer's Disease, and Parkinson's disease. Too much caffeine will shrink your breasts.
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rs762551, also known as -164A>C or -163C>A, is a SNP encoding the CYP1A2*1F allele of the CYP1A2 gene. For historic reasons, the rs762551(C) allele is considered the wild-type, even though it is the rarer allele in most populations. The rs762551(A) allele is the 'fast metabolizer' allele known as CYP1A2*1F; the (C) allele is by comparison a slower metabolizer of certain substrates (including caffeine). In terms of genotypes, only rs762551(A;A) individuals are considered fast metabolizers. Individuals who are rs762551(A;C) heterozygotes or rs762551(C;C) homozygotes are both considered slow metabolizers. The CYP1A2 gene encodes a member of the cytochrome p450 family of proteins, which metabolize nutrients and drugs. One well known substrate of CYP1A2 is caffeine; individuals who are ca...
Slightly increased lifespan?
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This SNP, a variant in the TP53 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the G allele encodes an arginine at position 72 of the protein (where there's normally a proline), and the SNP is commonly called the Arg72 variant, although P72R and Arg72Pro are also common in the literature. Minor allele homozygotes, i.e. rs1042522(C;C) genotypes, live on average 3 years longer than major allele (G;G) homozygotes, based on a study of 9,200+ Danish individuals. The increased longevity is speculated to be related to the i...
Generally European; Light skin; Possibly an increased risk of melanoma This SNP is associated with skin, hair, and eye colour, and risk of melanoma. Individuals with the G;G genotype are generally of European descent and have fair skin. In a population-based case-control study investigating a number of pigmentation-related SNPs and their correlation with cutaneous malignant melanoma (CMM) in a Caucasian Australian population, rs16891982 (variant F374L) was found to be associated with odds ratios of 3.44, 2.86, 1.68, and 1.68 for all study subjects (1,738 CMM cases and 4,517 controls); subjects with northern European ancestry (1,438 cases and 3,098 controls); northern European subjects adjusted for hair, eye, and skin colour; and northern European subjects adjusted for the MC1R genotype, r...
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This snp influences skin pigmentation. The allele p.L374F indicates light-skinned european ancestry c.1122C>G, p.Phe374Leu (NCBI dbSNP rs16891982) in SLC45A2 was associated with protection from malignant melanoma (OR, 0.41; 95% CI, 0.24-0.70; P=0.008 after adjustment for multiple testing) An association study conducted on a population of European origin concluded that the rare (in Europeans, at least) allele L374, i.e. rs16891982(C) in dbSNP orientation, significantly increases the possibility of having black hair color, with an odds ratio of around 7. This population-based case-control study investigated a number of pigmentation-related SNPs and their correlation with cutaneous malignant melanoma (CMM) in an Australian population. rs16891982 (variant F374L) was found to be associated w...
CYP1A2_1545T>C homozygote
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rs2470890 is a SNP in the CYP1A2 gene. The rs2470890(C) allele defines the CYP1A2_1545T>C variant. Low-penetrance alleles predisposing to sporadic colorectal cancers: a French case-controlled genetic association study. [PharmGKB:Curated Weakly associated with tardive dyskinesia and schizophrenia.]
Frequency: 15.9%
References:11
References:11
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rs17887200 and rs12951053 associated with ER negative breast cancer tumors (1.48 (1.11-1.93) p-trend = 0.01 and 1.29 (1.06-1.58) p-trend = 0.009, respectively) A study population including a total of 5,206 invasive ovarian cancer cases (2,829 of which were serous) and 8,790 controls found an association between rs12951053 and serous invasive cancer (median per allele odds ratio 1.19, CI: 1.01-1.38).
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Influences appearance gnxp A genomewide association study of skin pigmentation in a South Asian population. Complex signatures of selection for the melanogenic loci TYR, TYRP1 and DCT in humans.
associated with the absence of freckles
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Influences appearance The A allele of rs1042602 is associated with the absence of freckles [PharmGKB:Non-Curated GWAS Results: A genomewide association study of skin pigmentation in a South Asian population (Initial Sample Size: 363 with maxL* < 56 and 374 with maxL* > 63; 20% tails of distribution; Replication Sample Size: 116 low maxL*, 115 high maxL* individuals). This variant is associated with skin pigmentation by reflectance spectroscopy.] [OMIM:SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 3; SHEP3] [GWAS:Freckles] [GWAS:Skin pigmentation by reflectance spectroscopy]
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prostate cancer treatment response rs2279115 and rs7121 Complex haplotype structure of the human GNAS gene identifies a recombination hotspot centred on a single nucleotide polymorphism widely used in association studies. Polymorphism in maternal LRP8 gene is associated with fetal growth. Differential allelic expression in the human genome: a robust approach to identify genetic and epigenetic cis-acting mechanisms regulating gene expression. PTHR1 mutations associated with Ollier disease result in receptor loss of function. Functional genetic polymorphisms and female reproductive disorders: Part I: Polycystic ovary syndrome and ovarian response. A sensitive functional assay reveals frequent loss of genomic imprinting in human placenta. Association of the GNAS locus with severe malaria. Dev...
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[GWAS:Age-related macular degeneration]
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[GWAS:None]
Normal risk for cutaneous melanoma
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rs13181 is a SNP of the XPD/ERCC2 gene. A meta-analysis of 20 studies, comprising 2,308 cases, ultimately concluded that the rs13181(G) allele is associated with increased cutaneous melanoma risk (odds ratio 1.12, CI: 1.03-1.21, p = 0.01; population attributable risk = 9.6%). Polymorphisms in XPD and TP53 and mutation in human lung cancer. Decision forest analysis of 61 single nucleotide polymorphisms in a case-control study of esophageal cancer; a novel method. ERCC1 and ERCC2 polymorphisms and adult glioma. [Correlation of genetic polymorphisms in nucleotide excision repair system to sensitivity of advanced non-small cell lung cancer patients to platinum-based chemotherapy]. Bladder cancer predisposition: a multigenic approach to DNA-repair and cell-cycle-control genes. Risk of non-Hodgk...
Frequency: 46.9%
References:2
References:2
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[PharmGKB:Curated Variant was identified in a cohort of 54 Japanese individuals, who were administered the anti-arrhythmic drug amiodarone. (HapMap SNP)]
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[PharmGKB:Curated Risk or phenotype-associated allele: Not specified. Phenotype: This SNP was associated with clearance of docetaxel. Study size: 31. Study population/ethnicity: Patients with Non-Small-Cell Lung Carcinoma. Significance metric(s): p = 0.0097 (ANOVA); p = 0.0013 (QMIS); p = 0.0040 (KW) Type of association: PK.]
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A three-single-nucleotide polymorphism haplotype in intron 1 of OCA2 explains most human eye-color variation. Three genome-wide association studies and a linkage analysis identify HERC2 as a human iris color gene.
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Bisphosphonate-related osteonecrosis of the jaw is associated with polymorphisms of the cytochrome P450 CYP2C8 in multiple myeloma: a genome-wide single nucleotide polymorphism analysis. [OMIM:MYELOMA, MULTIPLE]
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[OMIM:DYSTROBREVIN-BINDING PROTEIN 1; DTNBP1]
blue/gray eyes more likely
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rs7495174 is located in intron 1 of the OCA2 gene. The (A) allele (in dbSNP orientation) is associated with blue or green eye color in Caucasians. . This SNP is 1 of 3 SNPs defining a haplotype that has been studied for association with eye color. The full details on the correspondence between the haplotype and eye color can be found on the OCA2 page. [PharmGKB:Curated A haplotype containing rs11855019, rs6497268 and rs7495174 was highly associated with eye color, hair color and skin pigmentation in a mostly Northern European twin study.] [OMIM:OCA2 GENE]
31 snps
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decreased risk of schizophrenia in limited study
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Associated with schizophrenia in a study of Croatians. Due to the limited number and diversity of the studied population, more study is needed to confirm any link. The G allele was associated with a decreased risk of schizophrenia.
Magnitude: 1.2
Frequency: 55.8%
Repute:Good
References:3
Frequency: 55.8%
Repute:Good
References:3
decreased risk of schizophrenia in limited study
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Associated with schizophrenia in a study of Croatians. Due to the limited number and diversity of the studied population, more study is needed to confirm any link. The C allele was associated with an decreased risk of schizophrenia. [PharmGKB:Curated This variant along with 3 other SNPs near DRD4 (4 SNP haplotype: rs3758653; rs916457; rs762502; rs11246226) is associated with tardive dyskinesia in male schizophrenia patients.]
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[PharmGKB:Curated This variant along with 3 other SNPs near DRD4 (4 SNP haplotype: rs3758653; rs916457; rs762502; rs11246226) is associated with tardive dyskinesia in male schizophrenia patients.]
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Association and synergistic interaction between promoter variants of the DRD4 gene in Japanese schizophrenics. [PharmGKB:Curated This variant along with 3 other SNPs near DRD4 (4 SNP haplotype: rs3758653; rs916457; rs762502; rs11246226) is associated with tardive dyskinesia in male schizophrenia patients.]
6 snps
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3.5x asthma risk in certain populations
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This SNP, in the GSTP1 gene influences asthma risk; the (A) allele encodes the Ile, while the (G) allele encodes the Val. This SNP is also known as GSTP1Val105, or GSTP1 Ile105Val. Despite evidence of antioxidant effects of vitamin E in vitro and in animal studies, large, randomized clinical trials have not substantiated a benefit of vitamin E in reducing inflammation in humans. In healthy control subjects, the effect of α-tocopherol supplementation on the production of inflammatory cytokines appears to be dependent on an individual's genotype. These genotype-specific differences may help explain some of the discordant results in studies that used vitamin E. Persons having the alleles AA or AG had an increase in interleukin-6 (IL-6) upon supplementing alpha-tocopherol (the most common...
Carrier of one CYP1A2*1F allele; Slow Caffeine Metabolizer. One copy of the slow caffeine metaboliser SNP, and one copy of the fast version. This makes you more strongly affected by drinking coffee, as caffeine is broken down slower in the liver. Supposedly this increases the risk of heart attacks, although other studies show caffeine is generally good for the heart. It also makes caffeine more effective at preventing Breast Cancer, Alzheimer's Disease, and Parkinson's disease. Too much caffeine will shrink your breasts.
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rs762551, also known as -164A>C or -163C>A, is a SNP encoding the CYP1A2*1F allele of the CYP1A2 gene. For historic reasons, the rs762551(C) allele is considered the wild-type, even though it is the rarer allele in most populations. The rs762551(A) allele is the 'fast metabolizer' allele known as CYP1A2*1F; the (C) allele is by comparison a slower metabolizer of certain substrates (including caffeine). In terms of genotypes, only rs762551(A;A) individuals are considered fast metabolizers. Individuals who are rs762551(A;C) heterozygotes or rs762551(C;C) homozygotes are both considered slow metabolizers. The CYP1A2 gene encodes a member of the cytochrome p450 family of proteins, which metabolize nutrients and drugs. One well known substrate of CYP1A2 is caffeine; individuals who are ca...
some risk linked to a number of metabolic conditions including obesity, coronary artery disease, insulin resistance and therefore diabetes, left ventricular hypertrophy, and hypertension. It has also been linked to how well a patient responds to Viagra (sildenafil).
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rs5443, a SNP in the G-protein beta3 subunit (GNB3) gene that is more commonly known as the C825T variant, has been linked to a number of metabolic conditions including obesity, coronary artery disease, insulin resistance and therefore diabetes, left ventricular hypertrophy, and hypertension. It has also been linked to how well a patient responds to Viagra (sildenafil). Several studies have been unable to replicate one or more of the associations in at least some populations between this SNP and these conditions. The more notable studies include: *rs5443(T) allele carriers are 2-3 fold more likely to be obese in Caucasian, Chinese, and African American populations. *rs5443(T) carriers are clearly at higher risk for hypertension, but this review indicates that whether they are also at incre...
Slower metaboliser for some drugs
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rs1045642, also known as C3435T, is a SNP located in the ABCB1 gene. It is often studied in conjunction with rs2032582. C3435T has been mentioned by: * A 'Silent' Polymorphism in the MDR1 Gene Changes Substrate Specificity (for example, to verapamil) * (R)-lansoprazole (Prevacid) concentrations are significantly increased in CYP2C19 extensive metabolizers with ABCB1 C3435T C allele. * In a Korean population, plasma concentrations of fexofenadine (Allegra) were 17% lower in 2677AA/3435CC subjects and 47% higher in the 2677TT/3435TT subjects compared to 2677GG/3435CC subjects. * In contrast, in this study no association was observed between the C3435T polymorphism and fexofenadine plasma or urine concentrations in a German Caucasian population. * A meta-analysis including 9 case-control stud...
7x less likely to respond to certain antidepressants. This version of a blood brain barrier protein blocks many common antidepressants from entering the brain, including: amitriptyline (Elavil), citalopram (Celexa), paroxetine (Paxil), and venlafaxine (Effexor). That makes those antidepressants 7 times less effective.
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rs2032583 is a SNP in the ABCB1 gene (also known as the MDR1 gene), which encodes a protein that transports certain molecules across the blood-brain barrier. SNPs in ABCB1 may thus influence the intracerebral concentrations of certain drugs and thus their efficacy or potential for adverse side effects. rs2032583 is one of 9 SNPs found within a tight linkage block (r<sup>2</sup> >= 0.8 ) such that the minor allele at any one of them predicts (with ~80%+ accuracy) that the other SNPs will also be the minor allele. The list of the 9 SNPs is shown below. When treated for depression with substrates of the protein encoded by ABCB1, carriers of one or two minor alleles at these ABCB1 SNPs have been reported to respond better than non-carriers. The antidepressant drugs that are know...
more likely to gain weight if taking olanzapine
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The ancestral allele is C. The rs7412(T) allele, also known as Arg176Cys, generally indicates the presence of an Apoε2 allele; see the ApoE page for a full discussion of the ApoE alleles and their association with Alzheimer's disease. Another SNP related to ApoE is rs429358. In a study of 67 mostly Caucasian patients prescribed the atypical antipsychotic olanzapine, carriers of a rs7412(C) allele were more likely to gain significant weight compared to rs7412(T;T) carriers, as assessed by physiogenomic analysis of corresponding weight profiles. Two other SNPs, rs5092 and rs4765623, were also significantly associated with weight profiles in these patients. Current limitations of SNP data from the public domain for studies of complex disorders: a test for ten candidate genes for obesity ...
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rs231775, also known as +49A/G, is a SNP in the CTLA4 gene. which is linked to Hashimoto thyroiditis In a meta-analysis of CTLA4 gene SNPs, rs231775 was most associated with vitiligo; however, the association seems to hold only in the subgroup of patients with other autoimmune diseases. rs231775 (CTLA4_+49_G/A P=0.0219) and rs733618 (CTLA4_-1722_T/C P=0.0096) susceptibility to Graves' disease associated with the development of placental abruption and preeclampsia, with women having the G allele being at risk rs231775 was not associated with type-1 diabetes in a study of 207 Portuguese patients. [PharmGKB:Curated This SNP affects risk for Autoimmune Thyroid Disorder (AITD). The G allele is generally thought to be the risk-conferring allele, but this study found that which allele confers ri...
~10% more likely to respond to citalopram
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rs1954787, located in an intron of the GRIK4 gene, was found to be associated with a somewhat increased rate of successful response to treatment of depression with the drug citalopram. From the abstract of this article: 'The effect size of (this) GRIK4 marker alone was modest, but homozygote carriers of the treatment-response-associated marker alleles of both the GRIK4 and HTR2A (see rs7997012) genes were 23% less likely to experience nonresponse to (citalopram) treatment relative to participants who did not carry any of these marker alleles.' * See also Anxiety Blog posting [PharmGKB:Curated A study in 1,816 eligible patients from the STAR*D cohort found that genetic variation in a kainic acid-type glutamate receptor is reproducibly associated with response to the antidepressant citalopr...
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[PharmGKB:Curated The Ala (C) allele of this SNP is associated with grade 3 to 4 neutropenia and diarrhea and is an independent predictor of diarrhea in patients with colorectal neoplasms.]
depends on [[rs1801252]]
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Also known as Arg389, variation at this SNP, located in the ADRB1 gene, may encode either the amino acid glycine or arginine at amino acid position 389 of the corresponding protein, the beta-1 adrenergic receptor (hence why it is frequently called Arg389Gly). This protein is the target of beta blocker drugs, and so how well the drug works to help lower a patients high blood pressure depends in part on this SNP. The status of this SNP is often reported together with the status of SNP rs1801252, which encodes an amino acid variant at position 49 of the same (ADRB1) protein. The rs1801253(G) allele encodes the glycine. One of the best known studies of the effects of these 2 separate SNPs on the average efficacy of the beta blocker metoprolol in lowering blood pressure (BP) can be summarized f...
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rs20455, often called Arg719 or 719Arg, is a reasonably well studied SNP in the KIF6 gene. The risk allele (encoding the arginine at position 719) is rs20455(C). An extensive 2010 meta-analysis, including over 17,000 patients, suggests this variant does not significantly influence coronary artery disease risk. This SNP is one of the 5 used by Celera's genetic risk score (GRS) for coronary heart disease (CHD). *rs20455, in the KIF6 gene *rs3900940, in the MYH15 gene *rs7439293, in the PALLD gene *rs2298566, in the SNX19 gene *rs1010, in the VAMP8 gene For each of the five variants, the GRS was increased by 1 if the subject was homozygous for the risk variant, unchanged if heterozygous, and decreased by 1 if the individual did not carry the variant. Therefore, individuals carrying all 10 pos...
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[PharmGKB:Curated This variant is in intron 4 of PICK1 and has been significantly associated with methamphetamine abusers with spontaneous relapse of psychosis.]
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rs2227956 in HSP70-hom, resulted in a significant association with noise-induced hearing loss [PharmGKB:Curated The C allele of this SNP is part of a haplotype that has been associated with protection from hypersensitivity to carbamazepine.] [OMIM:?]
Frequency: 41.1%
References:5
References:5
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rs12762549 and rs11045585 can be used to predict whether docetaxel will induced leukopenia/neutropenia, according to a study of ~100 Japanese patients. When patients were classified into three groups by the scoring system based on the genotypes of these two SNPs, patients with a score of 1 or 2 were shown to have a significantly higher risk of docetaxel-induced leukopenia/neutropenia as compared to those with a score of 0 (P = 0.0000057; odds ratio [OR], 7.00; 95% CI [confidence interval], 2.95-16.59). This prediction system correctly classified 69.2% of severe leukopenia/neutropenia and 75.7% of non-leukopenia/neutropenia into the respective categories. [PharmGKB:Curated In a case control study using samples from BioBank Japan, the G allele of rs12762549 was associated with docetaxel-ind...
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[PharmGKB:Curated A study on 50 subjects (25 patients who developed a distinct hearing loss during cisplatin therapy and in 25 patients without hearing impairment after cisplatin therapy)observed a higher frequency of the A-allele of rs2075252 in the LRP2 in the group with hearing impairment than in the group with normal hearing after cisplatin therapy.]
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[PharmGKB:Curated Risk or phenotype-associated allele: A allele. Phenotype: The A allele rs2894342, which lies in the promoter of MLN, is associated with carbamazepine (CBZ)-induced maculopapular exanthema (MPE)/ hypersensitivity syndrome (HSS). Study size: 175. Study population/ethnicity: 31 CBZ-induced MPE/HSS cases and 144 CBZ-tolerant controls of Chinese descent. Significance metric(s): p = 0.00342, OR = 2.88. Type of association: GN; PD; TOX; ADR.]
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rs7569963 is directly adjacent to CREB1. Associated with significantly (p = 0.005) increased chance of suicide in a study of 1447 citalopram users (male only subgroup, 539 in total). Two haplotypes (see below) also showed significant association with suicidality in the male subgroup. *rs2709376(C),rs2253206(A),rs7569963(A),rs7594560(T),rs4675690(C) - common haplotype, reduced chance of suicide in males, p = 0.004 *rs2709376(C),rs2253206(A),rs7569963(G),rs7594560(T),rs4675690(T) - increased chance of suicide in males, p = 0.009 [PharmGKB:Curated In a nested case-control study derived from the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) study this SNP in the CREB1 gene was associated with treatment-emergent suicidality among men with depression.]
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[PharmGKB:Curated This SNP on chromosome 1 was associated with the susceptibility to daunorubicin-induced cytotoxicity in the YRI population using International HapMap cell lines.]
slower responder
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This SNP in the ACE gene, also known as G12269A, is reported to influence how quickly African Americans respond to the anti-hypertensive drug ramipril. rs4344(A;A) and rs4344(G;G) homozygotes are able to reach lower blood pressure levels upon treatment with ramipril sooner than rs4344(A;G) heterozygotes. The odds ratio reported for this study, comparing both homozygotes to heterozygotes, is 1.86 (CI: 1.32-3.23). Note that this SNP is in almost complete linkage disequilibrium with the insertion/deletion ACE gene SNP.
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rs2306283 (Asn130Asp/N130D, A388G/388A>G) is a SNP within SLCO1B1 (Solute carrier organic anion transporter family member 1B1). A G at this location denotes the SLCO1B1*1B allele. among 8 healthy volunteers with *1B/*1B genotypes and 16 with the *1A/*1A genotype, *1B/*1B genotype associated with reduced plasma concentrations of repaglinide (but not nateglinide) consistent with increased hepatic uptake by SLCO1B1 (but w/ limited effects on nateglinide pharmacokinetics) news rs2306283 influences statin-related myopathy risk Genotyping panel for assessing response to cancer chemotherapy. Common variants in the SLCO1B3 locus are associated with bilirubin levels and unconjugated hyperbilirubinemia. Pazopanib-induced hyperbilirubinemia is associated with Gilbert's syndrome UGT1A1 polymorphism...
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[PharmGKB:Curated This SNP at chromosome 9 is significantly associated with HNRPD expression (located on chromosome 4), and daunorubicin IC50 in CEU population using International HapMap cell lines.]
Frequency: 52.3%
References:6
References:6
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Clinically relevant UGT1A10 variant. [PharmGKB:Curated *93 is a common variant of UGT1A1 in Caucasian and African-American populations. It is located in the Phenobarbital Response Enhancer Module (an upstream regulatory sequence) and may be important in predicting irinotecan response.]
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[OMIM:ERBB2 POLYMORPHISM]
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rs4675690 is in close proximity to CREB1, and adjacent to LOC151194. g2b2mh blog individuals with the TT genotype at rs4675690 (C/T) showed less disgust, but not happiness, desire or fear. T allele associated with increased chance of suicide (OR = 2.3, 95% CI 1.3-2.9, TT homozygotes vs CC homozygotes?) during the first 30 days (p > 0.05 after the first month) of citalopram treatment, in a study of 1447 citalopram users (male only subgroup, 539 in total). Two haplotypes (see below) also showed significant association with suicidality in the male subgroup. *rs2709376(C),rs2253206(A),rs7569963(A),rs7594560(T),rs4675690(C) - common haplotype, reduced chance of suicide in males, p = 0.004 *rs2709376(C),rs2253206(A),rs7569963(G),rs7594560(T),rs4675690(T) - increased chance of suicide in males...
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[PharmGKB:Curated The G allele of this SNP is associated with increased incidence of medium-severe nausea or vomiting, and with reduced leukocyte counts in gastric carcinoma and colon carcinoma patients treated with 5-fluorouracil. The elimination constant (Ke) for 5-fluorouracil was significantly lower in patients homozygous for the G allele.]
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[PharmGKB:Curated Risk or phenotype-associated allele: T allele. Phenotype: The T allele of rs3130690 (36 kb telomeric to HLA-B), which is strongly associated with the HLA-B*1502 allele, shows strong association with carbamazepine (CBZ)-induced Stevens-Johnson syndrome (SJS)/Toxic Epidermal Necrolysis (TEN, Lyell's syndrome) (OR = 254.6 for TT/TG genotype versus GG genotype; T allele only: p = 4.66x10(-42), Pc = 1.29x10(-39), OR = 45.65). Also, an extended haplotype with rs3130690 T, HLA-B*1502, and other alleles of major histocompatibility complex genes (A*1101-Cw*0801-HLABC-CA*119-rs3130690T-B*1502-MICA*019-DRB1*1202) was in strong association with CBZ-induced SJS/TEN. Study size: 204. Study population/ethnicity: 60 CBZ-induced SJS/TEN cases and 144 CBZ-tolerant controls of Chinese desce...
>3x increased risk for Alzheimer's; 1.4x increased risk for heart disease
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This SNP, located in the fourth exon of the ApoE gene, affects the amino acid at position 130 of the resulting protein. The more common rs429358 allele is (T). If the allele is (C) and the same chromosome also harbors the rs7412(C) allele, the combination is known as an APOE-ε4 allele. The APOE-ε4 allele has a strong influence on the risk of Alzheimer's disease. Both deCODEme and 23andMe (v3 chip) test for this SNP. Many studies have estimated the level of risk, and it varies depending on age, sex, ethnicity, and other factors. One meta-analysis estimated the odds ratios for homozygous rs429358(C;C) individuals compared to the more common ApoE3/ApoE3 homozygotes to be 12x for late-onset Alzheimer's and 61x for early-onset disease. Meta-analyses have also supported the association between t...
normal
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The (-) form of this SNP, representing a deletion of one nucleotide, causes a frameshift such that the resulting CYP2D6 protein is nonfunctional. The associated allele is also known as CYP2D6*6, and there are several subtypes but they are all nonfunctional. If two copies of this (or similar) changes are inherited, CYP2D6 poor metabolism ('PM') is observed. CYP2D6 poor metabolism may affect the efficacy or degree of side effects of drugs metabolized by CYP2D6, such as dextromorphan, sparteine, nortriptyline, venlafaxine and codeine. Response to serotonin reuptake inhibitors in OCD is not influenced by common CYP2D6 polymorphisms. [PharmGKB:Curated This variant is part of the CYP2D6*6 PM haplotype. Plasma concentrations of metoprolol were shown to be were 4.9-fold higher in the PMs, with gr...
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[PharmGKB:Curated Risk or phenotype-associated allele: G allele. Phenotype: The G allele of rs1264511 shows strong association with carbamazepine (CBZ)-induced maculopapular exanthema (MPE)/ hypersensitivity syndrome (HSS). Study size: 175. Study population/ethnicity: 31 CBZ-induced MPE/HSS cases and 144 CBZ-tolerant controls of Chinese descent. Significance metric(s): p = 0.001685, OR = 3.13. Type of association: GN; PD; TOX; ADR.]
normal; no change in warfarin metabolism
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rs1799853 is a SNP in the CYP2C9 gene and is linked to poor warfarin metabolism. Advanced knowledge of this may influence initial warfarin dosing by physicians. Warfarin is monitored through INR (international normalized ratio) and proper dosing is influenced by a variety of factors including warfarin metabolism and diet. rs1799853 is a SNP in the CYP2C9 gene. The rs1799853(T) allele encodes a variant amino acid, cysteine, which has been linked to poor metabolism of warfarin and thus sensitivity . The common nomenclature for this polymorphism is CYP2C9*2 (Cys amino acid, T allele; the SNP is also known as C430T or Cys144Arg). The CYP2C9*2 allele is also associated with higher sensitivity to the anti-epileptic drug phenytoin. The effect of CYP2C9 variants on drug metabolism should not be pr...
normal; no effect on warfarin metabolism
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SNP rs1057910(A), located in the cytochrome p450 CYP2C9 gene, most commonly encodes the amino acid isoleucine at position 359, and the resulting allele is also known as CYP2C9*1. rs1057910(C) encodes a leucine at this same position, and the resulting allele is called CYP2C9*3. This SNP is also known as Ile359Leu or A1075C. The effect of CYP2C9 variants on drug metabolism should not be predicted without also considering CYP2C9*2, defined as the common loss of function variant rs1799853(T) (NM_000771:c.430C>T, NP_000762:p.144R>C) Studies of the effects of these alleles include: * rs1057910(C;C)] genotypes may clear drugs like celecoxib (trade name Celebrex) twice as slowly as rs1057910(A;A) genotypes; the rs1057910(A;C) genotypes are in-between clearance rates. Lower clearance rates wi...
normal
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This SNP, located in an intron of the GRIA3 gene (also known as AMPA3), has been linked in one study to increased thoughts of suicide in patients taking the anti-depressant drug citalopram. The increased risk is calculated to be 1.9x. If the individual is also carrying two rs2518224(C) alleles, i.e. is a rs2518224(C;C) homozygote, the odds ratio for having suicidal thoughts is increased to ~15x (CI: 3.7 - 60.6). [PharmGKB:Curated This SNP in the GRIA3 gene was associated with treatment-emergent suicidal ideation during citalopram therapy in a clinically representative cohort of outpatients with major depressive disorder. DNA samples from 1,915 participants were genotyped.]
normal
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rs351855, a SNP in the fibroblast growth factor receptor 4 (FGFR4) gene, is also known as the Gly388Arg variant. The rs351855(T) allele encodes the risk (Arg) allele. The Arg form of this SNP is likely to cause a harder to treat version of node-positive breast cancer, including reducing the efficacy of Herceptin, based on a study of 372 patients. A study of ~500 Japanese prostate cancer patients found that individuals with a rs351855(T;T) genotype had a 2.2- and 1.9-fold increased risk of prostate cancer and benign prostate hyperplasia (BPH), and a 1.8-fold increased risk of metastatic prostate cancer compared to the (C;C) genotype. A meta-analysis published in 2011, surveying a total of 2,618 cases of prostate cancer, concluded that the odds ratio per rs351855(T) allele was 1.17 (CI: 1.07...
Common genotype: normal homocysteine levels
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rs1801133 is a SNP that is relatively common and has been studied for (relatively) a long time. Also known as C677T, Ala222Val, and A222V, it encodes a variant in the MTHFR gene, which encodes an enzyme involved in folate metabolism. Homozygous rs1801133(T;T) individuals have ~30% of the expected MTHFR enzyme activity, and rs1801133(C;T) heterozygotes have ~65% activity, compared to the most common genotype, rs1801133(C;C). This reduced activity (i.e. this SNP) has been linked at least once to each of the following disorders (though not necessarily reproducibly): * autism * cancer, including ** gastric cancer ** lung cancer ** head and neck cancer ** renal cancer * cleft lip and cleft palate * coronary artery disease * dementia * depression * hyperhomocysteinemia * migraine * neural tube d...
normal risk
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rs7997012, located in an intron of the HTR2A gene, was found to be associated with a somewhat increased rate of successful response to treatment of depression with the drug citalopram. From this article : 'HTR2A encodes the serotonin 2A receptor, which is downregulated by citalopram. Participants who were homozygous for the A allele had an 18% reduction in absolute risk of having no response to treatment, compared with those homozygous for the other allele.' * See also Anxiety Blog posting [PharmGKB:Curated Risk or phenotype-associated allele: A. Phenotype: Patients with the 5-HTR2A intron 2 (rs7997012) AA genotype suffered from more pronounced side effects compared to carriers of the GA or GG genotype. Study size: 124. Study population/ethnicity: Caucasian; Patients with psychiatric diso...
normal
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The rs1799971(G) allele in exon 1 of the mu opioid receptor OPRM1 gene causes the normal amino acid at residue 40, asparagine (Asn), to be replaced by aspartic acid (Asp). In the literature this SNP is also known as A118G, N40D, or Asn40Asp. Carriers of at least one rs1799971(G) allele appear to have stronger cravings for alcohol than carriers of two rs1799971(A) alleles, and are thus hypothesized to be more at higher risk for alcoholism. However, subsequent research results are mixed, and there are other studies both agreeing or disagreeing with this finding Among 200+ alcoholics treated with naltrexone, rs1799971(G) carriers receiving the drug (even without behavioral intervention) had an increased percentage of days abstinent (p = .07) and a decreased percentage of heavy drinking days (...
normal
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influences statin response *rs72559745 (SLCO1B1*1) AA AA *rs56061388 (SLCO1B1*3) TT TT *rs4149056 (SLCO1B1*5) TT TT *rs55901008 (SLCO1B1*6) TT TT rs4149056, also known as 37041T>C or V174A, is a SNP in the SLCO1B1 gene, which encodes the 'organic anion transporting polypeptide 1B1' (OATP1B1) protein. This protein, found primarily in the liver, regulates the uptake of numerous drugs and natural compounds. The rs4149056(C) SNP defines the SLCO1B1*5 allele. The rs4149056(C) allele gives rise to an amino acid change (from valine to alanine at residue 174) which has reduced uptake/transport activity. Therefore, drugs metabolized by OATP1B1 tend to build up to higher circulating concentrations than they would otherwise.. The drugs known (or in some cases, thought) to be transported less well ...
common in clinvar
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Technology to accelerate pangenomic scanning for unknown point mutations in exonic sequences: cycling temperature capillary electrophoresis (CTCE). Genetic variation in the one-carbon transfer pathway and ovarian cancer risk. Strong association of a common dihydropyrimidine dehydrogenase gene polymorphism with fluoropyrimidine-related toxicity in cancer patients. Genetic variation in TYMS in the one-carbon transfer pathway is associated with ovarian carcinoma types in the Ovarian Cancer Association Consortium. [PharmGKB:Curated Patients heterozygous for the C allele of this SNP exhibited increased incidence of medium-severe nausea and vomiting (as defined by WHO criteria) relative to those carrying only the T allele. The patient population consisted of individuals with gastric or colon ca...
normal
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This SNP, located in an intron of the GRIK2 gene, has been linked in one study to increased thoughts of suicide in patients using the anti-depressant drug citalopram. The risk is only seen for individuals carrying two rs2518224(C) alleles, i.e. the rs2518224(C;C) homozygotes. The odds ratio for these individuals is 8.2. If the individual also has at least one rs4825476(G) allele, the odds ratio for having suicidal thoughts is increased to ~15x (CI: 3.7 - 60.6). [PharmGKB:Curated This SNP in the GRIK2 gene was associated with treatment-emergent suicidal ideation during citalopram therapy in a clinically representative cohort of outpatients with major depressive disorder. DNA samples from 1,915 participants were genotyped.]
normal
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rs4244285 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*2 variant. This variant is the most common reason for poor metabolism of compounds like mephenytoin (an anti-convulsant), some antidepressants, the anti-platelet drug Plavix, and some drugs used for ulcer conditions of various types. The risk allele is rs4244285(A). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (trade name Prevacid). In Caucasians, SNPs in CYP2C19 are relatively rare (in contrast to SNPs in CYP2D6), but SNPs in this gene are common in Asians. Ulcer treatment with omeprazole to reduce Helicobacter pyl...
normal
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rs2231142, also known as Q141K and C421A, is a SNP in the ABCG2 gene, indicating a missense variant. 'Our data indicate that at least 10% of all gout cases in whites are attributable to this causal variant.' A is the risk allele. A large study totaling 7,699 participants in the Framingham cohort and 4,148 participants in the Rotterdam cohort was conducted, with genome-wide significant SNPs then replicated in 11,000+ Caucasian and ~4,000 African-American individuals who took part in the study of Atherosclerosis Risk in Communities (ARIC). This study calculated an odds ratio of 1.74 for rs2231142 (CI: 1.51-1.99, p = 3.3x10e-15). A genetic score comprised of this SNP plus 2 others may stratify risk for gout. Among non-small cell lung cancer patients treated with gefitinib, there's a 4-5x high...
common in clinvar
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rs1142345 is a SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The risk allele for this SNP is rs1142345(G), and when it is the only variant in the TPMT gene, it encodes the TPMT*3C allele. While still rare, it is more common in African-Americans (2.4% of all alleles) than in Caucasians. Note that if the same allele also carries the rs1800460(A) SNP, the allele is actually a TPMT*3A allele (OMIM). The medicine 6-Mercaptopurine is metabolized by TPMT. Individual differences in TPMT activity associated with this SNP are now used to determine appropriate dosage range and interval for treatment. 23an...
normal
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rs6413419, also known as 4768G>A or V179I, is a SNP in the CYP2E1 gene. The rs6413419(A) allele defines the CYP2E1*4 variant.
common in complete genomics
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23andMe reports that the A allele of rs3918290 is associated with the rare recessive disorder dihydropyrimidine dehydrogenase deficiency (DPD), also known as hereditary thymine-uraciluria or familial pyrimidinemia. Note that the terms used in the literature for this gene can be confusing, since the gene is in reverse orientation to the chromosome strand on the reference genome. pharmgkb - defines *2A allele, which has a significantly higher chance of 5-fluorouracil toxicity Fluorouracil Toxicity [PharmGKB:In-Depth Heterozygosity for the A allele of this SNP is associated with mucositis and leukopenia drug toxicity in cancer patients treated with fluorouracil. Heterozygous males were more likely than heterozygous females to develop severe toxicity. In this study, no A/A homozygotes were ob...
normal
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rs1800460 is a SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The risk allele for this SNP is rs1800460(A), and when it is the only variation in the TPMT gene, it encodes the TPMT*3B allele. While still rare, it is more common in Caucasians (4.5% of all alleles) than in African-Americans (0.8%). Note that if the same allele also carries the rs1142345(G) SNP, the allele is actually a TPMT*3A allele (OMIM). The medicine 6-Mercaptopurine is metabolized by TPMT. Individual differences in TPMT activity associated with this SNP are now used to determine appropriate dosage range and interval for treatm...
normal
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rs4986893 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*3 variant. This variant has been linked to poor metabolism of compounds like mephenytoin as well as proguanil, and it therefore has implications for malaria prophylaxis. The risk allele is rs4986893(A). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (Prevacid). Clopidogrel Efficacy [PharmGKB:Curated In contrast to other PPIs, esomeprazole-induced healing of GERD appears to be unrelated to the CYP2C19*3 variant.] [OMIM:MEPHENYTOIN, POOR METABOLISM OF]
common in clinvar
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minor form is a slow metaboliser according to pharmgkb [PharmGKB:In-Depth This variant results in enzyme inactivity and is considered to be part of the %22slow metabolizer%22 group; part of the CYP2A6*2 haplotype.] [OMIM:?] [GWAS:Smoking behavior]
common
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This SNP encodes a variation in the 33rd amino acid of the protein encoded by the TBX21 gene. Although 95% or so of all Caucasians carry two copies of the rs2240017(G) allele, as oriented in dbSNP orientation, and are thus rs2240017(G;G) homozygotes, a few individuals are rs2240017(C;G) heterozygotes. These heterozgotes are reported to improve better over time in response to corticosteroid treatment for asthma than the rs2240017(G;G) homozygotes. So far, studies have not linked, however, this SNP to any change in the overall risk of asthma itself. Although the effect observed was strong, in that treating rs2240017(C;G) heterozygotes ultimately (over 4 years) yields average airway responsiveness in the normal range (i.e. in the same range as for nonasthmatics), the authors point out that th...
more responsive to statin treatment
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rs17244841, also known as SNP 12, is located in the HMG-CoA reductase HMGCR gene. The protein encoded by this gene is the target for drugs designed to inhibit its action, in order to lower cholesterol levels. SNPs in the HMGCR gene may affect how well such drugs (typically statins) work. In a study of ~1,500 patients treated with 40mg/d of pravastatin, rs17244841(A;T) heterozgyotes had a mean decrease in total cholesterol of –32.8 mg/dL (–0.85 mmol/L), while the mean change for rs17244841(A;A) homozygotes was –42.0 mg/dL (–1.09 mmol/L), a reduction in overall efficacy of 21.8% (absolute difference, 9.2 mg/dL, CI: 3.8-14.6 mg/dL, p=.001). The drop in total cholesterol was almost completely due to the decrease in LDL...
normal for 23andMe appears common for 23andMe users
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rs1800462, also known as A80P, is a rare SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The risk allele for this SNP (in orientation to the dbSNP entry) is rs1800462(C), and it encodes the TPMT*2 allele. It may occur at a frequency of 1 in 200 alleles among Caucasians. wikipedia thiopurine drugs metabolized by TPMT include azathioprine, mercaptopurine, and thioguanine [PharmGKB:In-Depth The TPMT:238G>C SNP was cloned from a patient with severe mercaptopurine toxicity. It results in a non-synonymous protein change TPMT:Ala80Pro that has a 100-fold reduction in catalytic activity compared to w...
51 snps
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Impaired muscle performance. Likely endurance athlete. This is under-represented in elite strength and sprint athletes, consistent with previous reports of impaired muscle performance. However this is more common in endurance athletes. This SNP makes fast-twitch muscle fibers completely unable to produce alpha-actinin-3.
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This SNP, in the ACTN3 gene, encodes a premature stop codon in a muscle protein called alpha-actinin-3. The polymorphism alters position 577 of the alpha-actinin-3 protein. In the (C;C) genotype is often called RR. The truncated (T;T) is often called XX. (T;T) is under-represented in elite strength athletes, consistent with previous reports indicating that alpha-actinin-3 deficiency appears to impair muscle performance. The most common nucleotide at this position, (C), encodes an arginine (amino acid code R), the alternative T allele encodes a stop codon (X). Hence, the SNP is referred to as R577X, with homozygotes being either RR or XX and heterozygotes being RX. XX individuals completely lack the expression of alpha-actinin-3. An earlier report studying a relatively small number of Austr...
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[PharmGKB:Curated The -58C allele of the human beta2 bradykinin receptor gene has been associated with hypertension in a Chinese Han population and an African American population.]
complex; see details for increased risks
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Several susceptibilities have been linked to rs1042714, a SNP in the ADRB2 gene that is also known as the Q27E SNP. The rs1042714(C) allele encodes the glutamine (Gln; 'Q'), and the rs1042714(G) allele encodes the glutamic acid (Glu; 'E'). A study of 304 patients found that the Glu27 allele led to increased risk for idiopathic venous thromboembolism; the reported odds ratio was 1.40 (CI: 1.09-1.79, p=0.006) for carriers of at least one risk allele. A study of 334 families with at least one child with autism found that increased risk associated with the rs1042714(G;G) homozygous genotype; the odds ratio reported was between 1.33-1.60 (CI: 1.07-2.58). The risk was approximately doubled among mothers who had clinical markers for pregnancy related stress. In a study of 342 patients with type-2...
depends on [[rs1801252]]
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Also known as Arg389, variation at this SNP, located in the ADRB1 gene, may encode either the amino acid glycine or arginine at amino acid position 389 of the corresponding protein, the beta-1 adrenergic receptor (hence why it is frequently called Arg389Gly). This protein is the target of beta blocker drugs, and so how well the drug works to help lower a patients high blood pressure depends in part on this SNP. The status of this SNP is often reported together with the status of SNP rs1801252, which encodes an amino acid variant at position 49 of the same (ADRB1) protein. The rs1801253(G) allele encodes the glycine. One of the best known studies of the effects of these 2 separate SNPs on the average efficacy of the beta blocker metoprolol in lowering blood pressure (BP) can be summarized f...
normal
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rs1042713, also known as Arg16, G16R, and 16Arg>Gly, is a SNP in the adrenergic, beta-2-, surface receptor ADRB2 gene. The rs1042713(G) allele encodes the G/glycine form that is the more common one in most populations, while rs1042713(A) encodes the R/arginine residue at this position of the ADRB2 protein. A study of 1,182 young Scottish asthma patients (age, 3-22 years) concluded that rs1042713(A) alleles are significantly associated with 'exacerbations' of their condition, regardless of treatment regimens (odds ratio 1.30, CI: 1.09-1.55, p=0.003). This didn't hold true for patients using inhalers less than once per day; and it was particularly true for those receiving daily inhaled long- or short-acting beta(2)-agonist treatment (OR, 1.64, CI: 1.22-2.20, p=.001). This may therefore in...
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[OMIM:UNCOUPLING PROTEIN 3; UCP3]
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In 'Association of the ADRA2A polymorphisms with the risk of type 2 diabetes: a meta-analysis.' a meta-analysis of publications prior to September 2012 showed no overall association between rs553668 and T2D risk, but did find an association with very high (poor) P-value for Europeans under recessive gene model (GT=AA, OR=1.36, p=0.02, 95% CI: 1.05, 1.76). In 'Genetic association of adrenergic receptor alpha 2A with obesity and type 2 diabetes.' rs553668 was found to correlate with obesity in Swedish population, but not significantly for BMI-corrected T2D risk. ADRA2A is involved in sympathetic nervous system's inhibition of insulin secretion and lipolysis, so direct effect on T2D is usually sought, but the Swedish study suggest it could work through body mass. It also mentions that rs55366...
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Vascular endothelial growth factor gene polymorphisms in Behcet's disease. A functional variant of vascular endothelial growth factor is associated with severe ischemic complications in giant cell arteritis. Analysis of vascular endothelial growth factor (VEGF) functional variants in rheumatoid arthritis. Association between functional haplotypes of vascular endothelial growth factor and renal complications in Henoch-Schonlein purpura. Polymorphisms in the vascular endothelial growth factor gene and breast cancer in the Cancer Prevention Study II cohort. Vascular endothelial growth factor gene haplotypes in Kawasaki disease. Functional variation in VEGF is not associated with type 2 diabetes in a United Kingdom Caucasian population. VEGF, FGF1, FGF2 and EGF gene polymorphisms and psoriatic...
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Associated with baseline cholesterol levels in a study of 9,000+ individuals in Washington County, Maryland. [PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: The PPAR delta SNP rs2016520 A>G was associated with positive clincial response (partial or complete response) to treatment. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.0056 Type of association: PD; CO]
normal
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rs4994, also known as Trp64Arg or as the Arg64 variant, is a SNP in the ADRB3 gene. The rs4994(C) allele encodes the variant arginine. In a study of 600+ women initially referred for coronary angiography and then followed for 6 years, during which time 115 experienced a heart problem, rs4994(C) individuals were calculated to be at higher risk (adjusted hazard ratio 2.10, CI: 1.05-4.24). This risk was due to subtle increases in risk for all of the individual endpoints, and was only seen in women without obstructive coronary artery disease. Response to Diet and Exercise [PharmGKB:Curated Arg in position 64 associated with olanzapine-induced weight gain] [OMIM:OBESITY, SUSCEPTIBILITY TO]
common in complete genomics
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suggesting a positive association between the AG genotype, and possibly the G allele, and the likelihood of being an elite endurance athlete perhaps similar to rs1815739 NRF2 genotype improves endurance capacity in response to training.
11 snps
(hide) Eye color
Magnitude: 3.1
blue eyes are much more likely
Most people with this have some shade of blue eye color (some are more grey, some are more green), however one person with brown eyes has also observed this genoset. This spreadsheet is gathering more information on self reported eye color.
Magnitude: 2.5
homozygous for eye color haplotype #3
According to one publication this is blue eye color haplotype #3, however, feedback from Promethease users suggest it is not a reliable predictor of eye color.
Magnitude: 2.3
homozygous eye color haplotype #1
thumb|light brown gs255 eyes According to one publication, this is Blue eye color haplotype #1, however numerous Caucasian users have self reported brown eyes. It is clearly not the darker eye color found in asian or african populations, but it also is not particularly predictive of a reliable eye color. thumb|light blue gs255 eyes thumb|gray blue gs255 eyes
blond hair & blue eyes is 4x more likely
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rs1667394 increases susceptibility to Blond rather than brown hair 4.94 times for carriers of the A allele rs1667394 increases susceptibility to Blue rather than brown eyes 29.43 times for carriers of the A allele rs1667394 increases susceptibility to Blue rather than green eyes 6.74 times for carriers of the A allele For green versus blue eye color rs12913832 in OCA2/HERC2 has a score of 51.5 and an estimated allelic OR of 8.43 . The SNP rs1667394 in this same region has an estimated OR of (4.85–10.06). [OMIM:HECT DOMAIN AND RCC1-LIKE DOMAIN 2; HERC2] [GWAS:Eye color]
Magnitude: 2
Frequency: 61.9%
References:32
Frequency: 61.9%
References:32
blue eye color, 99% of the time
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rs12913832 is a SNP near the OCA2 gene that may be functionally linked to blue or brown eye color, due to a lowering of promoter activity of the OCA2 gene. Blue eye color is associated with the rs12913832(G;G) genotype. For green versus blue eye color rs12913832 in OCA2/HERC2 has a score of 51.5 and an estimated allelic OR of 8.43 . The SNP rs1667394 in this same region has an estimated OR of (4.85–10.06). rs12913832 is also part of a haplotype spanning 166kB on chromosome 15, defined by 13 SNPs listed below, that is found in 97% of all Caucasians with blue eyes. In this haplotype, variations in rs1129038 and rs12913832 are relatively common in Caucasians though rare among other racial groups. rs12913832-T (brown eye) homozygotes compared to rs12913832-C (blue eye). correlations with...
Generally European; Light skin; Possibly an increased risk of melanoma This SNP is associated with skin, hair, and eye colour, and risk of melanoma. Individuals with the G;G genotype are generally of European descent and have fair skin. In a population-based case-control study investigating a number of pigmentation-related SNPs and their correlation with cutaneous malignant melanoma (CMM) in a Caucasian Australian population, rs16891982 (variant F374L) was found to be associated with odds ratios of 3.44, 2.86, 1.68, and 1.68 for all study subjects (1,738 CMM cases and 4,517 controls); subjects with northern European ancestry (1,438 cases and 3,098 controls); northern European subjects adjusted for hair, eye, and skin colour; and northern European subjects adjusted for the MC1R genotype, r...
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This snp influences skin pigmentation. The allele p.L374F indicates light-skinned european ancestry c.1122C>G, p.Phe374Leu (NCBI dbSNP rs16891982) in SLC45A2 was associated with protection from malignant melanoma (OR, 0.41; 95% CI, 0.24-0.70; P=0.008 after adjustment for multiple testing) An association study conducted on a population of European origin concluded that the rare (in Europeans, at least) allele L374, i.e. rs16891982(C) in dbSNP orientation, significantly increases the possibility of having black hair color, with an odds ratio of around 7. This population-based case-control study investigated a number of pigmentation-related SNPs and their correlation with cutaneous malignant melanoma (CMM) in an Australian population. rs16891982 (variant F374L) was found to be associated w...
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[PharmGKB:Non-Curated GWAS Results: Two newly identified genetic determinants of pigmentation in Europeans (Initial Sample Size: 5,130 individuals; Replication Sample Size: 3,330 individuals; Risk/trait Allele: rs1408799-C). This variant is associated with Blue vs. green eyes.] [OMIM:TYROSINASE-RELATED PROTEIN 1; TYRP1] [GWAS:Eye color] [GWAS:Blue vs. green eyes]
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Influences appearance gnxp A genomewide association study of skin pigmentation in a South Asian population. Complex signatures of selection for the melanogenic loci TYR, TYRP1 and DCT in humans.
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eye color [GWAS:Eye color]
Frequency: 40.7%
References:0
References:0
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Influences appearance gnxp
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[GWAS:Eye color traits]
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[GWAS:Eye color traits]
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[GWAS:None]
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[GWAS:Eye color]
Frequency: 52.2%
References:10
References:10
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associated with hair color rs12896399 rs12203592 [OMIM:SOLUTE CARRIER FAMILY 24 (SODIUM/POTASSIUM/CALCIUM EXCHANGER), MEMBER] [GWAS:Black vs. blond hair color]
Frequency: 53.8%
References:1
References:1
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[GWAS:None]
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2865509/ http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2865509/table/pgen-1000934-t002/
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eye color http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2865509/ http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2865509/table/pgen-1000934-t002/ Digital quantification of human eye color highlights genetic association of three new loci.
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[GWAS:Eye color]
blue eye color if part of blue eye color haplotype
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rs4778241 is part of a haplotype spanning 166kB on chromosome 15, defined by 13 SNPs listed below, found in 97% of all Caucasians with blue eyes. In this haplotype, variations in rs1129038 and rs12913832 are relatively common in Caucasians though rare among other ethnic groups. The 'h-1' haplotype found in homozygous state in 97% of individuals with blue eye color is composed as follows : rs4778241(C)<br> rs1129038(A)<br> rs12593929(A)<br> rs12913832(G)<br> rs7183877(C)<br> rs3935591(G)<br> rs7170852(A)<br> rs2238289(T)<br> rs3940272(C)<br> rs8028689(T)<br> rs2240203(A)<br> rs11631797(G)<br> rs916977(G)<br> A three-single-nucleotide polymorphism haplotype in intron 1 of OCA2 explains most human eye-color variatio...
blue eye color if part of blue eye color haplotype
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rs916977 is part of a haplotype spanning 166kB on chromosome 15, defined by 13 SNPs listed below, found in 97% of all Caucasians with blue eyes. In this haplotype, variations in rs1129038 and rs12913832 are relatively common in Caucasians though rare among other ethnic groups. The 'h-1' haplotype found in homozygous state in 97% of individuals with blue eye color is composed as follows : rs4778241(C)<br> rs1129038(A)<br> rs12593929(A)<br> rs12913832(G)<br> rs7183877(C)<br> rs3935591(G)<br> rs7170852(A)<br> rs2238289(T)<br> rs3940272(C)<br> rs8028689(T)<br> rs2240203(A)<br> rs11631797(G)<br> rs916977(G)<br> [PharmGKB:Non-Curated GWAS results: Three genome-wide association studies and a linkage analysis identify H...
blue eye color if part of blue eye color haplotype
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rs3935591 is part of a haplotype spanning 166kB on chromosome 15, defined by 13 SNPs listed below, found in 97% of all Caucasians with blue eyes. In this haplotype, variations in rs1129038 and rs12913832 are relatively common in Caucasians though rare among other ethnic groups. The 'h-1' haplotype found in homozygous state in 97% of individuals with blue eye color is composed as follows : rs4778241(C) rs1129038(A) rs12593929(A) rs12913832(G) rs7183877(C) rs3935591(G) rs7170852(A) rs2238289(T) rs3940272(C) rs8028689(T) rs2240203(A) rs11631797(G) rs916977(G)
blue/gray eyes more possible
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rs1800407 is located in exon 13 of the OCA2 gene at amino acid position 419, and it is therefore also known as the R419Q variant. The (A) allele encodes the amino acid glutamine (instead of arginine), and it is associated with increased odds of having green/hazel eye color in some Caucasian populations. One copy of of rs1800407(A) is sufficient for this effect. [PMID 12163334, PMID 15889046; OMIM 203200.0012] According to tree scanning analysis, the proportion of eye colour variation explained by this nucleotide position is merely 4%. Thus, additional variation present in the OCA2 gene and perhaps some other pigment related genes must be taken into account in order to explain the high phenotypic variation in iris colour. Among rs12913832(A;A) individuals, the penetrance for green/hazel eye...
blue eye color if part of blue eye color haplotype
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rs7183877 is part of a haplotype spanning 166kB on chromosome 15, defined by 13 SNPs listed below, found in 97% of all Caucasians with blue eyes. In this haplotype, variations in rs1129038 and rs12913832 are relatively common in Caucasians though rare among other ethnic groups. The 'h-1' haplotype found in homozygous state in 97% of individuals with blue eye color is composed as follows : rs4778241(C)<br> rs1129038(A)<br> rs12593929(A)<br> rs12913832(G)<br> rs7183877(C)<br> rs3935591(G)<br> rs7170852(A)<br> rs2238289(T)<br> rs3940272(C)<br> rs8028689(T)<br> rs2240203(A)<br> rs11631797(G)<br> rs916977(G)<br>
Frequency: 89.4%
References:1
References:1
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[GWAS:Eye color]
blue eye color more likely
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rs1129038 is part of a haplotype spanning 166kB on chromosome 15, defined by 13 SNPs listed below, found in 97% of all Caucasians with blue eyes. In this haplotype, variations in rs1129038 and rs12913832 are relatively common in Caucasians though rare among other ethnic groups. The 'h-1' haplotype found in homozygous state in 97% of individuals with blue eye color is composed as follows : rs4778241(C)<br> rs1129038(A)<br> rs12593929(A)<br> rs12913832(G)<br> rs7183877(C)<br> rs3935591(G)<br> rs7170852(A)<br> rs2238289(T)<br> rs3940272(C)<br> rs8028689(T)<br> rs2240203(A)<br> rs11631797(G)<br> rs916977(G)<br> [OMIM:HECT DOMAIN AND RCC1-LIKE DOMAIN 2; HERC2] [GWAS:None]
blue/gray eyes possible
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rs1800401 is located in exon 7 of the OCA2 gene at amino acid position 305. The (T) allele encodes the amino acid tryptophan (instead of arginine), and it is one of several SNPs associated with increased odds of having brown or black eye color in Caucasians. One copy of of rs1800401(T) is sufficient for this effect. [PMID 12163334, PMID 15889046; OMIM 203200.0011] [OMIM:?]
slight increase in skin cancer risk
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rs1126809 is a SNP in the TYR tyrosinase gene. This SNP is also known as R402Q (or, 1205G>A) based on the amino acid change at position 402 from an arginine (R) to a glutamine (Q). The rs1126809(G) allele encodes the more common (R)/arginine, while the variant rs1126809(A) allele encodes the (Q)/glutamine. rs1126809(A) has previously been shown to affect eye color and sun sensitivity. Based on a study of 4,000+ skin cancer patients, it also conferred increased risk of cutaneous malignant melanoma (odds ratio 1.21, p = 2.8 x 10<sup>-7</sup>) and basal cell carcinoma (odds ratio 1.14, p = 6.1 x 10<sup>-4</sup>). rs1126809 is not associated with albinism. [PharmGKB:Curated This variant is associated with the risk of cutaneous melanoma and basal cell carcinoma. It i...
normal
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rs4911414 is a SNP near the ASIP (agouti signaling protein) gene on chromosome 20. This SNP is one of a tightly-linked pair that increases the likelihood of an individual being prone to sun sensitivity, in other words, freckles and sunburn, based on a study of 6,000+ Caucasians (5,000+ Icelanders + 1,000+ Dutch). The odds ratios, presumably on a dominant basis, and at least in the largest population (Icelanders) for 'freckles and burns vs. no freckles and tans' for the haplotype pair rs1015362(G) - rs4911414(T) is 3.91 (CI: 2.54-6.03) for males and 2.42 (CI: 1.52-3.86) for females, with an overall p=0.051. Based on a study by the same authors of 4,000+ skin cancer patients, this haplotype was seen to confer significant increased risk for cutaneous malignant melanoma (odds ratio 1.45, p = 1...
common on affy axiom data
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23andMe blog rs1393350 A 1.29 Melanoma rs1393350 increases susceptibility to Blond rather than brown hair 1.29 times for carriers of the A allele rs1393350 increases susceptibility to Blue rather than green eyes 1.52 times for carriers of the A allele rs1393350 increases susceptibility to Skin sensitivity to sun 1.26 times for carriers of the A allele A genome-wide association study identifies novel alleles associated with hair color and skin pigmentation. Genetic variants in pigmentation genes, pigmentary phenotypes, and risk of skin cancer in Caucasians. Digital quantification of human eye color highlights genetic association of three new loci. [OMIM:TYROSINASE; TYR] [GWAS:Tanning]
Magnitude: 0
Frequency: 70.8%
Repute:Good
References:20
Frequency: 70.8%
Repute:Good
References:20
common on affy axiom data
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plos rs12203592 showed the largest allele frequency difference between the Irish individuals and those individuals of Northern, Central European and Eastern European descent associated with hair color rs12896399 rs12203592 rs12203592 for freckling was previously associated with hair color, eye color, and tanning response to sunlight Squamous Cell Carcinoma [PharmGKB:Non-Curated GWAS Results: A Genome-Wide Association Study Identifies Novel Alleles Associated with Hair Color and Skin Pigmentation (Initial Sample Size: 2,287 women; Replication Sample Size: up to 8,465 individuals; Risk/trait Allele: rs12203592-T). This variant is associated with Black vs. red hair color.] [GWAS:Eye color] [GWAS:Black vs. red hair color]
Magnitude: 0
Frequency: 88.5%
Repute:Good
References:1
Frequency: 88.5%
Repute:Good
References:1
blue eye color more likely
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rs12593929 is part of a haplotype spanning 166kB on chromosome 15, defined by 13 SNPs listed below, found in 97% of all Caucasians with blue eyes. In this haplotype, variations in rs1129038 and rs12913832 are relatively common in Caucasians though rare among other ethnic groups. The 'h-1' haplotype found in homozgyous state in 97% of individuals with blue eye color is composed as follows : rs4778241(C)<br> rs1129038(A)<br> rs12593929(A)<br> rs12913832(G)<br> rs7183877(C)<br> rs3935591(G)<br> rs7170852(A)<br> rs2238289(T)<br> rs3940272(C)<br> rs8028689(T)<br> rs2240203(A)<br> rs11631797(G)<br> rs916977(G)<br>
blue eye color more likely
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rs2240203 is part of a haplotype spanning 166kB on chromosome 15, defined by 13 SNPs listed below, found in 97% of all Caucasians with blue eyes. In this haplotype, variations in rs1129038 and rs12913832 are relatively common in Caucasians though rare among other ethnic groups. The 'h-1' haplotype found in homozygous state in 97% of individuals with blue eye color is composed as follows : rs4778241(C)<br> rs1129038(A)<br> rs12593929(A)<br> rs12913832(G)<br> rs7183877(C)<br> rs3935591(G)<br> rs7170852(A)<br> rs2238289(T)<br> rs3940272(C)<br> rs8028689(T)<br> rs2240203(A)<br> rs11631797(G)<br> rs916977(G)<br>
blue eye color if part of blue eye color haplotype
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rs8028689 is part of a haplotype spanning 166kB on chromosome 15, defined by 13 SNPs listed below, found in 97% of all Caucasians with blue eyes. In this haplotype, variations in rs1129038 and rs12913832 are relatively common in Caucasians though rare among other ethnic groups. The 'h-1' haplotype found in homozygous state in 97% of individuals with blue eye color is composed as follows : rs4778241(C)<br> rs1129038(A)<br> rs12593929(A)<br> rs12913832(G)<br> rs7183877(C)<br> rs3935591(G)<br> rs7170852(A)<br> rs2238289(T)<br> rs3940272(C)<br> rs8028689(T)<br> rs2240203(A)<br> rs11631797(G)<br> rs916977(G)<br> [GWAS:Multiple myeloma (IgH translocation)]
blue/gray eyes more likely
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rs7495174 is located in intron 1 of the OCA2 gene. The (A) allele (in dbSNP orientation) is associated with blue or green eye color in Caucasians. . This SNP is 1 of 3 SNPs defining a haplotype that has been studied for association with eye color. The full details on the correspondence between the haplotype and eye color can be found on the OCA2 page. [PharmGKB:Curated A haplotype containing rs11855019, rs6497268 and rs7495174 was highly associated with eye color, hair color and skin pigmentation in a mostly Northern European twin study.] [OMIM:OCA2 GENE]
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Influences appearance gnxp Digital Quantification of Human Eye Color Highlights Genetic Association of Three New Loci[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2865509/] Common sequence variants on 20q11.22 confer melanoma susceptibility. Genome-wide association study identifies three loci associated with melanoma risk. Web-based, participant-driven studies yield novel genetic associations for common traits.
common in complete genomics
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Influences appearance gnxp associated with skin pigmentation in two samples of East Asian ancestry and it confirms previous evidence indicating that evolution towards light skin occurred, at least in part, independently in Europe and East Asia. The OCA2 gene has been under positive selection in Europe and East Asia, but different alleles have been selected in each region. 23andMe blog each rs1800414(C) was associated with a 1.3 melanin unit reduction in skin pigmentation. This SNP accounts for 9% of the variation in skin color seen in the study population.
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Influences appearance gnxp
3 genosets 39 snps
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Normal (A2/A2): Better avoidance of errors. Normal OCD risk, normal Tardive Diskinesia risk, lower ADHD risk. Less Alcohol dependence. Higher risk of Postoperative Nausea. Lower obesity. Bupropion is effective. This DRD2 TaqIA A2/A2 version causes a normal amount of Dopamine Receptors. Learns from mistakes more easily. Men may have a higher risk of Obsessive Compulsive Disorder but lower risk of ADHD. Women have higher Persistence. Higher risk of Tardive Diskinesia when taking dopamine receptor antagonists. Lower risk of alcoholism and smoking addiction. Faster recovery from traumatic brain injury. 1.6x risk of early postoperative nausea within 6 hours of surgery. Bupropion (Wellbutrin, Budeprion, Prexaton, Elontril, Aplenzin, Zyban, Voxra) works to quit smoking. Lower obesity due to incr...
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rs1800497, a SNP also known as the TaqIA (or Taq1A) polymorphism of the dopamine D2 receptor DRD2 gene (even though it is actually located over 10,000bp downstream of the gene), gives rise to the DRD2*A1 allele. This allele (rs1800497(T)) is associated with a reduced number of dopamine binding sites in the brain . Reduced response to errors and increased addictive behavior It has been postulated to play a role in alcoholism, smoking, and certain neuropsychiatric disorders. The reduced number of dopamine binding sites may play a role in nicotine addiction by causing an 'understimulated' state that can be relieved by smoking (and/or use of other drugs). A wide variety of reports have been published over more than ten years either linking rs1800497 to aspects of nicotine use and smoking cessa...
Less likely to live to 100. Unfortunately, this version of FOXO3 has reduced longevity. It has lower insulin sensitivity, increased oxidative stress, and increased risk of diabetes and heart disease.
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A study of 5 genes in 3,741 Japanese men, some of whom lived significantly longer than average (centarians), concluded that the FOXO3 gene (also known as FOXO3A) harbors several SNPs linked to longevity, including this SNP, rs2802292, as well as rs2764264 and rs13217795. The odds ratio for rs2802292(G;G) vs (T;T) carriers was 2.75 (p = 0.00009; adjusted p = 0.00135). It is not known yet if this correlation is specific to Japanese males. This is discussed extensively at geneticfuture as a longevity snp. *(T) shorter lifespan *(G) longer lifespan Quoted from the geneticfuture article: 'No-one should consider this association to be definitive until it's been replicated in independent cohorts. Secondly, the effects of this variant are likely to differ between groups. According to the HapMap da...
Increased risk of Male Pattern Baldness. One copy of the risk allele, and one copy of the normal allele. Verified in Europeans and Asians. Family Tree DNA, which tends to skew heterozygous results like this in the most positive light, reports this as less likely to go bald, but 23andMe doesn't mention it.
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spitoon rs2180439(T;T) have 2x increased odds of male pattern baldness. [PharmGKB:Non-Curated Susceptibility variants for male-pattern baldness on chromosome 20p11. (Initial Sample Size: 296 cases, 347 controls; Replication Sample Size: 319 cases, 234 controls); (Region: 20p11.22; Reported Gene: PAX1, BQ013595, BE789145; Risk Allele: rs2180439-C) This variant is associated with Male-pattern baldness.] [OMIM:ALOPECIA, ANDROGENETIC, 3; AGA3] [GWAS:Male-pattern baldness]
Impaired muscle performance. Likely endurance athlete. This is under-represented in elite strength and sprint athletes, consistent with previous reports of impaired muscle performance. However this is more common in endurance athletes. This SNP makes fast-twitch muscle fibers completely unable to produce alpha-actinin-3.
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This SNP, in the ACTN3 gene, encodes a premature stop codon in a muscle protein called alpha-actinin-3. The polymorphism alters position 577 of the alpha-actinin-3 protein. In the (C;C) genotype is often called RR. The truncated (T;T) is often called XX. (T;T) is under-represented in elite strength athletes, consistent with previous reports indicating that alpha-actinin-3 deficiency appears to impair muscle performance. The most common nucleotide at this position, (C), encodes an arginine (amino acid code R), the alternative T allele encodes a stop codon (X). Hence, the SNP is referred to as R577X, with homozygotes being either RR or XX and heterozygotes being RX. XX individuals completely lack the expression of alpha-actinin-3. An earlier report studying a relatively small number of Austr...
Carrier of one CYP1A2*1F allele; Slow Caffeine Metabolizer. One copy of the slow caffeine metaboliser SNP, and one copy of the fast version. This makes you more strongly affected by drinking coffee, as caffeine is broken down slower in the liver. Supposedly this increases the risk of heart attacks, although other studies show caffeine is generally good for the heart. It also makes caffeine more effective at preventing Breast Cancer, Alzheimer's Disease, and Parkinson's disease. Too much caffeine will shrink your breasts.
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rs762551, also known as -164A>C or -163C>A, is a SNP encoding the CYP1A2*1F allele of the CYP1A2 gene. For historic reasons, the rs762551(C) allele is considered the wild-type, even though it is the rarer allele in most populations. The rs762551(A) allele is the 'fast metabolizer' allele known as CYP1A2*1F; the (C) allele is by comparison a slower metabolizer of certain substrates (including caffeine). In terms of genotypes, only rs762551(A;A) individuals are considered fast metabolizers. Individuals who are rs762551(A;C) heterozygotes or rs762551(C;C) homozygotes are both considered slow metabolizers. The CYP1A2 gene encodes a member of the cytochrome p450 family of proteins, which metabolize nutrients and drugs. One well known substrate of CYP1A2 is caffeine; individuals who are ca...
Reduced risk of Baldness.
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nature Baldness OR = 1.60, P = 1.1 times 10-14). see also gs122 The risk allele is assumed to be rs1160312(A). Note that a haplotype consisting of rs201571(T) - rs6036025(G) has a perfect correlation (r2 = 1) with rs1160312(A), at least in the Caucasian population studied. [PharmGKB:Non-Curated Male-pattern baldness susceptibility locus at 20p11. (Initial Sample Size: 578 cases, 547 controls; Replication Sample Size: 1,351 cases, 2,485 controls); (Region: 20p11.22; Reported Gene: PAX1; Risk Allele: rs1160312-A) This variant is associated with Male-pattern baldness.] [OMIM:ALOPECIA, ANDROGENETIC, 3; AGA3] [GWAS:Male-pattern baldness]
Magnitude: 2
Frequency: 23.2%
Repute:Good
References:12
Frequency: 23.2%
Repute:Good
References:12
Wet earwax. Slightly better body odour. Heterozygous for wet earwax. This makes earwax wet, sticky, and honey-coloured, which is normal for non-Asians. Being heterozygous slightly improves body odour and may slightly reduce colostrum production for breast feeding. People with this usually still need to use deodorant.
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rs17822931, also known as c.538G>A or G180R, is a SNP in the ATP-binding cassette, sub-family C (CFTR/MRP), member 11 ABCC11 gene. The ABCC11 protein helps transport small molecules across apical membranes such as those in apocrine secretory cells. This SNP determines wet vs dry earwax as well as sweat production, and it is also associated with lipid secretion. It is commonly (T;T) for Asians and (C;C) for Europeans and Africans. A study of deodorant usage in a large (17,000+) population showed that rs17822931(T;T) individuals were at least 5-fold less likely to use deodorant, consistent with them being 'genotypically nonodorous'. Although not statistically significant, there was some evidence for a heterozygote effect, implying that individuals with a (C;C) genotype for this SNP were l...
Slightly increased lifespan?
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This SNP, a variant in the TP53 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the G allele encodes an arginine at position 72 of the protein (where there's normally a proline), and the SNP is commonly called the Arg72 variant, although P72R and Arg72Pro are also common in the literature. Minor allele homozygotes, i.e. rs1042522(C;C) genotypes, live on average 3 years longer than major allele (G;G) homozygotes, based on a study of 9,200+ Danish individuals. The increased longevity is speculated to be related to the i...
Less mental decline with age. One copy of the good version of the SIRT1 longevity gene. This is believed to slow the aging of the brain, and perhaps to increase longevity.
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rs3758391, a SNP in the SIRT1 gene, has been reported to potentially have some role in either longevity, or with higher statistical significance, better cognitive function in older individuals. SIRT1 is thought to regulate neuronal metabolism and survival in response to stress, and the equivalent gene in other species influences maximal life span. The study reporting improved cognition for carriers of rs3758391(T) alleles was based on over 1,000 Finnish adults over the age of 85, and a weak trend towards lower cardiovascular disease was also reported for this allele.
Smokes normal (lower) number of cigarettes if a smoker. Less nicotine dependence. Also smokes each cigarette less deeply. Therefore there is a reduced risk of lung cancer and a reduced (0.8x) risk of Peripheral Artery Disease. This doesn't affect whether people start smoking though.
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rs1051730, also known as D398N, is a SNP in the nicotinic acetylcholine receptor alpha 3 subunit CHRNA3 gene. In two recent (2008) studies, together comprising over 6,000 lung cancer patients of European ancestry, the rs1051730(T) allele was very significantly associated with increased risk. Having one copy (i.e. being a rs1051730(C;T) genotype) increased risk for lung cancer about 1.3x, and having two copies (rs1051730(T;T) individuals) represented 1.8x increased risk. Up to 14% of lung cancer incidence may be attributable to this allele. An independent study published at the same time concluded that (T) allele carriers for SNP rs1051730 are not at higher risk of becoming smokers compared to (C) carriers. However, if they do smoke, (T) carriers are quite likely to smoke more cigarettes th...
Back Pain: lower risk of Lumbar Disc Disease. This appears to reduce the risk of LDD, at least in Japanese people and women.
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The rs2073711 SNP (1184T→C ) is located in exon 8 of the cartilage intermediate layer protein gene (CILP). However, CILP gene is primarily known to be expressed abundantly in intervertebral discs, and was reported to have increased expression when degeneration occurs . For the rs2073711 SNP, the ancestral allele is T and the disease associated risk allele is C. A study of Asian patients with lumbar disc disease (LDD) implicates each copy of a (C) allele of SNP rs2073711 (as oriented with respect to dbSNP) as increasing risk about 1.6 fold. ==Background== Low back pain (LBP) is an enervating condition that affects 70-85% of all people during their lifetime . It can lead to decreased physical activity and quality of life, presenting considerable negative socioeconomic and health impact...
Faster aging. Increased risk for Dementia. Less good cholesterol. This reduces HDL ('good') cholesterol. HDL cholesterol removes cholesterol from artery walls and improves health. This SNP seems to be associated with higher blood pressure, less longevity, and more diseases of aging, in particular memory decline and dementia, and lower odds of living to 100, especially in Ashkenazi Jews. Attempting to raise HDL cholesterol may (or may not) be useful to mitigate the effects of this SNP.
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This SNP rs5882 in the CETP gene referred to as ILE405VAL and RSAI405V has been related to ageing and exceptional long life. A study in Ashkenazi Jews showed that individuals homozygotic for the G allele have significantly longer lifespans. New research also indicates that G homozygotes have an average of 70% less risk of dementia and Alzheimer's disease. The study also found that heterozygotes have a lower risk of dementia and Alzheimer's disease but more study is needed to determine the risk reduction for heterozygotes. See Association of a Functional Polymorphism in the Cholesteryl Ester Transfer Protein (CETP) Gene With Memory Decline and Incidence of Dementia and CETP Variant Linked to Slower Cognitive Decline and Reduced Dementia Risk . [PharmGKB:Curated Risk or phenotype-associated...
2-4x higher risk of sun sensitivity if part of risk haplotype. Increased risk of sunburns and freckles instead of tanning.
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rs1015362 is a SNP near the ASIP (agouti signaling protein) gene on chromosome 20. This SNP is one of a tightly-linked pair that increases the likelihood of an individual being prone to sun sensitivity, in other words, freckles and sunburn, based on a study of 6,000+ Caucasians (5,000+ Icelanders + 1,000+ Dutch). The odds ratios, presumably on a dominant basis, and at least in the largest population (Icelanders) for 'freckles and burns vs. no freckles and tans' for the haplotype pair rs1015362(G) - rs4911414(T) is 3.91 (CI: 2.54-6.03) for males and 2.42 (CI: 1.52-3.86) for females, with an overall p=0.051. Based on a study by the same authors of 4,000+ skin cancer patients, this haplotype was seen to confer significant increased risk for cutaneous malignant melanoma (odds ratio 1.45, p = 1...
Normal (higher) risk of physical impairment with age. This causes physical problems for older people, and Cerebral Small Vessel Disease in the brain.
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rs2811712 is a SNP associated with physical function in older individuals, and thus indirectly associated with longevity. In a study ultimately totaling over 3,300 elderly Caucasian individuals, the less common rs2811712(G) allele was associated with reduced physical impairment. Overall, severely limited physical function was present in 15.0% of the more common rs2811712(A;A) homozygotes, versus 7.0% of the rs2811712(G;G) homozygotes, yielding a per risk allele odds ratio of 1.48 (CI: 1.17-1.88, p=0.001). Association of single-nucleotide polymorphisms in the cell cycle genes with breast cancer in the British population. Consortium analysis of 7 candidate SNPs for ovarian cancer. Candidate gene analysis using imputed genotypes: cell cycle single-nucleotide polymorphisms and ovarian cancer r...
Alcohol Flush: Normal, doesn't flush. Normal hangovers. Normal risk of Alcoholism. Normal risk of Esophageal Cancer. Disulfiram is effective for alcoholism. Two working copies of Aldehyde Dehydrogenase (ALDH2) mean you won't turn bright red when you drink alcohol, unlike most Asians. After your body turns alcohol into the dangerous acetaldehyde, this gene quickly turns the acetaldehyde into vinegar. It also stops the acetaldehyde in cigarettes from causing Esophageal Cancer. It reduces hangovers compared to Asians, but less hangovers and flushing obviously increases the risk of alcoholism. Alcoholism can be treated effectively with the drug Disulfiram (Antabuse) which would stop this gene from working and cause the Asian flush in non-Asians. PMC2659709 [http://www.ncbi.nlm.nih.gov/pmc/art...
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rs671 is a classic SNP, well known in a sense through the phenomena known as the 'alcohol flush', also known as the 'Asian Flush' or 'Asian blush', in which certain individuals, often of Asian descent, have their face, neck and sometimes shoulders turn red after drinking alcohol. The rs671(A) allele of the ALDH2 gene is the culprit, in that it encodes a form of the aldehyde dehydrogenase 2 protein that is defective at metabolizing alcohol. This allele is known as the ALDH*2 form, and individuals possessing either one or two copies of it show alcohol-related sensitivity responses including facial flushing, and severe hangovers (and hence they are usually not regular drinkers). Perhaps not surprisingly they appear to suffer less from alcoholism and alcohol-related liver disease. Disulfiram (...
Probably MAOA 4 or 5 repeats: not Warrior Gene. People with this SNP usually also have either the 4 or 5 repeat (non-Warrior) version of MAOA which makes them less aggressive and less anti-social. If you are male, you inherited this from your mother. Do not confuse this with the completely different warrior/worrier gene.
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This is the best proxy for the number of repeats of the MAOA warrior gene. In 105 samples (69 males, 36 females) from the Stanley foundation brain collection, it was always A in people with the 4 or 5 repeat non-Warrior version and always G in people with the 3 repeat Warrior version. The combination rs909525(A) AND rs6323(G) AND rs3027399(G) indicate specifically that it is the 5 repeat version. The 2 repeat version and the 3.5 repeat version weren't mentioned. mentioned as potentially affecting white matter volume, sample size tiny
Can taste bitter. Normal tasting ability for bitterness. This makes turnip, cabbage, brussels sprouts, broccoli, and other cruciferous vegetables taste more interesting and less horribly bland. Coffee and dark beers also tastes more bitter. You can taste propylthiouracil (PROP), PTC, and related chemicals. On the other hand, you can't taste the unpleasant bitterness of the tropical fruit from the Bignay tree, it will taste sweet to you. You probably eat healthier.
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rs713598 is one of three SNPs that form the main haplotypes behind the ability to perceive as bitter the taste of the compound phenylthiocarbamide (PTC) and similar molecules in foods (like cabbage and raw broccoli) or drinks (like coffee and dark beers). The rs713598(G) allele, in the orientation shown in dbSNP, is the 'tasting' allele, and it is dominant to the 'non-tasting' allele rs713598(C), so having one copy is enough to have the bitter tasting ability. If you are a 'taster', you're also likely to carry at least one rs10246939(C) and one rs1726866(C) allele since, along with rs713598(G), these three SNPs form the most common tasting haplotype. If you lack these alleles, you're quite likely (~80%) to be a non-taster of bitterness, meaning that foods that may taste bitter to others ta...
Magnitude: 1.1
Repute:Bad
References:1
Repute:Bad
References:1
Less longevity for Ashkenazi Jewish women.
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rs34516635 is one of a small number of (rare) SNPs in the IGF1R gene found in a study of 384 Ashkenazi centenarians to potentially be associated with longevity and ageing. The rs34516635(A) allele was found somewhat more frequently (p=0.02) in female centenarians than in controls. No association was found for males. Higher IGF1 levels and an average decrease in maximal lifetime height of 2.5cm were also reported to be associated with (female Ashkenazi) centenarians.
complex; see details
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rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. In the literature, it is almost universally referred to as the IL6 '-174' polymorphism. It tends to be quite polymorphic in Caucasians, but Asian and African populations are almost monomorphic (for the (G) allele). It was first described in 1998, when it was shown that the rs1800795(C) allele produces less IL6 than the (G) allele, which supported the hypothesis that a protective genotype against systemic onset juvenile rheumatoid arthritis would be rs1800795(C;C), and indeed, few juvenile RA patients had that genotype. Studies on rs1800795 now include potential associations with heart disease, Kaposi's sarcoma, type-2 diabetes, stroke, obesity, Hodgkin's lymphoma, sudden ...
can taste bitter
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rs1726866 is one of three SNPs that form the main haplotypes behind the ability to perceive as bitter the taste of the compound phenylthiocarbamide (PTC) and similar molecules in foods (like cabbage and raw broccoli) or drinks (like coffee and dark beers). The rs1726866(C) allele is the 'tasting' allele, and it is dominant to the 'non-tasting' allele rs1726866(T), so having one copy is enough to have the bitter tasting ability. If you are a 'taster', you're also likely to carry at least one rs713598(G) and one rs10246939(C) allele since, along with rs1726866(C), these three SNPs form the most common tasting haplotype. If you lack these alleles, you're quite likely (~80%) to be a non-taster of bitterness, meaning that foods that may taste bitter to others taste far less bitter to you. (C;C)...
Magnitude: 0.1
Frequency: 47.8%
References:10
Frequency: 47.8%
References:10
can taste bitter
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rs10246939 is one of three SNPs that form the main haplotypes behind the ability to perceive as bitter the taste of the compound phenylthiocarbamide (PTC) and similar molecules in foods (like cabbage and raw broccoli) or drinks (like coffee and dark beers). The rs10246939(C) allele, in the orientation shown in dbSNP, is the 'tasting' allele, and it is dominant to the 'non-tasting' allele rs10246939(T), so having one copy is enough to have the bitter tasting ability. If you are a 'taster', you're also likely to carry at least one rs713598(G) and one rs1726866(C) allele since, along with rs10246939(C), these three SNPs form the most common tasting haplotype. If you lack these alleles, you're quite likely (~80%) to be a non-taster of bitterness, meaning that foods that may taste bitter to oth...
normal
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rs4911414 is a SNP near the ASIP (agouti signaling protein) gene on chromosome 20. This SNP is one of a tightly-linked pair that increases the likelihood of an individual being prone to sun sensitivity, in other words, freckles and sunburn, based on a study of 6,000+ Caucasians (5,000+ Icelanders + 1,000+ Dutch). The odds ratios, presumably on a dominant basis, and at least in the largest population (Icelanders) for 'freckles and burns vs. no freckles and tans' for the haplotype pair rs1015362(G) - rs4911414(T) is 3.91 (CI: 2.54-6.03) for males and 2.42 (CI: 1.52-3.86) for females, with an overall p=0.051. Based on a study by the same authors of 4,000+ skin cancer patients, this haplotype was seen to confer significant increased risk for cutaneous malignant melanoma (odds ratio 1.45, p = 1...
22 snps
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normal
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GRACILE syndrome is a very rare metabolic disorder that affects newborn infants of Finnish ancestry. rs28937590
1 snp
(hide) Folate
Slightly (~1.5x) higher risk for Caucasian mothers to give birth to NTD children There is a slightly higher risk (~1.5x at most) for Caucasian mothers with this genotype to give birth to children with neural tube defects; see discussion at rs2236225.
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rs2236225, also known as c.1958G>A, G1958A, p.Arg653Gln and R653Q, is a SNP in the MTHFD1 gene on chromosome 14. This SNP is best known for it's potential role in raising risk for neural tube defects, with some studies finding a slight effect in certain populations (for example, Irish and Italians) and other studies finding no effect (for example, in the Dutch). A 2014 meta-analysis of nine studies totaling 4,302 cases of children born with neural tube defects concluded that Caucasian mothers carrying one or two rs2236225(T) alleles were at slight increased risk, of about 1.5 - 1.7x, of having affected children compared to mothers with no (T) alleles. However, they cautioned that their results should be 'viewed with caution' given the statistical uncertainties inherent in these studies....
Frequency: 35.1%
References:2
References:2
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[PharmGKB:Non-Curated GWAS results: Genome-wide Association Study of Vitamin B6, Vitamin B12, Folate, and Homocysteine Blood Concentrations. (Initial Sample Size: 2,934 individuals; Replication Sample Size: 686 individuals); (Region: 10p13; Reported Gene(s): CUBN; Risk Allele: rs11254363-A); (p-value= 0.000001).This variant is associated with Folate pathway vitamins.] [GWAS:Folate pathway vitamins]
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[PharmGKB:Non-Curated GWAS results: Genome-wide Association Study of Vitamin B6, Vitamin B12, Folate, and Homocysteine Blood Concentrations. (Initial Sample Size: 2,934 individuals; Replication Sample Size: 686 individuals); (Region: 19q13.33; Reported Gene(s): FUT2; Risk Allele: rs602662-A); (p-value= 3E-20).This variant is associated with Folate pathway vitamins.] [OMIM:VITAMIN B12 PLASMA LEVEL QUANTITATIVE TRAIT LOCUS 1; B12QTL1] [GWAS:Folate pathway vitamins]
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Genome-wide significant predictors of metabolites in the one-carbon metabolism pathway. G allele associated with lower serum Vitamin B12. 'The TCN1 rs526934 G variant may reduce transport of cobalamin, resulting in lower plasma vitamin B12 levels.' [PharmGKB:Non-Curated GWAS results: Genome-wide Association Study of Vitamin B6, Vitamin B12, Folate, and Homocysteine Blood Concentrations. (Initial Sample Size: 2,934 individuals; Replication Sample Size: 686 individuals); (Region: 11q12.1; Reported Gene(s): TCN1; Risk Allele: rs526934-A); (p-value= 0.000002).This variant is associated with Folate pathway vitamins.] [GWAS:Folate pathway vitamins]
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rs1051266 (Arg27Cys, 80G>A) is a snp within SLC19A1 (Solute carrier family 19 (folate transporter), member 1). Cys (A) allele associated with reduced plasma folate women with GA and AA genotypes had higher red blood cell folate concentrations, not significantly associated with serum folate or homocysteine levels methotrexate (antifolate drug) uptake lowest in individuals with GG genotype than those with GA or AA genotypes [PharmGKB:Curated Risk or phenotype-associated allele: SLC19A1 80GG (27Arg/Arg) and GA (27His/Arg)>AA (27His/His) genotypes. Phenotype: A composite pharmacogenetic index (additive from zero to five) was calculated using the following values: ATIC 347CC or TSER*3/*3 or SLC19A1 80GG or SLC19A1 80GA genotypes were valued as 0, ATIC 347CG or TSER*2/*3 or SLC19A1 80AA g...
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[PharmGKB:Non-Curated GWAS results: Genome-wide Association Study of Vitamin B6, Vitamin B12, Folate, and Homocysteine Blood Concentrations. (Initial Sample Size: 2,934 individuals; Replication Sample Size: 686 individuals); (Region: 3p14.1; Reported Gene(s): PRICKLE2; Risk Allele: rs153734-T); (p-value= 0.000007).This variant is associated with Folate pathway vitamins.] [GWAS:Folate pathway vitamins]
normal Vitamin B6 blood concentration
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This is one of the SNPs reported by NutraHacker. Genetics and genomics of human aging. [PharmGKB:Non-Curated The C allele of this SNP is associated with lower blood concentration of vitamin B6 (Combined studies of Tuscan Italians ( inCHIANTI:N =1175 and Progetto Nutrizione study:N = 687) found 1.45 ng/mL lower vitamin B6 per copy of C (p = 8.3 x 10 (-18)))] [OMIM:?] [GWAS:Folate pathway vitamins]
Common genotype: normal homocysteine levels
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rs1801133 is a SNP that is relatively common and has been studied for (relatively) a long time. Also known as C677T, Ala222Val, and A222V, it encodes a variant in the MTHFR gene, which encodes an enzyme involved in folate metabolism. Homozygous rs1801133(T;T) individuals have ~30% of the expected MTHFR enzyme activity, and rs1801133(C;T) heterozygotes have ~65% activity, compared to the most common genotype, rs1801133(C;C). This reduced activity (i.e. this SNP) has been linked at least once to each of the following disorders (though not necessarily reproducibly): * autism * cancer, including ** gastric cancer ** lung cancer ** head and neck cancer ** renal cancer * cleft lip and cleft palate * coronary artery disease * dementia * depression * hyperhomocysteinemia * migraine * neural tube d...
8 snps
(hide) Forensically Useful Morphological Traits
Magnitude: 3.1
blue eyes are much more likely
Most people with this have some shade of blue eye color (some are more grey, some are more green), however one person with brown eyes has also observed this genoset. This spreadsheet is gathering more information on self reported eye color.
Carrier of one CYP2D6 decreased or non-functioning variant. Your body may have a reduced ability to process some medicines. You are a carrier for rs1065852(T;T)
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The wild type (normal) allele at this SNP is (C). The (T) variant indicates the presence of a non-wild type CYP2D6 variant, but it appears in many different variants so it can not be used to determine the presence of any particular variant. The most common variants it appears in are CYP2D6*10 and CYP2D6*4, but these are not the only ones. While this is the defining mutation for CYP2D6*10, it is not possible by itself for this mutation to determine a particular variant. In addition, the CYP2D6*4 variant includes this mutation, but the defining mutation 1846G>A SNP is not available in the common direct to consumer testing services. While it is not possible for this mutation to identify one particular variant, all the variants in which it appears have reduced or no CYP2D6 activity. If two ...
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Influences appearance gnxp A genomewide association study of skin pigmentation in a South Asian population. Complex signatures of selection for the melanogenic loci TYR, TYRP1 and DCT in humans.
associated with the absence of freckles
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Influences appearance The A allele of rs1042602 is associated with the absence of freckles [PharmGKB:Non-Curated GWAS Results: A genomewide association study of skin pigmentation in a South Asian population (Initial Sample Size: 363 with maxL* < 56 and 374 with maxL* > 63; 20% tails of distribution; Replication Sample Size: 116 low maxL*, 115 high maxL* individuals). This variant is associated with skin pigmentation by reflectance spectroscopy.] [OMIM:SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 3; SHEP3] [GWAS:Freckles] [GWAS:Skin pigmentation by reflectance spectroscopy]
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news three SNPs that appear to have different effects in men and women rs3846662 rs2304130 rs2083637 journal LDL-Cholesterol minor allele was associated with up to 2.2-fold lower expression Common SNPs in HMGCR in micronesians and whites associated with LDL-cholesterol levels affect alternative splicing of exon13. The HMG-CoA reductase gene and lipid and lipoprotein levels: the multi-ethnic study of atherosclerosis. Genetic loci associated with plasma concentration of low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, triglycerides, apolipoprotein A1, and Apolipoprotein B among 6382 white women in genome-wide analysis with replication. Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip. Analysis of recently identifie...
blue/gray eyes more possible
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rs1800407 is located in exon 13 of the OCA2 gene at amino acid position 419, and it is therefore also known as the R419Q variant. The (A) allele encodes the amino acid glutamine (instead of arginine), and it is associated with increased odds of having green/hazel eye color in some Caucasian populations. One copy of of rs1800407(A) is sufficient for this effect. [PMID 12163334, PMID 15889046; OMIM 203200.0012] According to tree scanning analysis, the proportion of eye colour variation explained by this nucleotide position is merely 4%. Thus, additional variation present in the OCA2 gene and perhaps some other pigment related genes must be taken into account in order to explain the high phenotypic variation in iris colour. Among rs12913832(A;A) individuals, the penetrance for green/hazel eye...
blue/gray eyes possible
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rs1800401 is located in exon 7 of the OCA2 gene at amino acid position 305. The (T) allele encodes the amino acid tryptophan (instead of arginine), and it is one of several SNPs associated with increased odds of having brown or black eye color in Caucasians. One copy of of rs1800401(T) is sufficient for this effect. [PMID 12163334, PMID 15889046; OMIM 203200.0011] [OMIM:?]
normal; no effect on warfarin metabolism
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SNP rs1057910(A), located in the cytochrome p450 CYP2C9 gene, most commonly encodes the amino acid isoleucine at position 359, and the resulting allele is also known as CYP2C9*1. rs1057910(C) encodes a leucine at this same position, and the resulting allele is called CYP2C9*3. This SNP is also known as Ile359Leu or A1075C. The effect of CYP2C9 variants on drug metabolism should not be predicted without also considering CYP2C9*2, defined as the common loss of function variant rs1799853(T) (NM_000771:c.430C>T, NP_000762:p.144R>C) Studies of the effects of these alleles include: * rs1057910(C;C)] genotypes may clear drugs like celecoxib (trade name Celebrex) twice as slowly as rs1057910(A;A) genotypes; the rs1057910(A;C) genotypes are in-between clearance rates. Lower clearance rates wi...
slight increase in skin cancer risk
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rs1126809 is a SNP in the TYR tyrosinase gene. This SNP is also known as R402Q (or, 1205G>A) based on the amino acid change at position 402 from an arginine (R) to a glutamine (Q). The rs1126809(G) allele encodes the more common (R)/arginine, while the variant rs1126809(A) allele encodes the (Q)/glutamine. rs1126809(A) has previously been shown to affect eye color and sun sensitivity. Based on a study of 4,000+ skin cancer patients, it also conferred increased risk of cutaneous malignant melanoma (odds ratio 1.21, p = 2.8 x 10<sup>-7</sup>) and basal cell carcinoma (odds ratio 1.14, p = 6.1 x 10<sup>-4</sup>). rs1126809 is not associated with albinism. [PharmGKB:Curated This variant is associated with the risk of cutaneous melanoma and basal cell carcinoma. It i...
normal
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rs2297480 is a SNP in the FDPS gene, which encodes an enzyme in the mevalonate pathway and therefore might alter the response to amino-bisphonate (drug) treatment of postmenopausal osteoporosis. A study of 234 Danish postmenopausal women treated for at least 2 years with amino-bisphonates concluded that rs2297480(C;C) homozygotes do not respond as successfully as (A;A) or (A;C) genotypes. [PharmGKB:Curated This variant impacted the response to long-term N-bisphosphonates treatment in a study of 234 Danish postmenopausal women. Patients with the homozygous CC genotype showed a decreased response of bone turnover markers to amino-bisphosphonate therapy.]
common in clinvar
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rs1805008, known as Arg160Trp or R160W, is one of several SNPs in the MC1R gene associated with red hair color (redheads), in this case in an Irish population although this has also been reported in Icelandic and Dutch populations . The risk allele is rs1805008(T), compared with the wild-type rs1805008(C) allele. blog about designing melanocortin analogs specific to these genotypes. See also OMIM 155555.0005 Melanoma Parkinson's disease [OMIM:SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 2; SHEP2]
normal risk
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rs1805007, known as Arg151Cys or R151C, one of several SNPs in the MC1R gene associated with red hair color (redheads), and in redheaded females, linked to being more responsive to the anesthetics pentazocine, nalbuphine, and butorphanol, often used by dentists The risk allele is rs1805007(T), compared with the wild-type rs1805007(C) allele. The risk allele has also been reported in several studies to be associated with increased risk for melanoma. For example, an odds ratio of 2.94 (CI: 1.04-8.31) has been reported for an Italian population , and similarly an odds ratio of 2.9 has been reported for a Polish population . Blog entry about designing melanocortin analogs specific to these genotypes. See also OMIM 155555.0004 Freckling [OMIM:SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 2; SHEP2]...
common in clinvar
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rs1805005, known as Val60Leu or V60L, is a SNP in the MC1R gene associated with light blond hair color in one study. The risk allele is rs1805005(T), compared with the wild-type rs1805005(G) allele. See also OMIM 155555.0006 [OMIM:?]
common in clinvar common for Caucasians on the 23andme platform
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rs2228479, known as Val92Met or V92M, is one of several SNPs in the MC1R gene commonly associated with red (or blond) hair and poor tanning, but note its high presence in one Asian population The risk allele is rs2228479(A), compared with the wild-type rs2228479(G) allele. See also OMIM 155555.0002 [OMIM:?]
normal
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Although the rs26722(T) alllele is relatively rare, at least statistically it seems to be associated with darker eye, hair, and skin color, all other things being equal. A genomewide association study of skin pigmentation in a South Asian population. A genome-wide association study identifies novel alleles associated with hair color and skin pigmentation. Association of the SLC45A2 gene with physiological human hair colour variation. Genome-wide association study of tanning phenotype in a population of European ancestry. Genetic variants in pigmentation genes, pigmentary phenotypes, and risk of skin cancer in Caucasians. Genetic determinants of hair and eye colours in the Scottish and Danish populations. [OMIM:PIGMENTATION OF HAIR, SKIN, AND EYES, VARIATION IN]
common in complete genomics
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A genome-wide association study identifies novel alleles associated with hair color and skin pigmentation. [GWAS:Tanning]
common in complete genomics
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Influences appearance gnxp associated with skin pigmentation in two samples of East Asian ancestry and it confirms previous evidence indicating that evolution towards light skin occurred, at least in part, independently in Europe and East Asia. The OCA2 gene has been under positive selection in Europe and East Asia, but different alleles have been selected in each region. 23andMe blog each rs1800414(C) was associated with a 1.3 melanin unit reduction in skin pigmentation. This SNP accounts for 9% of the variation in skin color seen in the study population.
common in complete genomics
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rs1805006, known as Asp84Glu or D84E, is one of several SNPs in the MC1R gene associated with higher risk of melanoma. The risk allele is rs1805006(A), compared with the wild-type rs1805006(C) allele. Allelic odds ratio for pale skin(P-value)=5.19(<1.0e-5)MC1R*D84E rs1805006 http://genepi.qimr.edu.au/contents/p/staff/Duffyetal_JID_520-528Jan10.pdf See also OMIM 155555.0003 [OMIM:?]
1 genoset 21 snps
(hide) Freckling
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An association between freckling and rs2153271 [GWAS:Freckling]
associated with the absence of freckles
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Influences appearance The A allele of rs1042602 is associated with the absence of freckles [PharmGKB:Non-Curated GWAS Results: A genomewide association study of skin pigmentation in a South Asian population (Initial Sample Size: 363 with maxL* < 56 and 374 with maxL* > 63; 20% tails of distribution; Replication Sample Size: 116 low maxL*, 115 high maxL* individuals). This variant is associated with skin pigmentation by reflectance spectroscopy.] [OMIM:SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 3; SHEP3] [GWAS:Freckles] [GWAS:Skin pigmentation by reflectance spectroscopy]
common in complete genomics
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plos the association between rs12203592 and hair color was independent of rs1540771, a SNP between the IRF4 and EXOC2 genes previously found to be associated with hair color. [PharmGKB:Non-Curated GWAS Results: Genetic determinants of hair, eye and skin pigmentation in Europeans (Initial Sample Size: 2,986 individuals; Replication Sample Size: 3,932 individuals). This variant is associated with freckles.] [OMIM:SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 8; SHEP8] [GWAS:Freckles]
Magnitude: 0
Frequency: 70.8%
Repute:Good
References:20
Frequency: 70.8%
Repute:Good
References:20
common on affy axiom data
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plos rs12203592 showed the largest allele frequency difference between the Irish individuals and those individuals of Northern, Central European and Eastern European descent associated with hair color rs12896399 rs12203592 rs12203592 for freckling was previously associated with hair color, eye color, and tanning response to sunlight Squamous Cell Carcinoma [PharmGKB:Non-Curated GWAS Results: A Genome-Wide Association Study Identifies Novel Alleles Associated with Hair Color and Skin Pigmentation (Initial Sample Size: 2,287 women; Replication Sample Size: up to 8,465 individuals; Risk/trait Allele: rs12203592-T). This variant is associated with Black vs. red hair color.] [GWAS:Eye color] [GWAS:Black vs. red hair color]
normal risk
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rs1805007, known as Arg151Cys or R151C, one of several SNPs in the MC1R gene associated with red hair color (redheads), and in redheaded females, linked to being more responsive to the anesthetics pentazocine, nalbuphine, and butorphanol, often used by dentists The risk allele is rs1805007(T), compared with the wild-type rs1805007(C) allele. The risk allele has also been reported in several studies to be associated with increased risk for melanoma. For example, an odds ratio of 2.94 (CI: 1.04-8.31) has been reported for an Italian population , and similarly an odds ratio of 2.9 has been reported for a Polish population . Blog entry about designing melanocortin analogs specific to these genotypes. See also OMIM 155555.0004 Freckling [OMIM:SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 2; SHEP2]...
8 snps
(hide) French-Canadian
common
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rs5370, also known as Lys198Asn or K198N, is a SNP in the endothelin-1 EDN1 gene on chromosome 6. The generally more common rs5370(G) allele encodes the Lys (K), and the rarer rs5370(T) allele encodes the Asn (N). Among the French-Canadian founder population of the Saguenay Lac St-Jean region of Quebec, rs5370(T) was associated with lower HDL cholesterol values in women (p = 1.3 x 10e-5), but not in men. In a study of 1,000+ Western Australians, no association was seen between HDL levels and rs5370. A study of ~400 rheumatoid arthritis patients found a 3x increase in the adjusted odds of being hypertensive for rs5370(T;T) homozygotes compared to (G;G) homozygotes (odds ratio 2.89, CI: 1.02 - 8.19, p=0.011). After adjustment for multiple potential confounders, haplotype analysis revealed an...
normal risk
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rs4762, a SNP in the angiotensin II AGT gene, has been reported to be associated with increased risk for developing pre-eclampsia, based on a study of ~180 French-Canadian women. The odds ratio associated with the rs4762(T) allele (encoding methionine) was 1.9 (CI:1.2–2.9, p=0.0033). Note that rs4762 is commonly referred to in the literature as 'T174M' or 'Thr174Met'; however, databases now indicate that the amino acid that varies is #207 (not 174), as the protein is currently numbered. rs4762 was also reported to play the major role in the 2.1 fold increased risk (CI: 1.4-3.4, p=0.0008) for pre-eclampsia of the rs3889728(A)-rs4762(T)-rs699(C) haplotype. Correction of population stratification in large multi-ethnic association studies. Ten renin-angiotensin system-relate...
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Autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS) is a neurodegenerative disorder first described in French-Canadian individuals from the Charlevoix and Saguenay-Lac-St-Jean regions of northeastern Quebec. Symptoms begin in early childhood and typically involve muscle overactivity and lack of muscle coordination, resulting in difficulty walking, moving the limbs, and speaking. https://www.23andme.com/you/journal/arsacs/overview/ rs281865117
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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Leigh syndrome is more common in some French-Canadian populations. [OMIM:LEIGH SYNDROME DUE TO CYTOCHROME c OXIDASE DEFICIENCY]
4 snps
(hide) GCH1
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A GCH1 Haplotype Associated with Susceptibility to Vasoocclusive Pain and Impaired Vascular Function in Sickle Cell Anemia
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Polymorphic Variation of the Guanosine Triphosphate Cyclohydrolase 1 Gene Predicts Outcome in Patients Undergoing Surgical Treatment for Lumbar Degenerative Disc Disease Lack of influence of GTP cyclohydrolase gene (GCH1) variations on pain sensitivity in humans. Genome-wide association to body mass index and waist circumference: the Framingham Heart Study 100K project.
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GTP cyclohydrolase and tetrahydrobiopterin regulate pain sensitivity and persistence. T allele associated with higher tolerance to pain. Do genetic predictors of pain sensitivity associate with persistent widespread pain? T allele associated with higher pain tolerance. GCH1 haplotype determines vascular and plasma biopterin availability in coronary artery disease effects on vascular superoxide production and endothelial function. Part of a haplotype, rs10483639(C)-rs3783641(A)-rs8007267(T), associated with lower levels of tetrahydrobiopterin.
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Polymorphic Variation of the Guanosine Triphosphate Cyclohydrolase 1 Gene Predicts Outcome in Patients Undergoing Surgical Treatment for Lumbar Degenerative Disc Disease
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GTP cyclohydrolase and tetrahydrobiopterin regulate pain sensitivity and persistence. C allele associated with higher tolerance to pain. Polymorphisms in the GTP cyclohydrolase gene (GCH1) are associated with ratings of capsaicin pain. C allele associated with higher tolerance to pain.
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GTP cyclohydrolase and tetrahydrobiopterin regulate pain sensitivity and persistence. T allele associated with higher tolerance to pain. Polymorphisms in the GTP cyclohydrolase gene (GCH1) are associated with ratings of capsaicin pain. T allele associated with higher tolerance to pain.
Frequency: 79.7%
References:0
References:0
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Polymorphic Variation of the COMT and GCH1 Genes In Patients Undergoing Surgical Treatment For Lumbar Degenerative Disc Disease Lack of influence of GTP cyclohydrolase gene (GCH1) variations on pain sensitivity in humans.
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[GWAS:None]
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Do genetic predictors of pain sensitivity associate with persistent widespread pain? C allele associated with higher pain tolerance. GCH1 haplotype determines vascular and plasma biopterin availability in coronary artery disease effects on vascular superoxide production and endothelial function. Part of a haplotype, rs10483639(C)-rs3783641(A)-rs8007267(T), associated with lower levels of tetrahydrobiopterin.
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GTP cyclohydrolase and tetrahydrobiopterin regulate pain sensitivity and persistence. A allele associated with higher tolerance to pain. Polymorphisms in the GTP cyclohydrolase gene (GCH1) are associated with ratings of capsaicin pain. A allele associated with higher tolerance to pain. Do genetic predictors of pain sensitivity associate with persistent widespread pain? A allele associated with higher pain tolerance. GCH1 haplotype determines vascular and plasma biopterin availability in coronary artery disease effects on vascular superoxide production and endothelial function. Part of a haplotype, rs10483639(C)-rs3783641(A)-rs8007267(T), associated with lower levels of tetrahydrobiopterin.
Magnitude: 0
Frequency: 75.0%
References:0
Frequency: 75.0%
References:0
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A GCH1 Haplotype Associated with Susceptibility to Vasoocclusive Pain and Impaired Vascular Function in Sickle Cell Anemia
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
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Also known as Lys224Arg, G allele is associated with Dopa-Responsive Dystonia. Dystonia with motor delay in compound heterozygotes for GTP-cyclohydrolase I gene mutations. Dopa-responsive dystonia in British patients: new mutations of the GTP-cyclohydrolase I gene and evidence for genetic heterogeneity. Autosomal dominant GTP-CH deficiency presenting as a dopa-responsive myoclonus-dystonia syndrome. [OMIM:?]
13 snps
(hide) GeneTest SNPs on Arrays
Possible risks. Complex. MTHFR rs1801131 is involved in converting 5-methylfolate (5MTHF) to tetrahydrofolate (THF). Unlike MTHFR C677T, this mutation does not lead to elevated homocysteine levels.
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rs1801131 is a SNP in the MTHFR gene, representing an A>C mutation at mRNA position 1298, resulting in a glu429-to-ala (E429A) substitution (hence this SNP is also known as A1298C or E429A). A diplotype (according to the authors, but perhaps actually a genoset) of rs1801131 and rs1801133 has been linked to increased risk for several types of brain cancer. The highest risk of meningioma was associated with heterozygosity for both MTHFR SNPs (odds ratio 2.11, CI: 1.42-3.12, p=0.002). The corresponding odds ratio for glioma was 1.23 (CI: 0.91-1.66, p=0.02. In general, risks were increased with genotypes associated with reduced MTHFR activity. rs1801131 shows no consistent association with schizophrenia overall in 12 studies totaling 3,000+ patients [PharmGKB:Curated Risk or phenotype-asso...
harmless ancestral galactosemia variant carrier This variant is evolutionarily ancestral, and in vitro studies fail to support an impact of this variant on enzyme activity.
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Galactosemia [OMIM:GALACTOSE-1-PHOSPHATE URIDYLYLTRANSFERASE; GALT]
Common genotype: normal homocysteine levels
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rs1801133 is a SNP that is relatively common and has been studied for (relatively) a long time. Also known as C677T, Ala222Val, and A222V, it encodes a variant in the MTHFR gene, which encodes an enzyme involved in folate metabolism. Homozygous rs1801133(T;T) individuals have ~30% of the expected MTHFR enzyme activity, and rs1801133(C;T) heterozygotes have ~65% activity, compared to the most common genotype, rs1801133(C;C). This reduced activity (i.e. this SNP) has been linked at least once to each of the following disorders (though not necessarily reproducibly): * autism * cancer, including ** gastric cancer ** lung cancer ** head and neck cancer ** renal cancer * cleft lip and cleft palate * coronary artery disease * dementia * depression * hyperhomocysteinemia * migraine * neural tube d...
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[GWAS:Hemoglobin levels]
Not a C282Y hemochromatosis carrier.
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rs1800562 represents a SNP that accounts for ~85% of all cases of hemochromatosis, a disorder whose symptoms include cirrhosis of the liver, diabetes, hypermelanotic pigmentation of the skin, and heart failure. OMIM indicates that liver cancer is responsible for about one-third of deaths of rs1800562(A;A) homozygotes, and since hemochromatosis is a relatively easily treated disorder if diagnosed, this is a form of preventable cancer. The rs1800562(A) allele is known as the C282Y or Cys282Tyr mutation, and it is found at a frequency of around 5-10% in many Caucasian populations, leading to an incidence of (A;A) homozygotes around 1 in 200. Early identification of rs1800562(A;A) homozygotes can prevent complications of hemochromatosis; however, the percentage of all (A;A) homozygotes who act...
normal/common
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rs6025 represents a SNP in the Factor V F5 gene, encoding a change in the protein from an arginine at position 506 to a glutamine. The resulting rs6025(A) allele encodes a mutation known as the Leiden mutation, R506Q, found in perhaps 3 to 5% of the individuals in most populations. About 1 in 10 individuals harboring the R506Q will experience clinically significant venous thromboembolism in their lifetimes (according to OMIM). Overall, the rs6025(A) allele appears to be necessary but not sufficient for the development of venous thromboembolism. Patients who are rs6025(A;G) heterozygotes but lack other risk-enhancing SNPs have a risk of recurrent deep venous thrombosis equal to patients with no such SNPs. In contrast, patients who are heterozygotes for both rs6025 and the prothrombin rs1799...
Magnitude: 0
Frequency: 98.4%
Repute:Good
References:7
Frequency: 98.4%
Repute:Good
References:7
common in clinvar
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rs11466023, also known as c.1105C>T, p.Pro369Ser or P369S, is a SNP in the MEFV gene. The risk allele is given as (A) by 23andMe, however in dbSNP orientation, the risk allele is (T). The symptoms of familial Mediterranean fever are caused by the person's own inflammatory response; it is not an infectious disease. The condition is more common among Turks, Sephardic Jews, and people of Arab and Armenian ancestry. [OMIM:FAMILIAL MEDITERRANEAN FEVER]
Magnitude: 0
Frequency: 99.1%
Repute:Good
References:9
Frequency: 99.1%
Repute:Good
References:9
normal
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[PharmGKB:Curated This variant is associated with risk of pancreatitits for HIV-infected individuals.] [OMIM:PANCREATITIS, CHRONIC, SUSCEPTIBILITY TO]
common in clinvar The rs1050828 G allele is located within the G6PD gene and is associated with 'normal' levels of glucose-6-phosphate dehydrogenase enzyme production.
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rs1050828 is a SNP residing in the G6PD gene and is located the X chromosome. G6PD codes for the enzyme glucose-6-phosphate dehydrogenase, which helps protect the cell from oxidative damage. Depending on genotype, an individual may possess one of two primary versions of the G6PD gene; type A and type B. Type A is predominantly found in people who have African ancestry. Mutations of G6PD can cause varying degrees of G6PD deficiency, which is a disease affecting red blood cells. For example, an G to A substitution mutation at the rs1050828 (also referred to as G202A) is associated with a reduction of G6PD. The G6PD deficient genotype A- (~8-20% reduction of G6PD) is typically defined by the possession of the rs1050828 A allele (rs1050828(A;A)). In addition, individuals who are type A- almost...
Not a H63D hemochromatosis carrier.
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rs1799945, also known as H63D or His63Asp, represents a SNP that accounts for a mild form of hereditary hemochromatosis (HH), an iron overload condition in which mutations of certain genes involved in iron metabolism disrupt the body’s ability to regulate uptake of iron, causing increased intestinal iron absorption. The most common form is caused by mutations in the HFE gene, which are inherited recessively. The gene for HH is closely linked to the HLA-A3 locus on the short arm of chromosome 6 . In 1996, HFE, a gene for HH, was found to have two missense mutations . A mutation at amino acid 282 (C282Y) was found to be homozygous in 83 percent of patients with HH. This is a point mutation from guanine to adenine, resulting in a missense mutation from cysteine to tyrosine. Such mutatio...
common in clinvar
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Profound biotinidase deficiency in two asymptomatic adults. Partial biotinidase deficiency is usually due to the D444H mutation in the biotinidase gene. Mutations causing profound biotinidase deficiency in children ascertained by newborn screening in the United States occur at different frequencies than in symptomatic children. [OMIM:?]
14 snps
(hide) Gs240
MI risk, aspirin resistance 23andMe blog lower odds of early stent thrombosis
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The 'A2' allele of the platelet specific alloantigen system is encoded by rs5918(C), and it has been implicated as increasing the risk of myocardial infarctions, heart disease, and resistance to blood-thinning benefits of aspirin. On its own, the A2 allele is implicated especially in early onset heart disease ; in combination with the 4G allele of the PAI1 gene, rs1799889, the increased risk of myocardial infarction in a Finnish study population was 4 fold higher (odds ratio = 4.5, p=0.001), particularly in males (odds ratio = 6.4, p=0.0005) . Olympic skater Sergei Grinkov, who had this risk factor, died of a heart attack at age 28. A2 allele carriers also appear to be relatively resistant to the anti-thrombotic (i.e. anti-clotting) actions normally associated with aspirin] use. A protecti...
normal risk (for autism)
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A common SNP in the CNTNAP2 gene, rs7794745, is associated with increased risk for autism based on a study of 148 affected children from families with two more autistic children. Related article A genome-wide association study of autism reveals a common novel risk locus at 5p14.1. Do candidate genes discriminate patients with an autism spectrum disorder from those with attention deficit/hyperactivity disorder and is there an effect of lifetime substance use disorders? A common genetic variant in the neurexin superfamily member CNTNAP2 is associated with increased risk for selective mutism and social anxiety-related traits. Genetic variation in CNTNAP2 alters brain function during linguistic processing in healthy individuals. [PharmGKB:Curated This common variant in CNTNAP2 is significantl...
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mentioned by gs240
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rs7766973 is a SNP in the jumonji, AT rich interactive domain 2 JARID2 gene. Significantly (p = 2 x 10e-7) but weakly associated with autism based on a GWAS study of 1,000+ affected families. However, upon attempted replication, rs7766973 did not meet genome-wide significance. Nonetheless, a French company (Integragen) announced in 2011 (that is was licensing the use of this SNP for identifying children at increased risk for autism, perhaps by combining rs7766973] with other autism-related SNPs.
Frequency: 69.7%
References:4
References:4
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mentioned by gs240
Frequency: 76.1%
References:3
References:3
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Haplotype rs12740310*C-rs3737296*G-rs12410279*A was overtransmitted (p(corrected)=0.0016), with a relative risk for autism of 1.8 in homozygous carriers [OMIM:MAP/MICROTUBULE AFFINITY-REGULATING KINASE 1; MARK1]
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nature The inheritance of the AC haplotype of rs1861972 – rs1861973 in en2, the C allele of rs1811399 in npas2, and the C allele of rs1234747 may contribute to autism by affecting microRNA rs1861972(A) + rs1861973(C) haplotype assoc. with '''protective''' effect against autism in a study of 818 Han Chinese (184 diag. autistics, 225 unrelated volunteers, 409 randomly selected) [OMIM:ENGRAILED 2; EN2]
7 snps
(hide) Gs247
Magnitude: 1.5
Normal Parkinson's Disease Risk
The (G;G) genotype at this position is considered protective against Parkinson's Disease, but you don't have it. You instead have the more common rs10513789(T;T) which does not reduce your risk. see also gs249 for the more common heterozygote form http://www.genomicslawreport.com/index.php/2012/06/01/patenting-and-personal-genomics-23andme-receives-its-first-patent-and-plenty-of-questions/
Magnitude: 1.25
Frequency: 55.8%
References:0
Frequency: 55.8%
References:0
Very common. Normal risk of Parkinson's disease. Approximately 55% of non-asian people have this genotype which is associated with slightly higher risk of Parkinson's disease when compared to genotype (G;G). It is notable because it is the first SNP patented by 23andMe rs10513789(T) increased risk of developing Parkinson's Disease GenomicsLawReport
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23andMe reports that the G allele of rs10513789 is associated with 0.8 times lower odds of Parkinson's disease. 23andMe has a patent covering this snp. http://blog.23andme.com/2012/05/28/announcing-23andmes-first-patent/ See also gs249 and gs248
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Mentioned in the 23andMe Parkinson's disease patent along with rs10513789
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[GWAS:None]
normal risk of developing Parkinson's Disease
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People with two copies of the T allele at rs6812193 appear to have a slightly lower risk of Parkinson's disease. The same researchers identified another risk allele for Parkinson's disease at rs11868035. plos [GWAS:Parkinson's disease]
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Mentioned in the 23andMe Parkinson's disease patent along with rs10513789
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[GWAS:None]
Magnitude: 0
Frequency: 75.2%
Repute:Good
References:4
Frequency: 75.2%
Repute:Good
References:4
common on affy axiom data
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Genomewide association study for susceptibility genes contributing to familial Parkinson disease. A unified framework for multi-locus association analysis of both common and rare variants. [GWAS:Parkinson's disease]
1 genoset 7 snps
(hide) Gs248
Magnitude: 1.25
Frequency: 55.8%
References:0
Frequency: 55.8%
References:0
Very common. Normal risk of Parkinson's disease. Approximately 55% of non-asian people have this genotype which is associated with slightly higher risk of Parkinson's disease when compared to genotype (G;G). It is notable because it is the first SNP patented by 23andMe rs10513789(T) increased risk of developing Parkinson's Disease GenomicsLawReport
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23andMe reports that the G allele of rs10513789 is associated with 0.8 times lower odds of Parkinson's disease. 23andMe has a patent covering this snp. http://blog.23andme.com/2012/05/28/announcing-23andmes-first-patent/ See also gs249 and gs248
Frequency: 82.3%
References:0
References:0
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see gs248 patented by 23andMe to diagnose Parkinson's disease
Magnitude: 0
Repute:Good
References:7
Repute:Good
References:7
normal
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First discovered in 2004, rs34637584 is a SNP indicating a position within the LRRK2 that encodes a variant protein. This SNP is commonly referred to as the G2019S variant (or, mutation) based on the potential change from glycine (encoded by rs34637584(G) allele) to serine (encoded by the rs34637584(A) allele) at position 2019 of the LRRK2 protein. One copy of a rs34637584(A) allele is sufficient to greatly increase one's risk for Parkinson's disease. It is considered a disease causing mutation because it is rarely found in healthy, elderly people without Parkinson's disease, and it has been found in both familial and sporadic types of the disease. While there are many different SNPs that can influence one's risk for Parkinson's disease, rs34637584 is an especially common cause of the dise...
3 snps
(hide) Gs249
Magnitude: 1.5
Normal Parkinson's Disease Risk
The (G;G) genotype at this position is considered protective against Parkinson's Disease, but you don't have it. You instead have the more common rs10513789(T;T) which does not reduce your risk. see also gs249 for the more common heterozygote form http://www.genomicslawreport.com/index.php/2012/06/01/patenting-and-personal-genomics-23andme-receives-its-first-patent-and-plenty-of-questions/
Magnitude: 1.25
Frequency: 55.8%
References:0
Frequency: 55.8%
References:0
Very common. Normal risk of Parkinson's disease. Approximately 55% of non-asian people have this genotype which is associated with slightly higher risk of Parkinson's disease when compared to genotype (G;G). It is notable because it is the first SNP patented by 23andMe rs10513789(T) increased risk of developing Parkinson's Disease GenomicsLawReport
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23andMe reports that the G allele of rs10513789 is associated with 0.8 times lower odds of Parkinson's disease. 23andMe has a patent covering this snp. http://blog.23andme.com/2012/05/28/announcing-23andmes-first-patent/ See also gs249 and gs248
1 genoset 1 snp
(hide) Gs250
Magnitude: 1.25
Frequency: 55.8%
References:0
Frequency: 55.8%
References:0
Very common. Normal risk of Parkinson's disease. Approximately 55% of non-asian people have this genotype which is associated with slightly higher risk of Parkinson's disease when compared to genotype (G;G). It is notable because it is the first SNP patented by 23andMe rs10513789(T) increased risk of developing Parkinson's Disease GenomicsLawReport
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23andMe reports that the G allele of rs10513789 is associated with 0.8 times lower odds of Parkinson's disease. 23andMe has a patent covering this snp. http://blog.23andme.com/2012/05/28/announcing-23andmes-first-patent/ See also gs249 and gs248
1 snp
(hide) Hair
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[GWAS:Hair morphology]
Frequency: 34.4%
References:4
References:4
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rs11803731, a SNP in the Trichohyalin gene (TCHH) gene, is estimated to account for 6% of the variance in hair morphology (ie hair curliness) based on a study of Australians of European ancestry. [OMIM:?] [GWAS:Hair morphology]
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[GWAS:Hair morphology]
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[GWAS:Hair morphology]
Frequency: 63.1%
References:1
References:1
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[GWAS:Hair morphology]
Frequency: 64.6%
References:1
References:1
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[GWAS:Hair morphology]
Magnitude: 0
Frequency: 82.3%
Repute:Good
References:1
Frequency: 82.3%
Repute:Good
References:1
Magnitude: 0
Frequency: 92.0%
Repute:Good
References:1
Frequency: 92.0%
Repute:Good
References:1
11 snps
(hide) Hair color
Generally European; Light skin; Possibly an increased risk of melanoma This SNP is associated with skin, hair, and eye colour, and risk of melanoma. Individuals with the G;G genotype are generally of European descent and have fair skin. In a population-based case-control study investigating a number of pigmentation-related SNPs and their correlation with cutaneous malignant melanoma (CMM) in a Caucasian Australian population, rs16891982 (variant F374L) was found to be associated with odds ratios of 3.44, 2.86, 1.68, and 1.68 for all study subjects (1,738 CMM cases and 4,517 controls); subjects with northern European ancestry (1,438 cases and 3,098 controls); northern European subjects adjusted for hair, eye, and skin colour; and northern European subjects adjusted for the MC1R genotype, r...
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This snp influences skin pigmentation. The allele p.L374F indicates light-skinned european ancestry c.1122C>G, p.Phe374Leu (NCBI dbSNP rs16891982) in SLC45A2 was associated with protection from malignant melanoma (OR, 0.41; 95% CI, 0.24-0.70; P=0.008 after adjustment for multiple testing) An association study conducted on a population of European origin concluded that the rare (in Europeans, at least) allele L374, i.e. rs16891982(C) in dbSNP orientation, significantly increases the possibility of having black hair color, with an odds ratio of around 7. This population-based case-control study investigated a number of pigmentation-related SNPs and their correlation with cutaneous malignant melanoma (CMM) in an Australian population. rs16891982 (variant F374L) was found to be associated w...
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[GWAS:Hair color]
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[GWAS:Hair color]
Frequency: 52.2%
References:10
References:10
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associated with hair color rs12896399 rs12203592 [OMIM:SOLUTE CARRIER FAMILY 24 (SODIUM/POTASSIUM/CALCIUM EXCHANGER), MEMBER] [GWAS:Black vs. blond hair color]
Frequency: 65.2%
References:1
References:1
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[GWAS:Hair color]
common in complete genomics
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plos the association between rs12203592 and hair color was independent of rs1540771, a SNP between the IRF4 and EXOC2 genes previously found to be associated with hair color. [PharmGKB:Non-Curated GWAS Results: Genetic determinants of hair, eye and skin pigmentation in Europeans (Initial Sample Size: 2,986 individuals; Replication Sample Size: 3,932 individuals). This variant is associated with freckles.] [OMIM:SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 8; SHEP8] [GWAS:Freckles]
Magnitude: 0
Frequency: 71.7%
Repute:Good
References:8
Frequency: 71.7%
Repute:Good
References:8
normal
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A 2007 study based on the Icelanders and Dutch concluded that individuals with an rs12821256(C) allele were ~2x fold more likely to have blond than brown hair color. The specific odds ratio claimed is 2.32, p = 5.5 x 10<sup>-14</sup>. [PharmGKB:Non-Curated GWAS Results: Genetic determinants of hair, eye and skin pigmentation in Europeans (Initial Sample Size: 2,986 individuals; Replication Sample Size: 3,932 individuals). This variant is associated with blond vs. brown hair.] [OMIM:KIT LIGAND; KITLG] [GWAS:Hair color] [GWAS:Blond vs. brown hair]
common in clinvar
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rs1805008, known as Arg160Trp or R160W, is one of several SNPs in the MC1R gene associated with red hair color (redheads), in this case in an Irish population although this has also been reported in Icelandic and Dutch populations . The risk allele is rs1805008(T), compared with the wild-type rs1805008(C) allele. blog about designing melanocortin analogs specific to these genotypes. See also OMIM 155555.0005 Melanoma Parkinson's disease [OMIM:SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 2; SHEP2]
normal risk
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rs1805007, known as Arg151Cys or R151C, one of several SNPs in the MC1R gene associated with red hair color (redheads), and in redheaded females, linked to being more responsive to the anesthetics pentazocine, nalbuphine, and butorphanol, often used by dentists The risk allele is rs1805007(T), compared with the wild-type rs1805007(C) allele. The risk allele has also been reported in several studies to be associated with increased risk for melanoma. For example, an odds ratio of 2.94 (CI: 1.04-8.31) has been reported for an Italian population , and similarly an odds ratio of 2.9 has been reported for a Polish population . Blog entry about designing melanocortin analogs specific to these genotypes. See also OMIM 155555.0004 Freckling [OMIM:SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 2; SHEP2]...
common in clinvar
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rs1805005, known as Val60Leu or V60L, is a SNP in the MC1R gene associated with light blond hair color in one study. The risk allele is rs1805005(T), compared with the wild-type rs1805005(G) allele. See also OMIM 155555.0006 [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
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This missense mutation influences red hair color and has been observed in the Spanish maternal ancestry of User:Corpas son.
13 snps
(hide) Hair curliness
straighter hair
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rs499697 the minor, derived allele is associated with curlier hair curl, 0.13 points per G. [GWAS:Common traits (Other)]
Frequency: 33.3%
References:1
References:1
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rs17646946 is a SNP on chromosome 1 that is apparently part of the trichohyalin-like 1 TCHHL1 gene. Trichohyalin is a protein found in hair follicle roots. In an interesting example of people-powered research, this SNP and one other were reported to be associated with hair curliness. Source: hair curl rs17646946 and rs7349332. source genetic future rs17646946 and hair curl with each A conferring a reduction in curliness of about 0.29 points on a scale from 0 to 5. See also: rs11803731 [GWAS:Common traits (Other)]
Frequency: 34.4%
References:4
References:4
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rs11803731, a SNP in the Trichohyalin gene (TCHH) gene, is estimated to account for 6% of the variance in hair morphology (ie hair curliness) based on a study of Australians of European ancestry. [OMIM:?] [GWAS:Hair morphology]
straighter hair; common
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hair curl rs17646946 and rs7349332. source genetic future Appearance [GWAS:Common traits (Other)]
4 snps
1 snp
(hide) Haplogroup Y (Y-DNA)
Normal risk of developing schizophrenia
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This snp is in the Pseudoautosomal region. rs6603272, part of a haplotype block spanning introns 4, 5 and 6 of the IL3RA gene, has been reported in a whole genome association study to be associated with schizophrenia. (The other SNPs in this block are rs6422441 and rs17883192.) The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with this allele is 2.74.
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Located in the Pseudoautosomal region
3 snps
(hide) Haplogroups
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haplogroups ,,,Palanichamy 2004 |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=HV |derived_haplogroup=H |ancestral_allele=T |derived_allele=C }}
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[haplogroup:?]
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haplogroups
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haplogroups ,23andMe |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H |derived_haplogroup=H4 |ancestral_allele=G |derived_allele=A }}
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haplogroups ,23andMe |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H1c |derived_haplogroup=H1c1 |ancestral_allele=A |derived_allele=G }}
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haplogroups
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haplogroups
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haplogroups same SNP as rs28358282 ,Achilli 2004 ('H2c') |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H2a |derived_haplogroup=H2a3 |ancestral_allele=T |derived_allele=C }}
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haplogroups
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haplogroups ,23andMe |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H2a |derived_haplogroup=H2a4 |ancestral_allele=C |derived_allele=T }}
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haplogroups ,23andMe |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H3 |derived_haplogroup=H3c |ancestral_allele=T |derived_allele=C }}
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haplogroups
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haplogroups
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haplogroups ,23andMe |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H3 |derived_haplogroup=H3a |ancestral_allele=T |derived_allele=C }}
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haplogroups
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haplogroups
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haplogroups
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haplogroups
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influences haplogroups http://en.wikipedia.org/wiki/Haplogroup_A_(mtDNA)
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haplogroups ,23andMe |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H1c |derived_haplogroup=H1c1 |ancestral_allele=T |derived_allele=G }}
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haplogroups ,Achilli 2004 ('H2c') |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H2a |derived_haplogroup=H2a3 |ancestral_allele=G |derived_allele=A }}
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haplogroups
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haplogroups
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haplogroups
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haplogroups ,23andMe |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H2 |derived_haplogroup=H2a1 |ancestral_allele=C |derived_allele=T }}
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haplogroups
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haplogroups
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haplogroups ,23andMe |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H2a |derived_haplogroup=H2a1 |ancestral_allele=G |derived_allele=A }}
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haplogroups
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haplogroups ,23andMe |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H1a |derived_haplogroup=H1f |ancestral_allele=T |derived_allele=C }}
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haplogroups
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haplogroups ,23andMe |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H1a |derived_haplogroup=H1f |ancestral_allele=A |derived_allele=G }}
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haplogroups
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haplogroups ,23andMe |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H1a |derived_haplogroup=H1f |ancestral_allele=T |derived_allele=C }}
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haplogroups ,23andMe |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H1c |derived_haplogroup=H1c2 |ancestral_allele=C |derived_allele=T }}
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haplogroups
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[haplogroup:?]
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haplogroups
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[haplogroup:?]
common on affy axiom data
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haplogroups ,,Shen 2004 |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H |derived_haplogroup=H1 |ancestral_allele=G |derived_allele=A }}
common on affy axiom data
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haplogroups |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H |derived_haplogroup=H2 |ancestral_allele=G |derived_allele=A }}
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haplogroups ,Carelli 2006 |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H2 |derived_haplogroup=H2a |ancestral_allele=G |derived_allele=A }}
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haplogroups
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haplogroups
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Haplogroups
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haplogroups
common on affy axiom data
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haplogroups ,Carelli 2006 |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H2a |derived_haplogroup=H2a2 |ancestral_allele=G |derived_allele=A }}
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
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haplogroups |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H1 |derived_haplogroup=H1a |ancestral_allele=A |derived_allele=G }}
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haplogroups
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haplogroups
73 snps
(hide) HLA
increased risk for psoriasis
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rs1265181 is a SNP in the HLA region of chromosome 6. A large study (>6,000 Chinese psoriasis patients and an equal number of controls) found a highly significant association between the minor rs1265181(G) allele and risk for psoriasis. A proxy for this allele is rs1265159(A). See also: 23andMe blog psoriasis [PharmGKB:Non-Curated GWAS results: Psoriasis genome-wide association study identifies susceptibility variants within LCE gene cluster at 1q21. (Initial Sample Size: 1,139 Chinese cases, 1,132 Chinese controls; Replication Sample Size: 5,721 Chinese cases, 7,340 Chinese controls); (Region: 6p21.33; Reported Gene(s): MHC; Risk Allele: rs1265181-?); (p-value= NS).This variant is associated with Psoriasis.] [GWAS:Psoriasis]
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People with one or two copies of the G allele at this SNP are 3.5 times more likely to suffer liver injury than TT carriers when taking the prescription nonsteroidal anti-inflammatory drug (NSAID) lumiracoxib. This new pain medication was approved in Europe in late 2006, but because of a higher incidence of liver injury and patient deaths than among patients using other NSAIDs, it was withdrawn from the market in most countries. It is still sold in some countries under the brand names Prexige and Joicela.
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Mapping the genetic architecture of gene expression in human liver. Association of MHC SNP genotype with susceptibility to type 1 diabetes: a modified survival approach. A large-scale replication study identifies TNIP1, PRDM1, JAZF1, UHRF1BP1 and IL10 as risk loci for systemic lupus erythematosus. Quantitative trait loci for CD4:CD8 lymphocyte ratio are associated with risk of type 1 diabetes and HIV-1 immune control. Genome-wide association study in Asian populations identifies variants in ETS1 and WDFY4 associated with systemic lupus erythematosus. The effect of single nucleotide polymorphisms from genome wide association studies in multiple sclerosis on gene expression. An application of Random Forests to a genome-wide association dataset: methodological considerations & new findings. D...
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This SNP is associated with a higher risk of liver injury in patients taking the nonsteroidal anti-inflammatory drug lumiracoxib, which has been withdrawn from most markets.
~5x increased risk of psoriasis
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23andMe blog psoriasis Chinese *rs1265159(A) 22.62x risk Proxy SNP for rs1265181 Note that in dbSNP orientation, the risk allele for this SNP is rs1265159(T); also, see rs1265181 for more information.
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[GWAS:None]
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HLA-B*5801 allele as a genetic marker for severe cutaneous adverse reactions caused by allopurinol. 'In particular, three SNPs in the MHC class III region have P values <10-7 (-log10 P value > 7, Fig. 1). These SNPs were rs3117583 of BAT3 (encoding for HLA-B associated transcript 3), rs1150793 of MSH5 (encoding mutS homolog), and rs2855804 of MICB (encoding MHC class I polypeptide-related sequence).'
Normal carbamazepine sensitivity; common in clinvar
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rs1061235(T) serves as a proxy for the HLA-A*3101 allele. The HLA-A*3101 allele, found in about 2 - 5% of Northern Europeans, is significantly associated with carbamazepine hypersensitivity syndrome, with odds ratios above 10. The presence of this HLA allele increases the risk from 5% to 26%, whereas its absence reduces the risk from 5% to 4%. [GWAS:None]
common in complete genomics
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Helps to identify HLA-B*1502 [PharmGKB:Curated Risk or phenotype-associated allele: allele 4. Phenotype: Combined alleles of rs3909184 (2) and rs2844682 (4) are tagging SNPs for HLA-B*1502 (0.011 allele frequency). Study size: 45. Study population/ethnicity: Unrelated Han Chinese from Beijing, China. Significance metric(s): Type of association: GN]
average
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In at least UK populations, and perhaps others, SNP rs2187668 is a tag SNP for the HLA-DRB1*0301 allele. The HLA-DRB1*0301 allele is the allele presenting the highest risk for developing lupus, and it appears to act in a dominant manner (i.e. inheriting 2 copies is no worse than inheriting 1 copy). In dbSNP orientation, the risk allele is rs2187668(A), with an odds ratio of 2.3x (CI: 1.7 - 3.2, permuted p < 0.0001). From individuals with the most common rs2187668(G;G) genotype, risk is reduced for celiac disease, with an odds ratio of 0.30x according to a study of ~800 patients. rs2187668(A) also tags the tightly linked DQB1*0201 allele, which in turn is linked to DQA1*0501; together, these are known as the DQ2.5 haplotype. This is the most common haplotype associated with celiac diseas...
common The rs2395029(T;T) genotype is the common genotype for this SNP, against which the rs2395029(T;G) and rs2395029(G;G) genotypes that are associated with reduced HIV viral load in HIV carriers are compared. See also rs9264942 and HIV.
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rs2395029 is a SNP in the major histocompatibility complex (MHC) region, and several studies have shown that the rs2395029(G) allele is 99.9% predictive of the presence of an HLA-B*5701 allele. This HLA allele, in turn, has been associated with several conditions. A study of 51 cases of flucloxacillin drug-induced liver injury (DILI), an important cause of serious liver disease, along with a replication study of another 23 cases, found that the rs2395029(G) carriers were at highly increased risk (odds ratio 80, p=8.7x10(-33)). * see also: 23andMe blog rs2395029(G;G) increases the odds of drug-induced liver injury in response to flucloxacillin by 45x This SNP is thought to be involved in determining the HIV viral load set point during the asymptomatic period of infection. This SNP is estima...
common
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Helps to identify HLA-B*1502 [PharmGKB:Curated Risk or phenotype-associated allele: allele 2. Phenotype: Combined alleles of rs3909184 (2) and rs2844682 (4) are tagging SNPs for HLA-B*1502 (0.011 allele frequency). Study size: 45. Study population/ethnicity: Unrelated Han Chinese from Beijing, China. Significance metric(s): Type of association: GN]
12 snps
(hide) HLA-B*1502
common in complete genomics
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Helps to identify HLA-B*1502 [PharmGKB:Curated Risk or phenotype-associated allele: allele 4. Phenotype: Combined alleles of rs3909184 (2) and rs2844682 (4) are tagging SNPs for HLA-B*1502 (0.011 allele frequency). Study size: 45. Study population/ethnicity: Unrelated Han Chinese from Beijing, China. Significance metric(s): Type of association: GN]
common
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Helps to identify HLA-B*1502 [PharmGKB:Curated Risk or phenotype-associated allele: allele 2. Phenotype: Combined alleles of rs3909184 (2) and rs2844682 (4) are tagging SNPs for HLA-B*1502 (0.011 allele frequency). Study size: 45. Study population/ethnicity: Unrelated Han Chinese from Beijing, China. Significance metric(s): Type of association: GN]
2 snps
(hide) HLA-B*5701
common The rs2395029(T;T) genotype is the common genotype for this SNP, against which the rs2395029(T;G) and rs2395029(G;G) genotypes that are associated with reduced HIV viral load in HIV carriers are compared. See also rs9264942 and HIV.
(hide)
rs2395029 is a SNP in the major histocompatibility complex (MHC) region, and several studies have shown that the rs2395029(G) allele is 99.9% predictive of the presence of an HLA-B*5701 allele. This HLA allele, in turn, has been associated with several conditions. A study of 51 cases of flucloxacillin drug-induced liver injury (DILI), an important cause of serious liver disease, along with a replication study of another 23 cases, found that the rs2395029(G) carriers were at highly increased risk (odds ratio 80, p=8.7x10(-33)). * see also: 23andMe blog rs2395029(G;G) increases the odds of drug-induced liver injury in response to flucloxacillin by 45x This SNP is thought to be involved in determining the HIV viral load set point during the asymptomatic period of infection. This SNP is estima...
1 snp
(hide) Intelligence
Magnitude: 2
Frequency: 26.5%
Repute:Good
References:0
Frequency: 26.5%
Repute:Good
References:0
better intracranial volume?
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associated with intracranial volume (12q14.3; N = 15,782; P = 1.12 × 10−12) http://www.genomesunzipped.org/2012/04/another-iq-gene-new-methods-old-flaws.php (C;C) has higher cranial capacity (about 2 teaspoons) and over 2% higher IQ. (C;T) is half this positive effect. Intelligence
very slight descrease in cortical thickness and IQ; see full description
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rs7171755 is a SNP near the synaptic cell adhesion glycoprotein-encoding NPTN gene. A study of ~1,500 adolescents determined that the rs7171755(A) allele is associated with a slightly thinner left hemisphere cortex and also a slight decrease in verbal and nonverbal intelligence (IQ). The differences were really quite slight; each copy of the risk allele decreased cortical thickness by 0.7%, and decreased verbal and nonverbal IQ by 1.8 and 1.4 points, respectively. This study awaits independent replication. Also, note that eight SNPs in the NPTN locus were reported as jointly showing significant association with cortical thickness in addition to rs7171755: rs7176637, rs11854138, rs8028749, rs12185108, rs1564492, rs899981, rs7178269 and rs4075802.
The (A;G) genotype averages 2.8 PIQ points higher than the (G;G), but averages 2.84 PIQ points lower than (A;A) genotype
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SNPs in the SNAP25 gene were initially linked to intelligence but have failed to replicate . While now suspect, the original work can be found in . The (A;A) genotype averaged 2.84 PIQ points higher than the (A;G) genotype, which averages 2.8 PIQ points higher than the (G;G) genotype (p=0.0002). Variance in this SNP may account for 3.4% of the phenotypic variance in PIQ. rs363050 is in close linkage with rs353016, with r2 = 0.98, such that the rs363050(A) allele typically is linked to the rs353016(T) allele. For SNPs rs363039 - rs363043 - rs353016, respectively, the haplotype C-T-T is most associated with higher intelligence in children, whereas the haplotype C-C-T is most associated in adults (SNPs oriented as in dbSNP). Measures of Intelligence
Frequency: 10.6%
References:1
References:1
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non sig. gwas, hit (p = 5 x 10^-6) for Stroop test performance [GWAS:Cognitive Performance]
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non sig. gwas, hit (p = 7 x 10^-7) - Animals [GWAS:Cognitive Performance]
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non sig. gwas, hit (p = 6 x 10^-6) for spatial span (SSP) length in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
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non sig. gwas, hit (p = 5 x 10^-6) - Immediate Story Recall [GWAS:Cognitive Performance]
Frequency: 17.7%
References:1
References:1
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non sig. gwas, hit (p = 8 x 10^-6) for forward digit span [GWAS:Cognitive Performance]
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non sig. gwas, hit (p = 5 x 10^-6) for Trails B performance [GWAS:Cognitive Performance]
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non sig. gwas, hit (p = 6 x 10^-6) principal component 1 (PC1) - CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
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SNPs in the SNAP25 gene were initially linked to intelligence but have failed to replicate . While now suspect, the original work can be found in and or this pdf poster show association between the CHRM2 gene and intelligence . In this study of ~300 Caucasians, the (G;G) genotype appeared to typically have a 4 point higher IQ than the (A;G) genotype, which had a 4 point higher IQ (on average) than the (A;A) genotype. A nearby SNP, rs324650, showed similar results to rs324640, and was in linkage disequilibrium (r2 = 0.90) with it.
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non sig. gwas, hit (p = 9 x 10^-6) principal component 1 (PC1) - CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
Frequency: 21.5%
References:1
References:1
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non sig. gwas, hit (p = 3 x 10^-6) for Controlled Oral Word Association (COWA) test performance [GWAS:Cognitive Performance]
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non sig. gwas, hit (p = 2 x 10^-6) for intra-extra dimensional set shift (IED) EDS errors in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
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non sig. gwas, hit (p = 4 x 10^-6) for Trails A performance [GWAS:Cognitive Performance]
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non sig. gwas, hit (p = 2 x 10^-6) for Trails B performance [GWAS:Cognitive Performance]
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non sig. gwas, top 25 GEE p-values, Boston Naming Test [GWAS:Cognitive test performance]
Frequency: 28.3%
References:1
References:1
(hide)
[GWAS:Cognitive performance]
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non sig. gwas, top 25 GEE p-values, measure of attention and executive function [PharmGKB:Non-Curated GWAS results: Genetic correlates of brain aging on MRI and cognitive test measures: a genome-wide association and linkage analysis in the Framingham Study (Initial Sample Size: 705 individuals (Framingham); Replication Sample Size: NR). This variant is associated with Cognitive test performance.] [GWAS:Cognitive test performance]
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non sig. gwas, hit (p = 3 x 10^-6) for paired associates learning (PAL) total errors at 6 patterns in the CANTAB (Cambridge Neuropsychological Test Automated Battery [GWAS:Cognitive performance]
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non sig. gwas, top 25 GEE p-values, Similarities [GWAS:Cognitive test performance]
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non sig. gwas, hit (p = 8 x 10^-6) for spatial span (SSP) length in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
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non sig. gwas, hit (p = 6 x 10^-6) - Animals [GWAS:Cognitive Performance]
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non sig. gwas, hit (p = 8 x 10^-6) for verbal recognition memory (VRM) free recall in the CANTAB (Cambridge Neuropsychological Test Automated Battery [GWAS:Cognitive performance]
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[GWAS:Cognitive performance]
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This is one of four SNPs in the first intron of the SNAP25 gene that have been correlated with increased intelligence based on studies of ~300 Caucasian subjects. In orientation to the dbSNP entry for this SNP, rather than as published, the (C;C) genotype averages ~2 PIQ points higher than the (C;T) genotype, which averages 2 PIQ points higher than the (T;T) genotype. For SNPs rs363039 - rs363043 - rs353016, respectively, the haplotype C-T-T is most associated with higher intelligence in children, whereas the haplotype C-C-T is most associated in adults (SNPs oriented as in dbSNP).
Frequency: 38.9%
References:1
References:1
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[GWAS:Cognitive performance]
Frequency: 38.9%
References:1
References:1
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non sig. gwas, hit (p = 5 x 10^-6) for intra-extra dimensional set shift (IED) EDS errors in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
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non sig. gwas, top hit for spatial working memory (SWM) 'between for 8 box stage' in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
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non sig. gwas, hit (p = 2 x 10^-6) for PC1 (principal component 1) among the cognitive tests performed [GWAS:Cognitive Performance]
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non sig. gwas, top hit for spatial span (SSP) length in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
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non sig. gwas, hit (p = 4 x 10^-6) for backwards digit span [GWAS:Cognitive Performance]
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non sig. gwas, hit (p = 3 x 10^-6) - Symbol Search [GWAS:Cognitive Performance]
Frequency: 43.4%
References:1
References:1
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non sig. gwas, hit (p = 4 x 10^-6) for Trails A performance [GWAS:Cognitive Performance]
(hide)
non sig. gwas, hit (p = 5 x 10^-6) for paired associates learning (PAL) total errors at 8 patterns in the CANTAB (Cambridge Neuropsychological Test Automated Battery [GWAS:Cognitive performance]
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non sig. gwas, hit (p = 1 x 10^-6) for forward digit span [GWAS:Cognitive Performance]
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non sig. gwas, top hit for spatial recognition memory (SRM) percent correct in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
Frequency: 44.2%
References:1
References:1
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non sig. gwas, hit (p = 4 x 10^-6) - Delayed Story Recall [GWAS:Cognitive Performance]
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4+ IQ points for breastfeeding with the AA or AG genotypes Breastfeeding and IQ [GWAS:Response to statin therapy]
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non sig. gwas, hit (p = 7 x 10^-6) for spatial working memory (SWM) strategy in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
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non sig. gwas, hit (p = 6 x 10^-6) principal component 1 (PC1) - CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
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non sig. gwas, top 25 GEE p-values, visual memory and organization [PharmGKB:Non-Curated GWAS results: Genetic correlates of brain aging on MRI and cognitive test measures: a genome-wide association and linkage analysis in the Framingham Study (Initial Sample Size: 705 individuals (Framingham); Replication Sample Size: NR). This variant is associated with Cognitive test performance.] [GWAS:Cognitive test performance]
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non sig. gwas, hit (p = 4 x 10^-6) for intra-extra dimensional set shift (IED) EDS errors in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
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intelligence related [PharmGKB:Curated Several studies showed an associaction of this SNP in DTNBP1 with schizophrenia and other psychotic disorders, including substance-induced psychosis]
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[GWAS:Cognitive performance]
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Rs1378810 is located in DNAJC13, a Hsp40 homolog. associated with an estimated 0.4% variance in g (p = 0.0007), from a sample (2650 children) within the Twins Early Development Study. The beneficial allele was T, and it is assumed to be oriented with respect to the positive strand (based on the affy genechip used). high LD with rs2133692 per HapMap data (with +Rs1378810(T;T) strongly matching with rs2133692(T;T)) cursory mention in [SciAm]
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non sig. gwas, hit (p = 4 x 10^-6) for PC1 (principal component 1) among the cognitive tests performed [GWAS:Cognitive Performance]
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non sig. gwas, hit (p = 3 x 10^-6) for Trails B performance [GWAS:Cognitive Performance]
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non sig. gwas, top hit for rapid visual information processing (RVP) hit probability in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
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non sig. gwas, hit (p = 2 x 10^-7) for forward digit span [GWAS:Cognitive Performance]
Frequency: 49.1%
References:1
References:1
(hide)
non sig. gwas, hit (p = 5 x 10^-6) for paired associates learning (PAL) total errors at 8 patterns in the CANTAB (Cambridge Neuropsychological Test Automated Battery [GWAS:Cognitive performance]
Frequency: 53.6%
References:1
References:1
(hide)
non sig. gwas, hit (p = 4 x 10^-6) for Trails A performance [GWAS:Cognitive Performance]
(hide)
non sig. gwas, hit (p = 5 x 10^-6) for Trails B performance [GWAS:Cognitive Performance]
(hide)
non sig. gwas, hit (p = 3 x 10^-6) - Animals [GWAS:Cognitive Performance]
(hide)
non sig. gwas, top 25 GEE p-values, visual memory and organization [GWAS:Cognitive test performance]
(hide)
non sig. gwas, top 25 GEE p-values, Boston Naming Test [GWAS:Cognitive test performance]
(hide)
non sig. gwas, top 25 GEE p-values, Boston Naming Test [GWAS:Cognitive test performance]
(hide)
[GWAS:Cognitive performance]
(hide)
non sig. gwas, top hit for intra-extra dimensional set shift (IED) EDS errors in the CANTAB (Cambridge Neuropsychological Test Automated Battery), noted as close to ME3 which has shown expression changes in a rat model of schizophrenia ( ) [GWAS:Cognitive performance]
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[GWAS:Cognitive performance]
(hide)
[GWAS:Cognitive performance]
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[GWAS:Cognitive performance]
Frequency: 63.1%
References:1
References:1
(hide)
[GWAS:Cognitive performance]
(hide)
non sig. gwas, top 25 GEE p-values, Wide-Range Achievement Test [GWAS:Cognitive test performance]
(hide)
non sig. gwas, hit (p = 7 x 10^-6) for Stroop test performance [GWAS:Cognitive Performance]
(hide)
non sig. gwas, hit (p = 5 x 10^-7) for Trails A performance [GWAS:Cognitive Performance]
(hide)
non sig. gwas, hit (p = 8 x 10^-6) - Animals [GWAS:Cognitive Performance]
(hide)
non sig. gwas, hit (p = 1 x 10^-6) - Animals [GWAS:Cognitive Performance]
(hide)
non sig. gwas, hit (p = 4 x 10^-6) for Test Trails A performance [GWAS:Cognitive Performance]
(hide)
[GWAS:Cognitive performance]
(hide)
[GWAS:Cognitive performance]
(hide)
non sig. gwas, hit (p = 3 x 10^-6) - Digit Symbol [GWAS:Cognitive Performance]
(hide)
[GWAS:Cognitive performance]
(hide)
[GWAS:Cognitive performance]
(hide)
non sig. gwas, hit (p = 8 x 10^-6) - Delayed Story Recall [GWAS:Cognitive Performance]
(hide)
[GWAS:Cognitive performance]
Frequency: 74.3%
References:1
References:1
(hide)
non sig. gwas, hit (p = 3 x 10^-6) for intra-extra dimensional set shift (IED) EDS errors in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
(hide)
non sig. gwas, top 25 GEE p-values, measure of attention and executive function [PharmGKB:Non-Curated GWAS results: Genetic correlates of brain aging on MRI and cognitive test measures: a genome-wide association and linkage analysis in the Framingham Study (Initial Sample Size: 705 individuals (Framingham); Replication Sample Size: NR). This variant is associated with Cognitive test performance.] [GWAS:Cognitive test performance]
(hide)
non sig. gwas, hit (p = 2 x 10^-6) - Delayed Story Recall [GWAS:Cognitive Performance]
(hide)
non sig. gwas, hit (p = 2 x 10^-6) - Immediate Story Recall [GWAS:Cognitive Performance]
(hide)
[GWAS:Cognitive performance]
(hide)
[GWAS:Cognitive performance]
Frequency: 79.6%
References:1
References:1
(hide)
non sig. gwas, hit (p = 3 x 10^-7) for Trails A performance [GWAS:Cognitive Performance]
(hide)
non sig. gwas, hit (p = 2 x 10^-6) for spatial recognition memory (SRM) percent correct in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
Frequency: 83.2%
References:1
References:1
(hide)
non sig. gwas, hit (p = 4 x 10^-7) for pattern recognition memory (PRM) percent correct in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
(hide)
non sig. gwas, top hit for pattern recognition memory (PRM) percent correct in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
(hide)
non sig. gwas, hit (p = 5 x 10^-6) for forward digit span [GWAS:Cognitive Performance]
(hide)
non sig. gwas, hit (p = 4 x 10^-7) for backwards digit span [GWAS:Cognitive Performance]
(hide)
Mentioned in retracted non sig. gwas, hit (p = 1 x 10^-6) for paired associates learning (PAL) total errors at 8 patterns in the CANTAB (Cambridge Neuropsychological Test Automated Battery [GWAS:Cognitive performance]
Frequency: 91.7%
References:1
References:1
(hide)
[GWAS:Cognitive performance]
Frequency: 95.6%
References:1
References:1
(hide)
[GWAS:Cognitive performance]
(hide)
non sig. gwas, top 25 GEE p-values, measure of attention and executive function [GWAS:Cognitive test performance]
References:1
(hide)
[GWAS:Cognitive performance]
(hide)
SNPs in the SNAP25 gene were initially linked to intelligence but have failed to replicate . While now suspect, the original work can be found in . The (T;T) genotype averages several PIQ points higher than the (C;T) genotype, which averages several PIQ points higher than the (C;C) genotype. For SNPs rs363039 - rs363043 - rs353016, respectively, the haplotype C-T-T is most associated with higher intelligence in children, whereas the haplotype C-C-T is most associated in adults (SNPs oriented as in dbSNP).
Magnitude: 0
Frequency: 54.0%
References:1
Frequency: 54.0%
References:1
(hide)
non sig. gwas, hit (p = 5 x 10^-6) for spatial working memory (SWM) strategy in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
common in complete genomics
(hide)
non sig. gwas, top 25 GEE p-values, visual memory and organization [GWAS:Cognitive test performance]
common in complete genomics
(hide)
non sig. gwas, top 25 GEE p-values, Boston Naming Test [PharmGKB:Non-Curated GWAS results: Genetic correlates of brain aging on MRI and cognitive test measures: a genome-wide association and linkage analysis in the Framingham Study (Initial Sample Size: 705 individuals (Framingham); Replication Sample Size: NR). This variant is associated with Cognitive test performance.] [GWAS:Cognitive test performance]
common in clinvar
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Mentioned in a 23andMe discussion on intelligence. Synonymous Polymorphisms at Splicing Regulatory Sites are Associated with CpGs in Neurodegenerative Disease-Related Genes.
common in complete genomics
(hide)
non sig. gwas, hit (p = 8 x 10^-6) for forward digit span [GWAS:Cognitive Performance]
Magnitude: 0
Frequency: 68.1%
Repute:Good
References:1
Frequency: 68.1%
Repute:Good
References:1
common on affy axiom data
(hide)
non sig. gwas, hit (p = 4 x 10^-6) for paired associates learning (PAL) total errors at 6 patterns in the CANTAB (Cambridge Neuropsychological Test Automated Battery [GWAS:Cognitive performance]
most common in all populations but having one copy of the rarer (C) allele is linked to increased executive function
(hide)
Variation in longevity gene KLOTHO is associated with greater cortical volumes
common in complete genomics
(hide)
non sig. gwas, hit (p = 3 x 10^-7) for paired associates learning (PAL) total errors at 6 patterns in the CANTAB (Cambridge Neuropsychological Test Automated Battery [GWAS:Cognitive performance]
common on affy axiom data
(hide)
non sig. gwas, hit (p = 5 x 10^-6) for Trails B performance [GWAS:Cognitive Performance]
common in complete genomics
(hide)
non sig. gwas, hit (p = 3 x 10^-6) for Stroop test performance [GWAS:Cognitive Performance]
common on affy axiom data
(hide)
non sig. gwas, hit (p = 2 x 10^-6) for Trails B performance [GWAS:Cognitive Performance]
Magnitude: 0
Frequency: 78.8%
Repute:Good
References:1
Frequency: 78.8%
Repute:Good
References:1
common on affy axiom data
(hide)
non sig. gwas, hit (p = 6 x 10^-6) for intra-extra dimensional set shift (IED) EDS errors in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
Magnitude: 0
Frequency: 79.6%
Repute:Good
References:1
Frequency: 79.6%
Repute:Good
References:1
common on affy axiom data
(hide)
non sig. gwas, hit (p = 6 x 10^-6) for paired associates learning (PAL) total errors at 6 patterns in the CANTAB (Cambridge Neuropsychological Test Automated Battery [GWAS:Cognitive performance]
Magnitude: 0
Frequency: 80.4%
Repute:Good
References:1
Frequency: 80.4%
Repute:Good
References:1
common on affy axiom data
(hide)
non sig. gwas, hit (p = 8 x 10^-6) for Controlled Oral Word Association (COWA) test performance [GWAS:Cognitive Performance]
common in complete genomics
(hide)
non sig. gwas, hit (p = 4 x 10^-6) for intra-extra dimensional set shift (IED) EDS errors in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
Magnitude: 0
Frequency: 83.1%
Repute:Good
References:1
Frequency: 83.1%
Repute:Good
References:1
common on affy axiom data
(hide)
non sig. gwas, top hit for paired associates learning (PAL) total errors at 8 patterns in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
common in complete genomics
(hide)
non sig. gwas, top 25 GEE p-values, measure of attention and executive function [GWAS:Cognitive test performance]
Magnitude: 0
Frequency: 86.5%
Repute:Good
References:1
Frequency: 86.5%
Repute:Good
References:1
common on affy axiom data
(hide)
non sig. gwas, hit (p = 2 x 10^-6) for pattern recognition memory (PRM) percent correct in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
Magnitude: 0
Frequency: 86.7%
Repute:Good
References:1
Frequency: 86.7%
Repute:Good
References:1
common on affy axiom data
(hide)
non sig. gwas, hit (p = 6 x 10^-6) for paired associates learning (PAL) total errors at 8 patterns in the CANTAB (Cambridge Neuropsychological Test Automated Battery [GWAS:Cognitive performance]
common in complete genomics
(hide)
non sig. gwas, hit (p = 6 x 10^-6) - Delayed Story Recall [GWAS:Cognitive Performance]
common in complete genomics
(hide)
non sig. gwas, hit (p = 7 x 10^-6) for verbal recognition memory (VRM) free recall in the CANTAB (Cambridge Neuropsychological Test Automated Battery [GWAS:Cognitive performance]
common in complete genomics
(hide)
non sig. gwas, hit (p = 6 x 10^-6) for paired associates learning (PAL) total errors at 6 patterns in the CANTAB (Cambridge Neuropsychological Test Automated Battery [GWAS:Cognitive performance]
common in complete genomics
(hide)
non sig. gwas, hit (p = 6 x 10^-8) for backwards digit span [GWAS:Cognitive Performance]
(hide)
[GWAS:Cognitive performance]
common in complete genomics
(hide)
non sig. gwas, hit (p = 2 x 10^-7) for paired associates learning (PAL) total errors at 8 patterns in the CANTAB (Cambridge Neuropsychological Test Automated Battery [GWAS:Cognitive performance]
Magnitude: 0
Frequency: 91.1%
Repute:Good
References:1
Frequency: 91.1%
Repute:Good
References:1
common in complete genomics
(hide)
non sig. gwas, hit (p = 7 x 10^-6) for Trails A performance [GWAS:Cognitive Performance]
common in complete genomics
(hide)
non sig. gwas, hit (p = 6 x 10^-6) - Animals [GWAS:Cognitive Performance]
common on affy axiom data
(hide)
non sig. gwas, top hit for paired associates learning (PAL) total errors at 6 patterns in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
Magnitude: 0
Frequency: 93.8%
Repute:Good
References:1
Frequency: 93.8%
Repute:Good
References:1
common in complete genomics
(hide)
non sig. gwas, hit (p = 8 x 10^-7) for spatial working memory (SWM) strategy in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
common on affy axiom data
(hide)
non sig. gwas, hit (p = 2 x 10^-6) for intra-extra dimensional set shift (IED) EDS errors in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
common in complete genomics
(hide)
non sig. gwas, hit (p = 4 x 10^-6) for intra-extra dimensional set shift (IED) EDS errors in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
common in complete genomics
(hide)
non sig. gwas, hit (p = 5 x 10^-6) for spatial working memory (SWM) strategy in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
common in complete genomics
(hide)
non sig. gwas, hit (p = 6 x 10^-7) - Animals [GWAS:Cognitive Performance]
(hide)
[GWAS:Cognitive performance]
Magnitude: 0
Frequency: 99.1%
Repute:Good
References:1
Frequency: 99.1%
Repute:Good
References:1
common in complete genomics
(hide)
non sig. gwas, hit (p = 2 x 10^-6) for intra-extra dimensional set shift (IED) EDS errors in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
common in complete genomics
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non sig. gwas, hit (p = 5 x 10^-6) for pattern recognition memory (PRM) percent correct in the CANTAB (Cambridge Neuropsychological Test Automated Battery) [GWAS:Cognitive performance]
common in complete genomics
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non sig. gwas, hit (p = 3 x 10^-6) - Animals [GWAS:Cognitive Performance]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
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non sig. gwas, hit (p = 6 x 10^-6) for Stroop test performance [GWAS:Cognitive Performance]
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In 2009, a large, multi-sample replication study failed to find any significant association with Intelligence for this or other SNPs in CHRM2 . Earlier work had observed that this snp (and perhaps its neighbors) influenced intelligence and alcohol dependence CHRM2 gene predisposes to alcohol dependence, drug dependence and affective disorders: results from an extended case-control structured association study. And the earlier and or this pdf poster show association between the CHRM2 gene and intelligence . In this study of ~300 Caucasians, the (T;T) genotype appeared to typically have a 4 point higher IQ than the (A;T) genotype, which had a 4 point higher IQ (on average) than the (A;A) genotype. A nearby SNP, rs324640, showed similar results to rs324650, and was in linkage disequilibrium (...
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rs174575, has been investigated with respect to increased intelligence in breastfed children but not yielded any clear result. *Although there was no difference in IQ linked to the SNP alone, breastfed children carrying one or two copies of rs174575(C) had a significant (6 point) increase in IQ compared to carriers of the same allele who were not breastfed. For children who were homozygous non-carriers, i.e. rs174575(G;G) individuals, there was no effect of breastfeeding on IQ. *did not replicate those findings. In contrast to their study, (G;G) children exhibited the greatest difference between feeding methods such that breastfed children performed similarly irrespective of child genotype whereas formula fed (G;G) children performed worse than other children on formula milk Breastfeeding ...
common on affy axiom data
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non sig. gwas, hit (p = 5 x 10^-6) for PC1 (principal component 1) among the cognitive tests performed [GWAS:Cognitive Performance]
135 snps
(hide) Major histocompatibility complex
1.1x increased risk for schizophrenia
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rs6932590 is a SNP that is postulated to have a role in conferring increased susceptibility for schizophrenia. rs6932590 lies in the major histocompatibility complex (MHC) region on chromosome 6, a region that codes for several genes with significant roles in autoimmunity, such as human leukocyte antigens. Specifically, rs6932590 lies in an intergenic region between PRSS16 (a serine protease expressed in the thymus that plays a role in positive T cell selection) and POM121L2 (a membrane glycoprotein) . The T allele at rs6932590 purportedly confers an increased risk for schizophrenia, with reported odds ratios of 1.16 and 1.31 . === Evidence === One large-scale case-controlled genome-wide association study (GWAS) that examined differential genotypes in individuals with schizophrenia, found ...
1 snp
(hide) Memory
Magnitude: 2
Frequency: 42.5%
Repute:Good
References:16
Frequency: 42.5%
Repute:Good
References:16
increased memory performance
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In a Swiss cohort: 'Carriers of KIBRA rs17070145 T allele had 24% better free recall performance 5 min after word presentation (P = 0.000004) and 19% better free recall performance 24 hours after word presentation (P = 0.0008) than did noncarriers.' In a US cohort: 'T allele carriers had significantly better memory scores than non-carriers in the Buschke's Selective Reminding Test (SRT). Performance on another episodic memory task, the Rey Auditory Verbal Learning Test (AVLT), was also significantly different between allele groups.' In another Swiss cohort, with a visual episodic memory task: 'T allele carriers also performed significantly better than did noncarriers in this population.' 'Functional magnetic resonance imaging detected KIBRA allele-dependent differences in hippocampal activ...
Resistance to Prion Disease (PrP 129 Met/Val heterozygote) This genotype codes for Met/Val heterozygote at codon 129 in PrP, the Prion Protein. This is strongly protective against development of Prion disease, including sporadic and infectious Creutzfeldt-Jakob disease. Studies in Papua New Guinea showed that this genotype prevents transmission of kuru , a form of Prion disease transmitted by cannibalism. So eat as many brains as you want!
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rs1799990, also known as Met129Val or M129V, is a SNP in the prion protein PRNP gene. The more common rs1799990(A) allele encodes the Met (methionine). Historically, since 1991 this SNP has been associated with risk for sporadic Creutzfeldt-Jakob disease, with homozygotes of both types apparently at increased risk compared to heterozygotes. More recently, this SNP has been related to long-term memory with (A;A) and (A;G) individuals recalling 17% more words than (G;G) individuals at 24h following learning. A further study of 12 individuals of each of the 3 possible genotypes showed that at both 30 minutes and 24 hour time lags, correlations between retrieval-related brain activity and retrieval success were negative for (G;) homozygotes (the more activity, the worse retrieval success), whi...
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g2b2mh blog In a population of healthy individuals, those that carry common variants (such as rs760761, rs1018381, rs2619522) located in the dysbindin (DTNBP1) gene, a risk factor for schizophrenia, show minor cognitive impairments such as decreased attentional capacity, worse performance on memory tasks, and alterations in schizotypal beliefs and experiences. [OMIM:DYSTROBREVIN-BINDING PROTEIN 1; DTNBP1]
Frequency: 37.2%
References:1
References:1
Frequency: 44.2%
References:2
References:2
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in all 4 ind. samples (1699 total indv.) associated with immediate recall, minor allele (C) carriers displayed worse short-term memory performance in a per allele fashion per HapMap data, the haplotype containing the C allele is in high LD with a (23andMe covered) haplotype consisting of rs4667867(A) (r^2 = 1), rs13421166(C), rs2126152(T), rs6432860(A) (+ the annotated SNP rs3812718(C) ) in the CEU+TSI sample
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rs4790904 is a mutation in the gene encoding PKCα (PRKCA). It has been linked to memory capacity in healthy subjects and to risk for post-traumatic stress disorder .
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anxiety-related personality traits, ADHD, schizophrenia part of a three marker haplotype rs737865-rs4680-rs165599 epistasis between SNPs in COMT (rs2097603, Val158Met (rs4680), rs165599) and polymorphisms in other schizophrenia susceptibility genes popular in pubmed is associated with bipolar disorder and influences prefrontal aspects of verbal memory in bipolar patients and healthy controls. [PharmGKB:Curated In a study of 78 African American and 65 white patients diagnosed with schizophrenia or schizoaffective disorder, this SNP in the COMT gene was found to have significant associations with response to risperidone over 2-12 weeks in both African-American and white patients.] [OMIM:CATECHOL-O-METHYLTRANSFERASE; COMT]
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g2b2mh blog In a population of healthy individuals, those that carry common variants (such as rs760761, rs1018381, rs2619522) located in the dysbindin (DTNBP1) gene, a risk factor for schizophrenia, show minor cognitive impairments such as decreased attentional capacity, worse performance on memory tasks, and alterations in schizotypal beliefs and experiences. The association between several SNPs in the DTNBP1 gene, most especially rs760761, and schizophrenia was confirmed in a new sample of 1021 cases and 626 controls from Ireland. Genetic variation in the 6p22.3 gene DTNBP1, the human ortholog of the mouse dysbindin gene, is associated with schizophrenia. Support for association of schizophrenia with genetic variation in the 6p22.3 gene, dysbindin, in sib-pair families with linkage and i...
normal cognitive ability
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g2b2mh blog In a population of healthy individuals, those that carry common variants (such as rs760761, rs1018381, rs2619522) located in the dysbindin (DTNBP1) gene, a risk factor for schizophrenia, show minor cognitive impairments such as decreased attentional capacity, worse performance on memory tasks, and alterations in schizotypal beliefs and experiences. [OMIM:DYSTROBREVIN-BINDING PROTEIN 1; DTNBP1]
normal
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rs1076560 is located in intron 6 of the dopamine receptor D2 gene. In one study of Japanese males, rs1076560(A) alleles were 1.3 fold more associated with Alcoholism than the rs1076560(C) alleles. The DRD2 risk allele A was more prevalent in the alcoholic patients than in the healthy controls. These data identify rs1076560 as a potentially important variable in the development of alcoholism. rs1076560 and the DAT 3'-VNTR variant influences memory Genetic variants altering dopamine D2 receptor expression or function modulate the risk of opiate addiction and the dosage requirements of methadone substitution [PharmGKB:Curated This variant is a potential marker for alcoholism. A allele was more prevalent in the alcoholic patients than in the healthy controls in a study consists of 248 alcohol...
complex; generally normal risk
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rs361525 is also known as the TNF-238 SNP, and occasionally the rs361525(A) allele is referred to as 238.2 (with the more common (G) allele being 238.1). This SNP in the tumor necrosis factor-alpha gene has been linked to a wide variety of conditions: * Breast cancer ** A large study of over 5,000 Caucasian women found that rs361525(A) allele carriers were at somewhat elevated risk for breast cancer compared to the (G;G) genotype, with an odds ratio per allele of 1.18, CI: 1.04-1.35, p(trend)= 0.008. ** However, a 2009 European study of 30,000 breast cancer cases, compared to 30,000 controls, found no association, or as they put it, 'persuasive evidence against an overall association between invasive breast cancer risk and (this SNP)'. * Graft versus host disease (GVHD) ** A study of ~100 ...
13 snps
(hide) Mendeliome
Generally European; Light skin; Possibly an increased risk of melanoma This SNP is associated with skin, hair, and eye colour, and risk of melanoma. Individuals with the G;G genotype are generally of European descent and have fair skin. In a population-based case-control study investigating a number of pigmentation-related SNPs and their correlation with cutaneous malignant melanoma (CMM) in a Caucasian Australian population, rs16891982 (variant F374L) was found to be associated with odds ratios of 3.44, 2.86, 1.68, and 1.68 for all study subjects (1,738 CMM cases and 4,517 controls); subjects with northern European ancestry (1,438 cases and 3,098 controls); northern European subjects adjusted for hair, eye, and skin colour; and northern European subjects adjusted for the MC1R genotype, r...
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This snp influences skin pigmentation. The allele p.L374F indicates light-skinned european ancestry c.1122C>G, p.Phe374Leu (NCBI dbSNP rs16891982) in SLC45A2 was associated with protection from malignant melanoma (OR, 0.41; 95% CI, 0.24-0.70; P=0.008 after adjustment for multiple testing) An association study conducted on a population of European origin concluded that the rare (in Europeans, at least) allele L374, i.e. rs16891982(C) in dbSNP orientation, significantly increases the possibility of having black hair color, with an odds ratio of around 7. This population-based case-control study investigated a number of pigmentation-related SNPs and their correlation with cutaneous malignant melanoma (CMM) in an Australian population. rs16891982 (variant F374L) was found to be associated w...
Frequency: 0.9%
References:1
References:1
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Analysis of variation in expression of autosomal dominant osteopetrosis type 2: searching for modifier genes. Polymorphisms of the CLCN7 gene are associated with BMD in women. CLCN7 polymorphisms and bone mineral density in healthy premenopausal white women and in white men.
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[OMIM:?]
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[OMIM:?]
normal
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rs213950, a SNP in the cystic fibrosis CFTR gene (but not one that is linked to cystic fibrosis), has been reported in a large study to be associated with type-1 diabetes. In an expanded follow-up study of >6,000 controls and 6,000 patients, the heterozygote odds ratio for this SNP was recalculated to be 1.09 (CI 1.04–1.15). [OMIM:CFTR POLYMORPHISM]
slight increase in skin cancer risk
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rs1126809 is a SNP in the TYR tyrosinase gene. This SNP is also known as R402Q (or, 1205G>A) based on the amino acid change at position 402 from an arginine (R) to a glutamine (Q). The rs1126809(G) allele encodes the more common (R)/arginine, while the variant rs1126809(A) allele encodes the (Q)/glutamine. rs1126809(A) has previously been shown to affect eye color and sun sensitivity. Based on a study of 4,000+ skin cancer patients, it also conferred increased risk of cutaneous malignant melanoma (odds ratio 1.21, p = 2.8 x 10<sup>-7</sup>) and basal cell carcinoma (odds ratio 1.14, p = 6.1 x 10<sup>-4</sup>). rs1126809 is not associated with albinism. [PharmGKB:Curated This variant is associated with the risk of cutaneous melanoma and basal cell carcinoma. It i...
normal risk
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RNA made containing the rs688(T) SNP, a variant near exon 12 of the low-density lipoprotein receptor (LDLR) that is a receptor for ApoE proteins, is spliced at lower efficiency in males. Presumably due to this, the rs688(T;T) genotype was associated with increased risk for Alzheimer's disease odds in males (odds ratio 1.49, CI: 1.13-1.97, uncorrected p=0.005), but not in females. The presence of the rs688(T) allele associates with increased total and LDL-cholesterol in female members of the Framingham Offspring Study; rs688 was not associated with significant differences in HDL-cholesterol. The largest rs688-associated cholesterol differences were observed in pre-menopausal women. Taken together, rs688, a SNP present in approximately 60% of Caucasians, is associated with significant 10% in...
common in clinvar
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Development of a fingerprinting panel using medically relevant polymorphisms. Genetic risk factors for hepatopulmonary syndrome in patients with advanced liver disease. Population based allele frequencies of disease associated polymorphisms in the Personalized Medicine Research Project. Genetic variants associated with Von Willebrand factor levels in healthy men and women identified using the HumanCVD BeadChip. von Willebrand factor plasma levels, genetic variations and coronary heart disease in an older population. [GWAS:Coagulation factor levels]
normal
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rs2464196 is a SNP that was originally associated with C-reactive protein levels, and given other findings that suggest C-reactive protein levels may be predictive of cancer risk, was thought to be linked to cancer risk. A large study pooling data from 3 Finnish studies totaling over 18,000 individuals concluded that while this SNP is not likely to be causative (relative to cancer), it and one other CRP SNP (rs1169300) are associated with increased risk for lung cancer. The odds ratio for minor alleles of either SNP was about 1.5x and 2x for heterozygotes and homozygotes, respectively. One other CRP SNP (rs1892534) was associated with increased overall cancer risk. CRP SNPs were not associated with colorectal, prostate or breast cancer risk. [PharmGKB:Curated In a candidate gene-based ass...
common in clinvar
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Susceptibility genes for gentamicin-induced vestibular dysfunction.
normal
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This SNP lies within the gene coding for ATM (Ataxia telegensia mutated), a main role of which is the repair of double-stranded DNA breaks. As such SNPs within this gene have been associated with susceptibility to cancer. Rs1801516(A,A) leads to homozygous expression of ATM(D1853N). Homozygotes for this mutation have been associated with increased likelihood of pancreatic cancer (OR, 2.55; 95% CI, 1.08-6.00; P = 0.032) . Despite early reports, the role of Rs1801516 in breas cancer is unclear . A meta-analysis concluded that this mutation was not a risk factor for developing breast cancer (GA vs GG:OR=1.18 (95%CI 0.90-1.53); AA vs GG:OR=0.77 (95%CI 0.58-1.03) . Similarly the (A,A) variant has been reported to be protective against Melanoma development (p=3.4×10−9, OR=0.84 overall...
common in clinvar you have the common genotype, but rare genotype has a beneficial effect on blood pressure and risk of myocardial infarction.
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[OMIM:MYOCARDIAL INFARCTION, DECREASED SUSCEPTIBILITY TO]
common in complete genomics
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15,000 individuals. Each copy of the minor T allele of SNP rs2228671 was related to a decrease of LDL-C levels by 0.19 mmol/L (95% confidence interval (CI) [0.13-0.24] mmol/L, p = 1.5x10(-10)) and a significantly lower risk of coronary artery disease (OR per copy of the T allele: 0.82, 95% CI [0.76-0.89], p = 2.1x10(-7)) [PharmGKB:Non-Curated GWAS results: Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. (Initial Sample Size: 17,797 individuals; Replication Sample Size: NR); (Region: 19p13.2; Reported Gene(s): LDLR; Risk Allele: rs2228671-G); (p-value= 0.00000000000004).This variant is associated with LDL cholesterol.] [OMIM:LOW DENSITY LIPOPROTEIN RECEPTOR; LDLR] [GWAS:Cholesterol, total]
Magnitude: 0
Frequency: 97.3%
Repute:Good
References:0
Frequency: 97.3%
Repute:Good
References:0
Magnitude: 0
Frequency: 98.1%
Repute:Good
References:1
Frequency: 98.1%
Repute:Good
References:1
common in clinvar
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[OMIM:MUSCULAR DYSTROPHY, CONGENITAL, 1C, WITH NEUROLOGIC ABNORMALITIES]
Magnitude: 0
Frequency: 98.4%
Repute:Good
References:7
Frequency: 98.4%
Repute:Good
References:7
common in clinvar
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rs11466023, also known as c.1105C>T, p.Pro369Ser or P369S, is a SNP in the MEFV gene. The risk allele is given as (A) by 23andMe, however in dbSNP orientation, the risk allele is (T). The symptoms of familial Mediterranean fever are caused by the person's own inflammatory response; it is not an infectious disease. The condition is more common among Turks, Sephardic Jews, and people of Arab and Armenian ancestry. [OMIM:FAMILIAL MEDITERRANEAN FEVER]
Magnitude: 0
Frequency: 99.1%
Repute:Good
References:0
Frequency: 99.1%
Repute:Good
References:0
common in clinvar
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rs28897743, also known as 7235G>T, c.7007G>T and p.Gly2313AlafsX31, as well as Arg2336His or R2336H, is a variant in the BRCA2 gene considered pathogenic for breast cancer in ClinVar and UMD. This variant meets the criteria published in 2013 by the ACMG regarding incidental findings in exome or genome sequencing, as a variant that they do recommend informing a patient about. 23andMe has another SNP for this position, named i5009343.
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
common in clinvar
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rs11539445, also known as c.572G>A, p.Gly191Asp and G191D, or c.572G>T, p.Gly191Val and G191V, as is a variant in the YARS2 gene on chromosome 12. The minor allele rs11539445(T) is relatively common, with an ExAC database frequency of 0.1259, and over 1,000 homozygotes observed. This implies that G191V is a benign variation. However, the minor allele rs11539445(A), encoding G191D, is reported to be pathogenic in OMIM, at least when inherited recessively, based on a 2013 study. Frequency data about this allele is not reported so far as we know, indicating it is likely to be extremely rare, and if the 2013 report holds up, is to be considered pathogenic (at least when inherited in two copies or as a compound heterozygote).
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
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rs12948217, also known as Y231X or Tyr231Ter, is a SNP in the ASPA gene. According to 23andMe, only the A allele at rs12948217 confers risk to Canavan disease. A person with the CC, CT, or TT alleles is not a carrier; someone with the AC or AT alleles is a carrier; and people with two AA alleles are affected with the disease. [OMIM:[[Canavan disease]]]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
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rs28937594, also known as c.2228T>C, p.Met743Thr, M743T and most commonly in the literature M712T, is a mutation in the GNE gene on chromosome 9. The very rare rs28937594(C) allele is the most common mutation leading to autosomal recessive inclusion body myopathy 2 (IBM2 or HIBM) in Middle Eastern populations. See also OMIM 603824.0005 [OMIM:INCLUSION BODY MYOPATHY, AUTOSOMAL RECESSIVE]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:6
Repute:Good
References:6
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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A variant of the SLC10A2 gene encoding the apical sodium-dependent bile acid transporter is a risk factor for gallstone disease. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common/normal
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rs1064651, also known as Asp448His or D448H, is a SNP in exon 9 of the GBA gene on chromosome 1. As the protein was originally numbered, though, this variation occurred at amino acid 409 (rather than 448), so the scientific literature still often refers to this mutation as Asp409His or D409H. Mutations in both copies of a person's GBA gene may lead to Gaucher's disease, an autosomal recessive disorder. When one of the mutations is the D409H mutation, the clinical description may be Gaucher disease type 3C, involving valvular heart disease. However, the clinical presentation appears to be highly variable as well as dependent on which two mutations are present. For more information, see OMIM 606463.0006. Be aware that since this mutation is due to a G>C (tranversion) when oriented in the ...
45 snps
(hide) Menopause
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[GWAS:Menopause]
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[GWAS:Menopause]
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[GWAS:Menopause]
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[GWAS:Menopause]
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[GWAS:Menopause]
Frequency: 32.4%
References:1
References:1
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[GWAS:Menopause]
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[GWAS:Menopause]
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23andMe blog rs1172822(T) Menopause about 25 weeks earlier [OMIM:?] [GWAS:Menopause]
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rs4806660 is a SNP on chromosome 19. A case control study of ~2,000 women found that each rs4806660(C) allele was associated with an average decrease in age at menopause of ~1 month. This also meant that each rs4806660(T) allele yielded an odds ratio of 1.45 (CI: 1.32–1.59, p = 8.88 x 10e-16) of not having early menopause, defined as occurring before the age of 46. Overall, women homozygous for the 'early' alleles at all 4 SNPs found in this study were ~4 times more likely to undergo menopause early compared to women who had a total of 3 or less risk alleles. However, the ability to predict which women will actually undergo early menopause using these 4 SNPs is still low. [OMIM:?]
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23andMe blog rs365132(T) Menopause about 20 weeks later [OMIM:?] [GWAS:Menarche and menopause (age at onset)]
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23andMe blog rs2153157(A) Menopause about 15 weeks later [OMIM:MENOPAUSE, NATURAL, AGE AT, QUANTITATIVE TRAIT LOCUS 1; MENOQ1] [GWAS:Menarche and menopause (age at onset)]
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[OMIM:?] [GWAS:Menopause]
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rs9379896 is a SNP on chromosome 6. A case control study of ~2,000 women found that each rs9379896(C) allele was associated with an average increase in age at menopause of ~1 month. This also meant that each rs9379896(T) allele yielded an odds ratio of 1.13 (CI: 1.01–1.27, p = 3.8 x 10e-2) of early menopause, defined as occurring before the age of 46. Overall, women homozygous for the 'early' alleles at all 4 SNPs found in this study were ~4 times more likely to undergo menopause early compared to women who had a total of 3 or less risk alleles. However, the ability to predict which women will actually undergo early menopause using these 4 SNPs is still low.
common on affy axiom data
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23andMe blog rs7333181(A) Menopause about 27 weeks later [OMIM:MENOPAUSE, NATURAL, AGE AT, QUANTITATIVE TRAIT LOCUS 1; MENOQ1] [GWAS:Menopause]
Magnitude: 0
Frequency: 76.1%
Repute:Good
References:1
Frequency: 76.1%
Repute:Good
References:1
Magnitude: 0
Frequency: 82.3%
Repute:Good
References:8
Frequency: 82.3%
Repute:Good
References:8
common on affy axiom data
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rs16991615 is a nonsynonymous SNP on chromosome 20. A case control study of ~2,000 women found that each rs16991615(A) allele was associated with an average increase in age at menopause of 11 months. This also meant that each rs16991615(G) allele yielded an odds ratio of 1.85 (CI: 1.51–2.2, p = 1.45 x 10e-9) of early menopause, defined as occurring before the age of 46. Overall, women homozygous for the 'early' alleles at all 4 SNPs found in this study were ~4 times more likely to undergo menopause early compared to women who had a total of 3 or less risk alleles. However, the ability to predict which women will actually undergo early menopause using these 4 SNPs is still low. * see also 23andMe blog [OMIM:?] [GWAS:Menarche and menopause (age at onset)]
17 snps
(hide) Mental health
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g2b2mh blog In a population of healthy individuals, those that carry common variants (such as rs760761, rs1018381, rs2619522) located in the dysbindin (DTNBP1) gene, a risk factor for schizophrenia, show minor cognitive impairments such as decreased attentional capacity, worse performance on memory tasks, and alterations in schizotypal beliefs and experiences. [OMIM:DYSTROBREVIN-BINDING PROTEIN 1; DTNBP1]
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origins blog rs833070 and rs2146323. Individuals with the CC genotype at rs833070 and rs2146323 displayed smaller hippocampal volumes than T-allele and A-allele carriers, respectively. bdmh2 blog coverage of rs833070 and rs2146323
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associated with vulnerability to nicotine addiction in men. g2b2mh blog rs1044396 mediates effects of nicotine self-medication via parietal cortex. subjects with the (T;T) genotype showed robust brain activity in the parietal cortex while subjects with the (C;C) genotype showed very little change in activity. [PharmGKB:Curated This variant is closely linked to rs2236196 and has been associated with the intensification of nicotine dependence.] [OMIM:CHOLINERGIC RECEPTOR, NEURONAL NICOTINIC, ALPHA POLYPEPTIDE 4; CHRNA4]
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origins blog linked to brain mophology via a haplotype block with rs833070 and rs2146323, Large-scale evaluation of candidate genes identifies associations between VEGF polymorphisms and bladder cancer risk. A genetic association analysis of cognitive ability and cognitive ageing using 325 markers for 109 genes associated with oxidative stress or cognition. Polymorphisms in the VEGFA and VEGFR-2 genes and neovascular age-related macular degeneration. Vascular endothelial growth factor gene polymorphisms and ovarian cancer survival. Genetics of VEGF serum variation in human isolated populations of cilento: importance of VEGF polymorphisms. Contribution of VEGF polymorphisms to variation in VEGF serum levels in a healthy population.
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rs4675690 is in close proximity to CREB1, and adjacent to LOC151194. g2b2mh blog individuals with the TT genotype at rs4675690 (C/T) showed less disgust, but not happiness, desire or fear. T allele associated with increased chance of suicide (OR = 2.3, 95% CI 1.3-2.9, TT homozygotes vs CC homozygotes?) during the first 30 days (p > 0.05 after the first month) of citalopram treatment, in a study of 1447 citalopram users (male only subgroup, 539 in total). Two haplotypes (see below) also showed significant association with suicidality in the male subgroup. *rs2709376(C),rs2253206(A),rs7569963(A),rs7594560(T),rs4675690(C) - common haplotype, reduced chance of suicide in males, p = 0.004 *rs2709376(C),rs2253206(A),rs7569963(G),rs7594560(T),rs4675690(T) - increased chance of suicide in males...
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g2b2mh blog rs833070 and rs2146323. Individuals with the CC genotype at rs833070 and rs2146323 displayed smaller hippocampal volumes than T-allele and A-allele carriers, respectively.
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origins associated with an independent aspect of decision making in a learning paradigm Association analysis of the protein phosphatase 1 regulatory subunit 1B (PPP1R1B) gene with nicotine dependence in European- and African-American smokers. Genetic analysis of the gene coding for DARPP-32 (PPP1R1B) in Japanese patients with schizophrenia or bipolar disorder. Reduced prefrontal cortex DARPP-32 mRNA in completed suicide victims with schizophrenia. The biological basis of anger: associations with the gene coding for DARPP-32 (PPP1R1B) and with amygdala volume. Dopaminergic genes predict individual differences in susceptibility to confirmation bias. Variation of the gene coding for DARPP-32 (PPP1R1B) and brain connectivity during associative emotional learning.
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g2b2mh blog In a population of healthy individuals, those that carry common variants (such as rs760761, rs1018381, rs2619522) located in the dysbindin (DTNBP1) gene, a risk factor for schizophrenia, show minor cognitive impairments such as decreased attentional capacity, worse performance on memory tasks, and alterations in schizotypal beliefs and experiences. The association between several SNPs in the DTNBP1 gene, most especially rs760761, and schizophrenia was confirmed in a new sample of 1021 cases and 626 controls from Ireland. Genetic variation in the 6p22.3 gene DTNBP1, the human ortholog of the mouse dysbindin gene, is associated with schizophrenia. Support for association of schizophrenia with genetic variation in the 6p22.3 gene, dysbindin, in sib-pair families with linkage and i...
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asthma related influences sleep patterns [http://originsgenomeresources.net/musings/?p=62] [OMIM:ASTHMA SUSCEPTIBILITY 2]
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rs964201 and rs2442496 arose approximately 50,000 years ago and show strong positive selection in the lineage leading to humans [http://originsgenomeresources.net/musings/?p=68]
normal cognitive ability
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g2b2mh blog In a population of healthy individuals, those that carry common variants (such as rs760761, rs1018381, rs2619522) located in the dysbindin (DTNBP1) gene, a risk factor for schizophrenia, show minor cognitive impairments such as decreased attentional capacity, worse performance on memory tasks, and alterations in schizotypal beliefs and experiences. [OMIM:DYSTROBREVIN-BINDING PROTEIN 1; DTNBP1]
common/normal Val/val (normal) variant of the Val66Met snp in the BDNF gene that codes for brain-derived neurotrophic factor. Met/met is associated with susceptibility to neuropsychiatric disorders.
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rs6265, also known as Val66Met, is a SNP in brain-derived neurotrophic factor BDNF gene. The more common G allele encodes the Val, while the A allele encodes Met. Met/A allele associated with introversion The A allele may also be protective against depression when subjected to repeated defeat g2b2mh blog On a driving-based motor learning task subjects with this genotype showed greater error during short-term learning and poorer retention over 4 days, relative to subjects without the polymorphism. The presence of this BDNF polymorphism is associated with differences in brain motor system function, altered short-term plasticity, and greater error in short-term motor learning. Wired discusses the research as does 23andMe blog. Alzheimer's disease risk for non ApoE4 carriers is affected by the...
common in complete genomics
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rs964201 is an A/G SNP located in the ASPM gene. The G-allele of this SNP as well as the A-allele of rs3762271 another SNP located in the ASPM gene and rs2442496 a SNP in the MCPH1 gene arose approximately 50,000 years ago and show strong positive selection in the lineage leading to humans. A comment is found at g2b2mh.
common in complete genomics
(hide)
origins associated with an independent aspect of decision making in a learning paradigm
14 snps
(hide) Micronutrient Metabolism
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Association of a common nonsynonymous variant in GLUT9 with serum uric acid levels in old order amish.
Frequency: 50.8%
Repute:Bad
References:60
Repute:Bad
References:60
increased type-2 diabetes risk; higher gestational diabetes risk
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rs10830963 was associated with an increased risk of type-2 diabetes in our Han Chinese cohort (OR 1.16, 95% CI 1.03-1.31, p = 0.015). As previously described, the risk variant was also associated with increased fasting plasma glucose, showing an increase of 0.068 mmol/l (95% CI 0.036-0.100, p = 4 x 10(-5)) per risk allele rs10830962, rs4753426, and rs10830963 were significantly associated with higher fasting plasma glucose concentrations and reduced OGTT- and IVGTT-induced insulin release. rs3781638 displayed significant association with lower fasting plasma glucose levels and increased OGTT-induced insulin release A study totaling 19,000+ Europeans concluded that rs10830963 had the most influence of any MTNR1B gene SNP on the risk for type-2 diabetes. Specifically, the (G) allele increase...
6 snps
(hide) MicroRNA
higher cancer risk ? (ambiguous flip)
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(C;C) predisposes to papillary thyroid carcinoma. Among 42 patients with familial breast cancer and 82 patients with ovarian cancer, those with at least one rs2910164(C) SNP tended to have been diagnosed at an earlier age than those with only (G) alleles. For the breast cancer patients, the difference in median age was between 45 vs 56 (p = 0.029) and for ovarian cancer patients, 45 vs 50, (p = 0.014). (G;G) males were two-fold more susceptible to hepatocellular carcinoma (OR = 2.016, 95% CI = 1.056-3.848, P = 0.034) perhaps an ambiguous flip? [OMIM:MICRO RNA 146A; MIRN146A]
0.43x decreased risk for esophageal cancer
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rs6505162 is a SNP located in the pre-miRNA region of mir423. The major allele is rs6505162(C). A study of 346 Caucasians with esophageal cancer found that compared with the homozygous wild-type genotype of rs6505162, individuals with the heterozygous and homozygous variant genotype had a significantly reduced esophageal cancer risk with odds ratios of 0.58 (CI: 0.41-0.82) and 0.43 (CI: 0.27-0.68), respectively. After stratifying by gender, smoking, and age, the authors discovered that the protective effect was significant only for individuals under 64 years of age, regardless of sex or whether they smoked. Other unfavorable genotypes (ie SNPs) were also identified that were not as significant as rs6505162, and the overall risk of esophageal cancer increased with increasing numbers of unfa...
~1.2x increased risk for cancer
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microRNA 1,009 breast cancer cases and 1,093 controls in a population of Chinese women *rs3746444 in hsa-mir-499 A>G OR 1.25; 95% CI, 1.02-1.51 Genetic variants of miRNA sequences and non-small cell lung cancer survival. MicroRNA polymorphisms: the future of pharmacogenomics, molecular epidemiology and individualized medicine. Comprehensive analysis of the impact of SNPs and CNVs on human microRNAs and their regulatory genes. SNPs in human miRNA genes affect biogenesis and function. Common genetic variants in pre-microRNAs are associated with risk of coal workers' pneumoconiosis. MicroRNA polymorphisms: a giant leap towards personalized medicine. Common genetic variants in pre-microRNAs and risk of gallbladder cancer in North Indian population. Association of pre-microRNAs genetic varia...
Frequency: 0.0%
References:0
References:0
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Comprehensive analysis of the impact of SNPs and CNVs on human microRNAs and their regulatory genes.
Frequency: 26.5%
References:0
References:0
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discussed in nature Single nucleotide polymorphisms of microRNA machinery genes modify the risk of renal cell carcinoma. Genetic variations in microRNA-related genes are novel susceptibility loci for esophageal cancer risk. Comprehensive analysis of the impact of SNPs and CNVs on human microRNAs and their regulatory genes. Genetic Polymorphisms in MicroRNA-Related Genes as Predictors of Clinical Outcomes in Colorectal Adenocarcinoma Patients.
Frequency: 36.3%
References:1
References:1
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Comprehensive analysis of the impact of SNPs and CNVs on human microRNAs and their regulatory genes. Tissue effect on genetic control of transcript isoform variation. Fine-scale variation and genetic determinants of alternative splicing across individuals.
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nature The inheritance of the AC haplotype of rs1861972 – rs1861973 in en2, the C allele of rs1811399 in npas2, and the C allele of rs1234747 may contribute to autism by affecting microRNA rs1861972(A) + rs1861973(C) haplotype assoc. with '''protective''' effect against autism in a study of 818 Han Chinese (184 diag. autistics, 225 unrelated volunteers, 409 randomly selected) [OMIM:ENGRAILED 2; EN2]
Magnitude: 0
Frequency: 44.2%
References:63
Frequency: 44.2%
References:63
normal
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miRNA sequences and non-small cell lung cancer rs11614913 SNP in hsa-mir-196a2 was associated with survival in individuals with NSCLC. Specifically, survival was significantly decreased in individuals who were homozygous CC at SNP rs11614913. microRNA 1,009 breast cancer cases and 1,093 controls in a population of Chinese women *rs11614913 in hsa-mir-196a2 T>C 1.23; 95% confidence interval [CI], 1.02-1.48 *rs3746444 in hsa-mir-499 A>G OR 1.25; 95% CI, 1.02-1.51 Single nucleotide polymorphisms of microRNA machinery genes modify the risk of renal cell carcinoma. Genetic variations in microRNA-related genes are novel susceptibility loci for esophageal cancer risk. Signatures of purifying and local positive selection in human miRNAs. MicroRNA polymorphisms: the future of pharmacogenomics...
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nature The inheritance of the AC haplotype of rs1861972 – rs1861973, the C allele of rs1811399, and the C allele of rs1234747 may contribute to autism by affecting microRNA rs1861972(A) + rs1861973(C) haplotype assoc. with '''protective''' effect against autism in a study of 818 Han Chinese (184 diag. autistics, 225 unrelated volunteers, 409 randomly selected) [OMIM:ENGRAILED 2; EN2]
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nature The inheritance of the AC haplotype of rs1861972 – rs1861973, the C allele of rs1811399, and the C allele of rs1234747 may contribute to autism by affecting microRNA
normal
(hide)
microRNA 749 Swedish incident breast cancer cases with detailed clinical data and up to 15 years of follow-up together with 1493 matched controls. The strongest association was between the rs743554(T) allele of the ITGB4 gene and estrogen receptor negative (ER-) tumors (odds ratio 2.09, CI: 1.19-3.67) and worse survival compared to the wild type genotype carriers (hazard ratio [HR] 2.11, CI: 1.21-3.68). The poor survival was significantly associated with the aggressive tumour characteristics: high grade, lymph node metastasis and high stage.
Magnitude: 0
Frequency: 85.8%
Repute:Good
References:1
Frequency: 85.8%
Repute:Good
References:1
Magnitude: 0
Frequency: 86.4%
Repute:Good
References:0
Frequency: 86.4%
Repute:Good
References:0
common in complete genomics
(hide)
Association of the tag SNPs in the human SKT gene (KIAA1217) with lumbar disc herniation. Comprehensive analysis of the impact of SNPs and CNVs on human microRNAs and their regulatory genes.
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seems to have a microrna snp near 8q24 rs10109700 rs7832031 Comprehensive resequence analysis of a 136 kb region of human chromosome 8q24 associated with prostate and colon cancers.
Magnitude: 0
Frequency: 90.0%
Repute:Good
References:1
Frequency: 90.0%
Repute:Good
References:1
(hide)
seems to have a microrna snp near 8q24 rs10109700 rs7832031
Magnitude: 0
Frequency: 93.7%
Repute:Good
References:0
Frequency: 93.7%
Repute:Good
References:0
Magnitude: 0
Frequency: 96.9%
Repute:Good
References:0
Frequency: 96.9%
Repute:Good
References:0
Magnitude: 0
Frequency: 98.5%
Repute:Good
References:1
Frequency: 98.5%
Repute:Good
References:1
Magnitude: 0
Frequency: 99.1%
Repute:Good
References:2
Frequency: 99.1%
Repute:Good
References:2
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:0
Frequency: 100.0%
Repute:Good
References:0
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:1
Frequency: 100.0%
Repute:Good
References:1
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:0
Frequency: 100.0%
Repute:Good
References:0
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:0
Frequency: 100.0%
Repute:Good
References:0
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:1
Frequency: 100.0%
Repute:Good
References:1
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:1
Frequency: 100.0%
Repute:Good
References:1
common in complete genomics
(hide)
Comprehensive analysis of the impact of SNPs and CNVs on human microRNAs and their regulatory genes.
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:0
Frequency: 100.0%
Repute:Good
References:0
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:0
Frequency: 100.0%
Repute:Good
References:0
common in complete genomics
(hide)
Comprehensive analysis of the impact of SNPs and CNVs on human microRNAs and their regulatory genes.
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:0
Frequency: 100.0%
Repute:Good
References:0
common in complete genomics
(hide)
Comprehensive analysis of the impact of SNPs and CNVs on human microRNAs and their regulatory genes.
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in complete genomics
(hide)
endothelial dysfunction seen in hypertensive subjects. notable that the authors initiated their own dbsnp entry and cite the ss# in the abstract as well as relating to microRNA
59 snps
(hide) Mitochondrial Haplogroup
Magnitude: 3
Mitochondrial Haplogroup H3
European maternal ancestry. Mitochondrial Haplogroup H3 represents a smaller fraction of European genome than H1 but has a somewhat similar distribution with peak among Basques (13.9%), Galicians (8.3%) and Sardinians (8.5%). Its importance decreases towards the northeast of the continent ==See Also== *mtDNA Haplogroup H *i1000015 *i3001487 == Links == *Ian Logan's mtDNA Website *Wikipedia mtDNA
Magnitude: 1.5
Mitochondrial Haplogroup H
Haplogroup H probably evolved in West Asia ~30k years ago and arrived to Europe 20-25k years ago, spreading rapidly to the southwest of the continent. About one half of Europeans are of mtDNA haplogroup H. The haplogroup is also common in North Africa and the Middle East. The majority of the European populations have an overall haplogroup H frequency of 40%–50%. Frequencies decrease in the southeast of the continent, reaching 20% in the Near East and Caucasus, and <10% in the Persian Gulf, Northern India and Central Asia and up to the Northern reaches of Scandinavia. wikipedia provides more info. This is a mitochondrial haplogroup and a subclade of HV. haplograph provides this image *N **R ***R0 ****HV *****H
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haplogroups ,,,Palanichamy 2004 |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=HV |derived_haplogroup=H |ancestral_allele=T |derived_allele=C }}
G2706A+, probably MT-Haplogroup H. One of the 2 ancestral mitochondrial mutations needed for mitochondrial Haplogroup H. This is a non-synonymous mutation in the mitochondrial ribosome, and possibly in the neuroprotective protein humanin. Haplogroup H has been associated with increased risk of age-related neurological diseases, suggesting that this mutation (or some other) may slightly reduce the effectiveness of mitochondria or humanin.
(hide)
,,,Palanichamy 2004 |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=HV |derived_haplogroup=H |ancestral_allele=G |derived_allele=A }} More commonly known as G2706A, this is one of the two ancestral mitochondrial mutations that define Mitochondrial Haplogroup H. However, this is also a mutation which changes both the RNA of the mitochondrial ribosome (potentially changing its shape and function) and the protective protein humanin which is encoded from the RNA of the ribosome itself.
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haplogroups
Frequency: 100.0%
References:0
References:0
Frequency: 100.0%
References:0
References:0
(hide)
haplogroups
(hide)
haplogroups
References:0
References:0
References:0
References:0
References:0
(hide)
haplogroups
References:1
(hide)
|tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H2 |derived_haplogroup=H2b |ancestral_allele=T |derived_allele=C }}
A11467G-, not MT-Haplogroup U or K. Normal version of A11467G. Not mitochondrial Haplogroup U or K.
(hide)
More commonly known as A11467G, or 11467. One of 3 Mitochondrial mutations that together define Mitochondrial Haplogroup U, and its descendants. This is a synonymous change that still codes for the exact same amino acid, so it probably has no biological effect.
12308-, not MT-Haplogroup U or K. MT-L2 gene is normal, not mitochondrial haplogroup U or K. Possibly decreased risk of Age-related Macular Degeneration.
(hide)
Commonly known as A12308G or 12308, this is one of the three defining mitochondrial DNA mutations of Haplogroup U. G means Haplogroup U, A means not Haplogroup U. Medically, this is part of the mitochondrial tRNA gene MT-L2, responsible for building mitochondrial proteins containing the amino acid Leucine. This only affects the 13 proteins encoded by mitochondrial DNA, not the thousands of other mitochondrial proteins encoded by the normal DNA in the nucleus.
G12372A-, not MT-Haplogroup U or K Normal healthy mitochondrial SNP. Not Mitochondrial Haplogroup U or K.
(hide)
More commonly known as G12372A, or just 12372. One of the 3 SNPs that defines Mitochondrial Haplogroup U and its descendants. The minor allele is synonymous, so it makes no biological difference.
common on affy axiom data
(hide)
haplogroups ,,Shen 2004 |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H |derived_haplogroup=H1 |ancestral_allele=G |derived_allele=A }}
Magnitude: 0
Frequency: 85.9%
References:1
Frequency: 85.9%
References:1
Magnitude: 0
Frequency: 88.5%
Repute:Good
References:0
Frequency: 88.5%
Repute:Good
References:0
Magnitude: 0
Frequency: 89.1%
Repute:Good
References:0
Frequency: 89.1%
Repute:Good
References:0
Magnitude: 0
Frequency: 89.2%
Repute:Good
References:0
Frequency: 89.2%
Repute:Good
References:0
Magnitude: 0
Frequency: 89.2%
Repute:Good
References:0
Frequency: 89.2%
Repute:Good
References:0
Magnitude: 0
Frequency: 90.8%
Repute:Good
References:0
Frequency: 90.8%
Repute:Good
References:0
Magnitude: 0
Frequency: 92.3%
Repute:Good
References:0
Frequency: 92.3%
Repute:Good
References:0
Magnitude: 0
Frequency: 95.3%
Repute:Good
References:0
Frequency: 95.3%
Repute:Good
References:0
common on affy axiom data
(hide)
haplogroups |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H |derived_haplogroup=H2 |ancestral_allele=G |derived_allele=A }}
Magnitude: 0
Frequency: 95.4%
Repute:Good
References:0
Frequency: 95.4%
Repute:Good
References:0
(hide)
haplogroups ,Carelli 2006 |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H2 |derived_haplogroup=H2a |ancestral_allele=G |derived_allele=A }}
Magnitude: 0
Frequency: 96.8%
Repute:Good
References:0
Frequency: 96.8%
Repute:Good
References:0
Magnitude: 0
Frequency: 96.9%
Repute:Good
References:0
Frequency: 96.9%
Repute:Good
References:0
Magnitude: 0
Frequency: 96.9%
Repute:Good
References:0
Frequency: 96.9%
Repute:Good
References:0
common on affy axiom data
(hide)
Two novel pathogenic mitochondrial DNA mutations affecting organelle number and protein synthesis. Is the tRNA(Leu(UUR)) gene an etiologic hot spot? Mutational analysis of the mitochondrial 12S rRNA gene in Chinese pediatric subjects with aminoglycoside-induced and non-syndromic hearing loss. The role of selection in the evolution of human mitochondrial genomes.
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:0
Frequency: 100.0%
Repute:Good
References:0
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:0
Frequency: 100.0%
Repute:Good
References:0
Magnitude: 0
Frequency: 100.0%
References:0
Frequency: 100.0%
References:0
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:0
Frequency: 100.0%
Repute:Good
References:0
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:0
Frequency: 100.0%
Repute:Good
References:0
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:0
Frequency: 100.0%
Repute:Good
References:0
(hide)
haplogroups
(hide)
haplogroups
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
References:0
References:0
common on affy axiom data
(hide)
haplogroups ,Carelli 2006 |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H2a |derived_haplogroup=H2a2 |ancestral_allele=G |derived_allele=A }}
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
(hide)
|tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H1 |derived_haplogroup=H1c |ancestral_allele=T |derived_allele=C }}
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
(hide)
haplogroups |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H1 |derived_haplogroup=H1a |ancestral_allele=A |derived_allele=G }}
Magnitude: 0
References:0
References:0
(hide)
haplogroups
(hide)
haplogroups
2 genosets 83 snps
(hide) MtDNA Haplogroup
Magnitude: 1.5
Mitochondrial Haplogroup H
Haplogroup H probably evolved in West Asia ~30k years ago and arrived to Europe 20-25k years ago, spreading rapidly to the southwest of the continent. About one half of Europeans are of mtDNA haplogroup H. The haplogroup is also common in North Africa and the Middle East. The majority of the European populations have an overall haplogroup H frequency of 40%–50%. Frequencies decrease in the southeast of the continent, reaching 20% in the Near East and Caucasus, and <10% in the Persian Gulf, Northern India and Central Asia and up to the Northern reaches of Scandinavia. wikipedia provides more info. This is a mitochondrial haplogroup and a subclade of HV. haplograph provides this image *N **R ***R0 ****HV *****H
(hide)
haplogroups ,,,Palanichamy 2004 |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=HV |derived_haplogroup=H |ancestral_allele=T |derived_allele=C }}
G2706A+, probably MT-Haplogroup H. One of the 2 ancestral mitochondrial mutations needed for mitochondrial Haplogroup H. This is a non-synonymous mutation in the mitochondrial ribosome, and possibly in the neuroprotective protein humanin. Haplogroup H has been associated with increased risk of age-related neurological diseases, suggesting that this mutation (or some other) may slightly reduce the effectiveness of mitochondria or humanin.
(hide)
,,,Palanichamy 2004 |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=HV |derived_haplogroup=H |ancestral_allele=G |derived_allele=A }} More commonly known as G2706A, this is one of the two ancestral mitochondrial mutations that define Mitochondrial Haplogroup H. However, this is also a mutation which changes both the RNA of the mitochondrial ribosome (potentially changing its shape and function) and the protective protein humanin which is encoded from the RNA of the ribosome itself.
Frequency: 100.0%
References:0
References:0
Frequency: 100.0%
References:0
References:0
Frequency: 100.0%
References:0
References:0
(hide)
haplogroups
Frequency: 100.0%
References:0
References:0
(hide)
haplogroups
(hide)
,23andMe |tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H1a |derived_haplogroup=H1b |ancestral_allele=T |derived_allele=G }}
(hide)
haplogroups
(hide)
This version of the test for rCRS position 16166 tests for ether A or G.
References:0
References:0
References:0
References:0
References:0
References:1
(hide)
|tree=PhyloTree |tree_build=7 |ancestral_haplogroup=H2 |derived_haplogroup=H2b |ancestral_allele=T |derived_allele=C }}
A11467G-, not MT-Haplogroup U or K. Normal version of A11467G. Not mitochondrial Haplogroup U or K.
(hide)
More commonly known as A11467G, or 11467. One of 3 Mitochondrial mutations that together define Mitochondrial Haplogroup U, and its descendants. This is a synonymous change that still codes for the exact same amino acid, so it probably has no biological effect.
12308-, not MT-Haplogroup U or K. MT-L2 gene is normal, not mitochondrial haplogroup U or K. Possibly decreased risk of Age-related Macular Degeneration.
(hide)
Commonly known as A12308G or 12308, this is one of the three defining mitochondrial DNA mutations of Haplogroup U. G means Haplogroup U, A means not Haplogroup U. Medically, this is part of the mitochondrial tRNA gene MT-L2, responsible for building mitochondrial proteins containing the amino acid Leucine. This only affects the 13 proteins encoded by mitochondrial DNA, not the thousands of other mitochondrial proteins encoded by the normal DNA in the nucleus.
G12372A-, not MT-Haplogroup U or K Normal healthy mitochondrial SNP. Not Mitochondrial Haplogroup U or K.
(hide)
More commonly known as G12372A, or just 12372. One of the 3 SNPs that defines Mitochondrial Haplogroup U and its descendants. The minor allele is synonymous, so it makes no biological difference.
Magnitude: 0
Frequency: 85.9%
References:1
Frequency: 85.9%
References:1
Magnitude: 0
Frequency: 88.5%
Repute:Good
References:0
Frequency: 88.5%
Repute:Good
References:0
Magnitude: 0
Frequency: 89.1%
Repute:Good
References:0
Frequency: 89.1%
Repute:Good
References:0
Magnitude: 0
Frequency: 89.2%
Repute:Good
References:0
Frequency: 89.2%
Repute:Good
References:0
Magnitude: 0
Frequency: 89.2%
Repute:Good
References:0
Frequency: 89.2%
Repute:Good
References:0
Magnitude: 0
Frequency: 90.8%
Repute:Good
References:0
Frequency: 90.8%
Repute:Good
References:0
Magnitude: 0
Frequency: 92.3%
Repute:Good
References:0
Frequency: 92.3%
Repute:Good
References:0
Magnitude: 0
Frequency: 95.3%
Repute:Good
References:0
Frequency: 95.3%
Repute:Good
References:0
Magnitude: 0
Frequency: 95.4%
Repute:Good
References:0
Frequency: 95.4%
Repute:Good
References:0
Magnitude: 0
Frequency: 96.8%
Repute:Good
References:0
Frequency: 96.8%
Repute:Good
References:0
Magnitude: 0
Frequency: 96.9%
Repute:Good
References:0
Frequency: 96.9%
Repute:Good
References:0
Magnitude: 0
Frequency: 96.9%
Repute:Good
References:0
Frequency: 96.9%
Repute:Good
References:0
common on affy axiom data
(hide)
Two novel pathogenic mitochondrial DNA mutations affecting organelle number and protein synthesis. Is the tRNA(Leu(UUR)) gene an etiologic hot spot? Mutational analysis of the mitochondrial 12S rRNA gene in Chinese pediatric subjects with aminoglycoside-induced and non-syndromic hearing loss. The role of selection in the evolution of human mitochondrial genomes.
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:0
Frequency: 100.0%
Repute:Good
References:0
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:0
Frequency: 100.0%
Repute:Good
References:0
Magnitude: 0
Frequency: 100.0%
References:0
Frequency: 100.0%
References:0
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:0
Frequency: 100.0%
Repute:Good
References:0
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:0
Frequency: 100.0%
Repute:Good
References:0
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haplogroups
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
References:0
References:0
1 genoset 116 snps
(hide) Musical aptitude
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Strongest association for ability to discriminate sound patterns found in study of 767 Finnish individuals belonging in 76 families , involved in musical aptitude. Posterior probability of LD 70% to trait Karma Music Test KMT. Long non-coding RNA not linked to any known gene, that may have expression in human brain. Near LRRIQ3 Leucine-rich repeats and IQ motif containing 3. A genome-wide linkage and association study of musical aptitude identifies loci containing genes related to inner ear development and neurocognitive functions
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Region with strongest linkage for ability to discriminate pitch found in study of 767 Finnish individuals belonging in 76 families , involved in musical aptitude. Posterior Probability of Linkage given as 86% to trait Carl Seashore's subtest of pitch (SP). Located next to the region harboring the protocadherin 7 gene, PCDH7 which has been suggested to play a role in cochlear and amygdaloid complexes. This SNP is in LIMCH1 LIM and calponin homology domains 1 gene, which is thought to be unlikely to be responsible, probably a combination of SNP's frequently inherited with it are involved. The study suggests rs13146789 in PCDH7 as one likely causal variant. A genome-wide linkage and association study of musical aptitude identifies loci containing genes related to inner ear development and neu...
Frequency: 54.5%
References:1
References:1
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Strong association for ability to discriminate pitch found in Finnish study of 767 individuals belonging in 76 families . Posterior probability of LD given as 34% to trait Carl Seashore's subtest of pitch SP, but 84% to overall tested musical aptitude. Situated in protocadherin 7 gene, PCDH7 which has been suggested to play a role in cochlear and amygdaloid complexes. A genome-wide linkage and association study of musical aptitude identifies loci containing genes related to inner ear development and neurocognitive functions
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Strongest association with combined capacities for music perception (pitch, duration, sound patterns) found in study of 767 Finnish individuals belonging in 76 families , involved in musical aptitude. Posterior probability of LD 98%. This region is located a few dozen kilobases upstream of the GATA binding protein 2 GATA2 gene. GATA2 regulates the development of cochlear hair cells and the inferior colliculus (IC), which are important in tonotopic mapping. SNP is surrounded by known regulatory regions, and may itself be in one. A genome-wide linkage and association study of musical aptitude identifies loci containing genes related to inner ear development and neurocognitive functions
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Category:needs help Category:interestingThis paper implicates this snp as playing a role in heart disease. Having a G at this position is considered normal. Having an A at this position reduces the risk of heart disease. Approximate 15% of all people carry this allele. '''Technical note:''' This applies to many other snps, but here is the first clean case I've encountered. dbsnp shows ss3839 and ss16241517 are being read 'fwd' ss16940640 and ss44449258 are being read in 'rev'. This has C/T alleles when read forward, and A/G when read in reverse. Since the authors of the paper above describe this as an A/G snp, it seems they are reading in reverse. Often papers include even less information, and can leave some ambiguity about these important details. GATA2 is associated with familial early-...
5 snps
(hide) NAT2
NAT2 Rapid metabolizer.
NAT2 Rapid metabolizer source This is ostensibly the 'normal' type of metabolizer, who carries two rapid (active) acetylator alleles such as NAT2*4. NAT2 rapid acetylators can be typically be administered drugs which are substrates of the NAT2 enzyme following standard dosing practices. This prediction and that of gs154 of NAT2 metabolizer phenotype is based on using 2 SNPs, rs1041983 and rs1801280. An alternative prediction of NAT2 metabolizer status based on using more SNPs (6) is used by genosets gs138, gs139, and gs140.
Magnitude: 1.5
NAT2 intermediate metabolizer
NAT2 Intermediate metabolizer source Generally this means a person is carrying one rapid (normal) NAT2 allele plus one slow allele. This appears to be the most common form. Intermediate acetylators may benefit by slightly lower than average drug dosages of the drugs metabolized by NAT2 for optimal therapeutic response.
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rs1208 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The risk allele for this SNP is rs1208(G). [PharmGKB:Curated in vitro study; PK: 20-fold reduction in Vmax vs wild type] [OMIM:?]
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rs1799929 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The risk allele for this SNP is rs1799929(T). When this SNP is indicative of carrying a NAT2*5A allele, the following may be relevant: A study (based on only 42 patients) found that women with the NAT2*5A slow genotype (which presumably means rs1799929(T;T)) had a significantly higher risk of cervical cancer compared with individuals with the NAT2*5A fast genotype (i.e. carriers of only one rs1799929(T) allele), with a reported odds ratio of 7.469 (CI: 1.6-33.3, p=0.008). [PharmGKB:Curated in vitro study; PK: 20-fold reduction...
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rs1801280, also known as T341C, is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The allele associated with slow NAT2 metabolization for this SNP is rs1801280(C). Genosets gs154 and gs156 evaluate predicated NAT2 metabolizer phenotype based on rs1041983 and rs1801280. [PharmGKB:Curated in vitro study; PK: 20-fold reduction in Vmax vs wild type] [OMIM:?]
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rs1041983, also known as C282T, is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The allele associated with slow NAT2 metabolization for this SNP is rs1041983(T). Genosets gs154 and gs156 evaluate predicated NAT2 metabolizer phenotype based on rs1041983 and rs1801280. [PharmGKB:Curated in vitro study; PK: 22-fold reduction in Vmax vs wild type]
common in complete genomics Predicted to be a NAT2 slow metabolizer.
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With 99% sensitivity and 95% specificity, at least in Caucasian populations, rs1495741 is reported to classify the NAT2 phenotype of an individual; it therefore is a candidate to replace the 7-SNP panel used in genosets such as gs138, gs139, and gs140. The rs1495741(A;A), (A;G) and (G;G) genotypes predicted slow, intermediate, and rapid NAT2 acetylation phenotypes, respectively. [GWAS:None]
Normal common for Caucasians on the 23andme platform
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rs1799930 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. Also known as G590A. The risk allele for this SNP is rs1799930(A). [PharmGKB:Curated in vitro study; PK: 22-fold reduction in Vmax vs wild type] [OMIM:?]
common in complete genomics common for Caucasians on the 23andme platform
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rs1801279 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The risk allele for this SNP is rs1801279(A). [PharmGKB:Curated Homozygous A allele is slow acetylator phenotype (altered rates of metabolism of arylamines). May be associated with higher risk for bladder cancer and lower risk for colorectal cancer.]
common in clinvar
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rs1799931 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The risk allele for this SNP is rs1799931(A). [PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: The NAT2:rs1799931 G variant was associated with toxicity in response to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.003 Type of association: CO; TOX] [OMIM:?]
common in complete genomics
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[PharmGKB:Curated Homozygous A allele is slow acetylator phenotype.]
2 genosets 12 snps
(hide) NatGeo
reduced risk (0.84x) for late-onset (adult) asthma Found in 38% of all Caucasions, this genotype is associated with a reduced risk (relative risk = 0.84) for late-onset (adult) asthma.
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rs1837253 is a SNP found a bit upstream of the thymic stromal lymphopoietin TSLP gene on chromosome 5. The TSLP protein plays a role in inflammation of cells in the trachea and alveoli therefore may have a causative role in certain types of asthma. The rs1837253(T) allele has been found to reduce the risk of developing late-onset (adult) asthma in several studies, and it is recognized by the CPMC Study as one they report to their participants. [GWAS:None]
Normal risk of sexual dysfunction when taking SSRI Antidepressants.
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rs6311 (-1438A>G / A-1438G or -1438G>A / G-1438A) is a SNP located upstream (and within the promoter region of) HTR2A. Multiple Regulatory Variants Modulate Expression of 5-Hydroxytryptamine 2A Receptors in Human Cortex. The minor A allele of rs6311 reduces expression of a previously unannotated extension of the 5' untranslated region of HTR2A mRNA. rs6311 together with rs6314 have a modest effect on depression severity, when examined in the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) study. Three (rs643627-rs594242-rs6311: A-C-T), two (rs594242-rs6311: C-T) and a single functional (rs6311: T) marker were protective against suicidal behavior. The complementary markers (rs594242-rs6311: G-C and rs6311: C) were associated with increased risk for non-violent and impu...
1.3x increased risk for Crohn's disease with ileal involvement
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rs3814570 is a SNP in the transcription factor 7-like 2 (T-cell specific, HMG-box) TCF7L2 gene. A study of 784 Crohn's disease patients with ileal involvement concluded that rs3814570 was associated with increased risk, but not with risk for colonic Crohn's disease or ulcerative colitis. The odds ratio was 1.27 (CI: 1.07 - 1.52, p = 0.00737). Evidence for association between polycystic ovary syndrome (PCOS) and TCF7L2 and glucose intolerance in women with PCOS and TCF7L2.
Magnitude: 1.5
Frequency: 63.3%
Repute:Bad
References:1
Frequency: 63.3%
Repute:Bad
References:1
Slightly increased risk of developing prostate cancer
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rs13149290 is one of seven SNPs found in a combined study of over 1,000 patients to be associated with increased risk for prostate cancer. The risk allele for this SNP is (C); and while the odds ratio was not specifically reported, the probability of false significance (not permuted though) was given as p=2.5 x 10e-5, using a dominant model of risk.
Magnitude: 1.25
Frequency: 55.8%
References:0
Frequency: 55.8%
References:0
Very common. Normal risk of Parkinson's disease. Approximately 55% of non-asian people have this genotype which is associated with slightly higher risk of Parkinson's disease when compared to genotype (G;G). It is notable because it is the first SNP patented by 23andMe rs10513789(T) increased risk of developing Parkinson's Disease GenomicsLawReport
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23andMe reports that the G allele of rs10513789 is associated with 0.8 times lower odds of Parkinson's disease. 23andMe has a patent covering this snp. http://blog.23andme.com/2012/05/28/announcing-23andmes-first-patent/ See also gs249 and gs248
more likely to go bald more likely to go bald
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Along with rs201571 serves as a proxy for rs1160312. related to baldness
Frequency: 0.0%
References:2
References:2
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rs12467557 increases susceptibility to Substance dependence, Nicotine 1.81 times for carriers of the C allele
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[GWAS:None]
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[PharmGKB:Curated This variant is significantly associated with late-onset Alzheimer disease (LOAD) in a GWAS study with 492 LOAD cases and 498 cognitive controls using Illumina's HumanHap550 beadchip.]
Frequency: 4.4%
References:1
References:1
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[GWAS:None]
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[GWAS:None]
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rs231725 associated with primary biliary cirrhosis
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[GWAS:None]
Frequency: 7.9%
References:2
References:2
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[GWAS:None]
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[GWAS:None]
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[PharmGKB:Curated This variant is associated with hip bone size in a genome-wide association study (GWAS) consisting of 1,000 homogeneous unrelated Caucasian subjects.]
Frequency: 9.7%
References:1
References:1
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[PharmGKB:Curated In a GWAS of 3497 Dutch subjects from the Netherlands Study of Depression and Anxiety or from the Netherlands Twin Registry, this SNP was found to be associated with Current Smoking (p = 0.00008365;OR for minor allele G:1.212).]
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[GWAS:None]
Frequency: 11.5%
References:1
References:1
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[GWAS:None]
Frequency: 12.4%
References:1
References:1
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
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mentioned by gs240
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[GWAS:None]
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[GWAS:None]
if less milk in teenage females, less bone?
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A very small study of 117 healthy European peri- and postmenarcheal girls (14.9 +/- 1.6 years) were followed for 4 years along with their calcium intake. Girls with rs4516035(C;T) and (C;C) genotypes had 13% lower spine mineral content if their milk intakes were below 260 mL/day, compared to either genotype-matched girls with higher milk intakes or to girls with the (T;T) genotype. If this is real, it suggests that rs4516035(C;T) and (C;C) female teens need more milk than rs4516035(T;T) girls to have optimal bone density. rs4516035 and the more aggressive tumour location in head-neck and trunk (OR=1.54, p=0.020)
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[GWAS:None]
Frequency: 19.5%
References:1
References:1
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[GWAS:None]
Frequency: 19.5%
References:0
References:0
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[GWAS:None]
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finds no association between rs11832 and pulmonary emphysema
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[GWAS:None]
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[GWAS:None]
0.74x decreased risk for Non-hodgkin's lymphoma
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rs4833103 is a SNP located in a cluster of toll-like receptor genes. In a pooled analysis including three population-based case-control studies of Non-Hodgkin's lymphoma (1,946 cases, 1,808 controls), two SNPs in moderate linkage disequilibrium were significantly associated with NHL: rs10008492 (odds ratio for (C;T) genotype 1.12, CI: 0.97-1.30; OR(T;T) 1.40, CI: 1.15-1.71; p(trend)=0.001) and rs4833103 (OR(A;C) 0.75, CI: 0.64-0.88; OR(A;A) 0.74, CI: 0.62-0.90; p(trend)=0.002; p(dominant)=0.0002).
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Associated with bipolar disorder in individuals of European ancestry. [GWAS:Bipolar disorder and schizophrenia]
Frequency: 22.0%
References:1
References:1
Frequency: 22.1%
References:2
References:2
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[GWAS:None]
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[GWAS:None]
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[GWAS:Cardiac Troponin-T levels]
Frequency: 23.0%
References:1
References:1
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[GWAS:None]
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This SNP was associated with amyotrophic lateral sclerosis (ALS) based on a study of 1,152 patients.
~10% more likely to respond to citalopram
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rs1954787, located in an intron of the GRIK4 gene, was found to be associated with a somewhat increased rate of successful response to treatment of depression with the drug citalopram. From the abstract of this article: 'The effect size of (this) GRIK4 marker alone was modest, but homozygote carriers of the treatment-response-associated marker alleles of both the GRIK4 and HTR2A (see rs7997012) genes were 23% less likely to experience nonresponse to (citalopram) treatment relative to participants who did not carry any of these marker alleles.' * See also Anxiety Blog posting [PharmGKB:Curated A study in 1,816 eligible patients from the STAR*D cohort found that genetic variation in a kainic acid-type glutamate receptor is reproducibly associated with response to the antidepressant citalopr...
Frequency: 25.7%
References:1
References:1
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
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Genomewide association study for susceptibility genes contributing to familial Parkinson disease.
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association with restless leg syndrome
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[GWAS:None]
Frequency: 28.3%
References:1
References:1
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Association study of polymorphisms in the excitatory amino acid transporter 2 gene (SLC1A2) with schizophrenia.
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[GWAS:None]
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A second-generation genomewide screen for asthma-susceptibility alleles in a founder population. [GWAS:None]
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[GWAS:None]
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discussed in nature Single nucleotide polymorphisms of microRNA machinery genes modify the risk of renal cell carcinoma. Genetic variations in microRNA-related genes are novel susceptibility loci for esophageal cancer risk. Comprehensive analysis of the impact of SNPs and CNVs on human microRNAs and their regulatory genes. Genetic Polymorphisms in MicroRNA-Related Genes as Predictors of Clinical Outcomes in Colorectal Adenocarcinoma Patients.
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[GWAS:None]
Frequency: 29.5%
References:1
References:1
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[GWAS:None]
Frequency: 30.1%
References:1
References:1
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[GWAS:None]
Frequency: 31.0%
References:1
References:1
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23andMe blog multiple sclerosis rs17066096 IL22RA2 G 1.14 [GWAS:None]
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[PharmGKB:Curated This variant is associated with end-of-induction minimal risidual disease (MRD) in childhood acute lymphoblastic leukemia (ALL) from 2 independent cohorts (GWAS result). Risk Allele: T, MAF= 0.40, combined P value= 5.62E-04.]
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[GWAS:None]
Frequency: 31.5%
References:2
References:2
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
Frequency: 33.6%
References:1
References:1
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[GWAS:Periodontal disease-related phenotypes]
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rs1741981 and rs2547547 influence risk for postoperative hepatocellular carcinoma tumor recurrence up to 2.2x Detection of fetomaternal genotype associations in early-onset disorders: evaluation of different methods and their application to childhood leukemia.
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[GWAS:Breast cancer]
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[PharmGKB:Curated This variant is significantly associated with late-onset Alzheimer disease (LOAD) in a GWAS study with 492 LOAD cases and 498 cognitive controls using Illumina's HumanHap550 beadchip.]
Frequency: 35.4%
References:1
References:1
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[PharmGKB:Curated This variant is significantly associated with late-onset Alzheimer disease (LOAD) in a GWAS study with 492 LOAD cases and 498 cognitive controls using Illumina's HumanHap550 beadchip.]
Frequency: 35.4%
References:1
References:1
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
Frequency: 37.2%
References:4
References:4
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[GWAS:Adiponectin levels]
Frequency: 37.2%
References:2
References:2
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the rs1411766 locus may be commonly involved in conferring susceptibility to diabetic nephropathy among subjects with type 1 or type 2 diabetes across different ethnic groups.
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Comprehensive follow-up of the first genome-wide association study of multiple sclerosis identifies KIF21B and TMEM39A as susceptibility loci. [GWAS:None]
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[GWAS:None]
Frequency: 38.1%
References:1
References:1
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
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[PharmGKB:Curated Risk or phenotype-associated allele: not stated Phenotype: Using a Quantitative Transmission Disequilibrium Test (QTDT), this variant was significantly associated with etoposide toxicity based upon IC50 values in cell lines from 30 parent-child trios. Study size: 89. Study population/ethnicity: 89 Yorubans. Significance metric(s): p = 0.00003. Type of association: FA; GN.]
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[GWAS:None]
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[GWAS:None]
Frequency: 38.9%
References:0
References:0
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
Frequency: 39.8%
References:1
References:1
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
Frequency: 40.2%
References:1
References:1
Frequency: 40.2%
Repute:Bad
References:5
Repute:Bad
References:5
1.19x increased risk for T2D
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rs11868035 is one of several SNPs associated with the SREBF1 gene that show a modest association with type-2 diabetes. A study of ~2,000 Caucasian patients (and 10,000+ controls) led to an odds ratio of 1.19 (CI: 1.07-1.33, p=0.002) for the minor (risk) allele, rs11868035(A), in the orientation as in dbSNP. type-2 diabetes rs2297508(C) and rs11868035(C) This SNP rs11868035 and rs1057217 are associated with increased risk of schizophrenia in German and Scandinavian samples. This SNP and rs6812193 are reported to affect risk of Parkinson's disease. plos Polymorphisms in the gene encoding sterol regulatory element-binding factor-1c are associated with type 2 diabetes. [PharmGKB:Curated This SNP in the SREBF1 gene was strongly associated with schizophrenia in German, Danish and Norwegian samp...
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[PharmGKB:Curated In a GWAS of 3497 Dutch subjects from the Netherlands Study of Depression and Anxiety or from the Netherlands Twin Registry, this SNP was found to be associated with Current Smoking (p = 0.0000151;OR for minor allele C:0.785).]
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[GWAS:None]
Frequency: 40.7%
References:1
References:1
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[PharmGKB:Curated In a GWAS of 3497 Dutch subjects from the Netherlands Study of Depression and Anxiety or from the Netherlands Twin Registry, this SNP was found to be associated with Smoking Initiation (p = 0.00007691; OR for minor allele A:1.256)]
Frequency: 40.7%
References:3
References:3
Frequency: 40.7%
References:1
References:1
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Chromosome 15q25.1 genetic markers associated with level of response to alcohol in humans.
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[GWAS:None]
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ADHD GIT1 is associated with ADHD in humans and ADHD-like behaviors in mice
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
Frequency: 41.5%
References:1
References:1
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[GWAS:None]
Frequency: 41.6%
References:1
References:1
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Identification of a novel risk locus for progressive supranuclear palsy by a pooled genomewide scan of 500,288 single-nucleotide polymorphisms. [GWAS:None]
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rs4693596(C;C) 2x odds of myopathy when taking statins. Statin Response
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
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[PharmGKB:Curated Risk or phenotype-associated allele: A allele. Phenotype: The A allele rs2894342, which lies in the promoter of MLN, is associated with carbamazepine (CBZ)-induced maculopapular exanthema (MPE)/ hypersensitivity syndrome (HSS). Study size: 175. Study population/ethnicity: 31 CBZ-induced MPE/HSS cases and 144 CBZ-tolerant controls of Chinese descent. Significance metric(s): p = 0.00342, OR = 2.88. Type of association: GN; PD; TOX; ADR.]
Frequency: 42.9%
References:1
References:1
Frequency: 42.9%
References:1
References:1
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[GWAS:None]
Frequency: 43.1%
References:0
References:0
Frequency: 43.4%
References:3
References:3
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[GWAS:None]
Frequency: 43.8%
References:1
References:1
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[GWAS:None]
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[GWAS:Height]
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[GWAS:None]
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[GWAS:None]
Frequency: 44.2%
References:1
References:1
Frequency: 44.2%
References:2
References:2
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[GWAS:None]
Frequency: 44.2%
References:1
References:1
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[GWAS:None]
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[GWAS:None]
Frequency: 45.1%
References:1
References:1
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[GWAS:None]
Frequency: 45.1%
References:1
References:1
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
Frequency: 46.0%
References:1
References:1
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[GWAS:None]
Frequency: 46.0%
References:1
References:1
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[GWAS:None]
Frequency: 46.0%
References:1
References:1
1.4x increased gastric cancer risk. Increased risk of Acute Graft-Versus-Host Disease after Unrelated Bone Marrow Transplantation
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rs2275913, also known as G-197A, is a SNP in the IL17A gene. A study of 811 Japanese subjects (524 without gastric cancer and 287 with gastric cancer) reported an odds ratio of 1.42 (CI: 1.09-1.85, p=0.01) for the rs2275913(A) allele, and 3.02 (CI: 1.86-4.91, p<0.0001) for the (A;A) genotype, with gastric cancer. This 'A'-allele of this SNP is also functionally associated with acute Graft-Versus-Host Disease after unrelated bone marrow transplantation
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[GWAS:Cognitive performance]
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[GWAS:None]
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[PharmGKB:Curated Risk or phenotype-associated allele: not stated Phenotype: Using a Quantitative Transmission Disequilibrium Test (QTDT), this variant was significantly associated with etoposide toxicity based upon IC50 values in cell lines from 30 parent-child trios. Study size: 176. Study population/ethnicity: 87 European descent Caucasians and 89 Yorubans. Significance metric(s): p = 0.00007. Type of association: FA; GN.]
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[GWAS:None]
Frequency: 46.4%
References:6
References:6
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Association of Toll-like receptor 4 gene polymorphisms with normal tension glaucoma. Association analysis of Toll-like receptor 4 polymorphisms with autoimmune pancreatitis. Lack of association between toll-like receptor 4 gene polymorphisms and sarcoidosis-related uveitis in Japan. Traffic-related air pollution, oxidative stress genes, and asthma (ECHRS). Sequence variants in the TLR4 and TLR6-1-10 genes and prostate cancer risk. Results based on pooled analysis from three independent studies.
Frequency: 46.4%
References:0
References:0
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The enabled homolog gene polymorphisms are associated with susceptibility and progression of childhood IgA nephropathy.
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[GWAS:None]
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[GWAS:None]
Frequency: 46.8%
References:1
References:1
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[PharmGKB:Curated Risk or phenotype-associated allele: not stated Phenotype: Using a Quantitative Transmission Disequilibrium Test (QTDT), this variant was significantly associated with etoposide toxicity based upon IC50 values in cell lines from 30 parent-child trios. Study size: 87. Study population/ethnicity: 87 European descent Caucasians. Significance metric(s): p = 0.00006. Type of association: FA; GN.]
Frequency: 46.9%
References:0
References:0
(hide)
[GWAS:None]
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[PharmGKB:Curated This SNP on 5p14.1 was associated with autism spectrum disorder in a combined analysis of four GWAS data sets with a total of more than 10,000 subjects of European ancestry. This SNP is in an intergenic region between CDH10 and CDH9 that contains several highly conserved genomic elements.]
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
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[GWAS:None]
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[PharmGKB:Curated Risk or phenotype-associated allele: not stated Phenotype: Using a Quantitative Transmission Disequilibrium Test (QTDT), this variant was significantly associated with etoposide toxicity based upon IC50 values in cell lines from 30 parent-child trios. Study size: 176. Study population/ethnicity: 87 European descent Caucasians and 89 Yorubans. Significance metric(s): p = 0.00009. Type of association: FA; GN.]
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[GWAS:None]
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[PharmGKB:Curated Risk or phenotype-associated allele: A Phenotype: This SNP was associated with a greater reduction in total cholesterol after at least 1 week of statin use. This was not replicated in a second cohort. Study size: 546 (original cohort); 100 (replication cohort). Study population/ethnicity: People taking statins; age 55 or older; Rotterdam Study; Netherlands. Significance metric(s): p = 0.05 (original); p = 0.975 (replication) Type of association: PD.]
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[GWAS:None]
Frequency: 47.8%
References:1
References:1
(hide)
[PharmGKB:Curated In a GWAS of 3497 Dutch subjects from the Netherlands Study of Depression and Anxiety or from the Netherlands Twin Registry, this SNP was found to be associated with Smoking Initiation (p = 0.00004278; OR for minor allele C:1.255)]
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[GWAS:None]
Frequency: 48.2%
References:1
References:1
(hide)
[GWAS:None]
(hide)
[GWAS:None]
Frequency: 48.6%
References:1
References:1
Frequency: 48.7%
References:5
References:5
(hide)
This SNP was identified as a 'core' SNP helping to define one (of nine total) runs of homozygosity (ROH) potentially associated with increased risk for schizophrenia. Each region consists of at least 100 consecutive SNPs, generally spanning 500KB or more, for which both chromosomes in an individual were homozygous. The overall odds ratio for schizophrenia associated with inheriting 1, 2, or 3 of these 9 ROHs was calculated to be 3.3, 5.4, or 24, respectively, with 95% confidence intervals of (1.9-5.7), (3.7-16.1), and (6.9-83.9), respectively. This particular SNP, rs7582658, was deemed to be the core SNP of a region on chromosome 2 with 274 SNPs spanning 2282KB from 2:188489676 to 2:190772106 (build 35). Potentially independent of the ROH, the risk allele for this SNP in the orientation as...
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[GWAS:None]
Frequency: 49.6%
References:1
References:1
(hide)
[GWAS:None]
(hide)
[GWAS:None]
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[GWAS:None]
Frequency: 50.4%
References:1
References:1
(hide)
[PharmGKB:Curated In a GWAS of 3497 Dutch subjects from the Netherlands Study of Depression and Anxiety or from the Netherlands Twin Registry, this SNP was found to be associated with Smoking Initiation (p = 0.000004333; OR for minor allele T:0.786)]
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(C;C) greater odds of longevity Replication of an association of variation in the FOXO3A gene with human longevity using both case-control and longitudinal data. Association of the FOXO3A locus with extreme longevity in a southern Italian centenarian study.
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Meta-analysis of three genome-wide association studies identifies susceptibility loci for colorectal cancer at 1q41, 3q26.2, 12q13.13 and 20q13.33.
Frequency: 51.3%
References:1
References:1
Frequency: 51.3%
References:1
References:1
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[PharmGKB:Curated Risk or phenotype-associated allele: A allele. Phenotype: Decreased fasting insulin. Study size: 4681. Study population/ethnicity: Replication study of Swedish control subjects. Significance metric(s): p = 0.001. Type of association: FA; GN.]
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[GWAS:None]
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[GWAS:None]
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Gene-environment interaction effects on the development of immune responses in the 1st year of life. Algorithm for automatic genotype calling of single nucleotide polymorphisms using the full course of TaqMan real-time data. A functional SNP of interferon-gamma gene is important for interferon-alpha-induced and spontaneous recovery from hepatitis C virus infection. Interferon gamma allelic variants: sex-biased multiple sclerosis susceptibility and gene expression. Host genetic factors and vaccine-induced immunity to hepatitis B virus infection. A single nucleotide polymorphism (A --> G) in intron 3 of IFNgamma gene is associated with asthma. Host genetic factors and vaccine-induced immunity to HBV infection: haplotype analysis. IFNG genotype and sex interact to influence the risk of chi...
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[GWAS:None]
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[GWAS:Colorectal cancer]
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Lack of replication of genetic predictors for the rheumatoid arthritis response to anti-TNF treatments: a prospective case-only study. [PharmGKB:Curated This variant is significantly associated with the efficacy of anti-TNF treatment in rheumatoid arthritis (Adjusted P-value: 0.00003; OR: 5.5 (1.8, 20.2)). The study is a genome-wide association study using the Illumina HapMap300 SNP chip on 89 RA patients prospectively followed after beginning of anti-TNF therapy.]
Frequency: 53.1%
References:0
References:0
(hide)
[GWAS:None]
Frequency: 54.0%
References:1
References:1
(hide)
[GWAS:None]
Frequency: 54.9%
References:0
References:0
(hide)
23andMe blog blood pressure
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[GWAS:None]
(hide)
[GWAS:None]
Frequency: 55.4%
References:1
References:1
(hide)
[PharmGKB:Curated This variant is associated with hip fracture in a GWAS study consisting of 403 chinese females (266 with hip fracture and 177 control subjects).]
Frequency: 55.8%
References:1
References:1
(hide)
[GWAS:None]
Frequency: 56.6%
References:0
References:0
(hide)
Follow-up examination of linkage and association to chromosome 1q43 in multiple sclerosis.
(hide)
associated with specific patterns of brain activity. rs3087454 rs1355920 rs7520974 rs885834
Frequency: 57.5%
References:1
References:1
(hide)
[GWAS:None]
Frequency: 57.5%
References:1
References:1
(hide)
[PharmGKB:Curated Risk or phenotype-associated allele: not stated Phenotype: Using a Quantitative Transmission Disequilibrium Test (QTDT), this variant was significantly associated with etoposide toxicity based upon IC50 values in cell lines from 30 parent-child trios. In combination, rs10018204, rs11222869, rs16965867, rs1846644, and rs6539870 were significant predictors of etoposide IC50, accounting for 55% of the etoposide IC50 variation in Caucasians. Study size: 87. Study population/ethnicity: 87 European descent Caucasians. Significance metric(s): p = 0.00009. Type of association: FA; GN.]
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Tooth Development [GWAS:None]
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[GWAS:None]
(hide)
[GWAS:None]
(hide)
GTP cyclohydrolase and tetrahydrobiopterin regulate pain sensitivity and persistence. T allele associated with higher tolerance to pain. Do genetic predictors of pain sensitivity associate with persistent widespread pain? T allele associated with higher pain tolerance. GCH1 haplotype determines vascular and plasma biopterin availability in coronary artery disease effects on vascular superoxide production and endothelial function. Part of a haplotype, rs10483639(C)-rs3783641(A)-rs8007267(T), associated with lower levels of tetrahydrobiopterin.
Frequency: 58.4%
References:1
References:1
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[GWAS:None]
(hide)
[GWAS:None]
(hide)
[GWAS:None]
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mentioned as potentially affecting grey matter volume, sample size tiny
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[GWAS:None]
Frequency: 62.8%
References:1
References:1
(hide)
Follow-up examination of linkage and association to chromosome 1q43 in multiple sclerosis.
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[GWAS:None]
Frequency: 64.6%
References:1
References:1
(hide)
[GWAS:None]
(hide)
[GWAS:None]
(hide)
[GWAS:None]
(hide)
[GWAS:None]
(hide)
[GWAS:None]
Frequency: 66.7%
References:1
References:1
Frequency: 67.3%
References:1
References:1
(hide)
[GWAS:None]
Frequency: 69.0%
References:1
References:1
(hide)
[GWAS:None]
Frequency: 69.9%
References:1
References:1
(hide)
[GWAS:None]
(hide)
[GWAS:None]
Frequency: 72.6%
References:1
References:1
(hide)
[GWAS:None]
Frequency: 72.6%
References:1
References:1
Frequency: 72.6%
References:1
References:1
(hide)
[GWAS:None]
(hide)
Elevated expression and genetic association links the SOCS3 gene to atopic dermatitis. Elevated expression and polymorphisms of SOCS3 influence patient response to antiviral therapy in chronic hepatitis C. Lack of association between the tagging SNP A+930-->G of SOCS3 and type 2 diabetes mellitus: meta-analysis of four independent study populations. Gene expression and hepatitis C virus infection. Polymorphisms near SOCS3 are associated with obesity and glucose homeostasis traits in Hispanic Americans from the Insulin Resistance Atherosclerosis Family Study.
Frequency: 73.5%
References:1
References:1
Frequency: 73.5%
References:2
References:2
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Association between liver X receptor alpha gene polymorphisms and risk of metabolic syndrome in French populations. Functional and genetic analysis in type 2 diabetes of liver X receptor alleles--a cohort study. Genetic variation within the NR1H2 gene encoding liver X receptor beta associates with insulin secretion in subjects at increased risk for type 2 diabetes. Associations between common genetic polymorphisms in the liver X receptor alpha and its target genes with the serum HDL-cholesterol concentration in adolescents of the HELENA Study. Liver X receptor alpha gene polymorphisms and variable cardiovascular outcomes in patients treated with antihypertensive therapy: results from the INVEST-GENES study.
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[GWAS:None]
Frequency: 75.9%
References:1
References:1
(hide)
[GWAS:None]
Frequency: 76.1%
References:1
References:1
(hide)
[GWAS:None]
Frequency: 78.0%
References:1
References:1
(hide)
[PharmGKB:Curated This variant is associated with end-of-induction minimal risidual disease (MRD) in childhood acute lymphoblastic leukemia (ALL) from 2 independent cohorts (GWAS result). Risk Allele: A, MAF= 0.15, combined P value= 4.89E-05. It is also associated with etoposide clearance.]
Frequency: 78.8%
References:1
References:1
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[GWAS:None]
(hide)
[GWAS:None]
(hide)
[GWAS:None]
(hide)
[GWAS:None]
(hide)
[GWAS:None]
(hide)
[PharmGKB:Curated in a GWAS of subjects of African ancestry(African American plus African Caribbean), this SNP was found to be significantly associated with Asthma . This finding was not significantly replicated in 4 additional case-control studies of African Americans nor in tested family and case-control panels of UK and German subjects. Risk or phenotype-associated allele: A. Phenotype: increased risk for asthma. Study size/population/ethnicity: 1) 935 African American asthmatic cases and control subjects from the Baltimore-Washington area (2) 929 African Caribbean asthmatic subjects and their family members from Barbados . Significance metric(s): combined p = 3.05 x 10(-6); OR = 0.65(95% CI= 0.49 -0.87). Type of association: CO; GN.]
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Population substructure and control selection in genome-wide association studies.
(hide)
[GWAS:None]
(hide)
[GWAS:None]
(hide)
[GWAS:None]
(hide)
[GWAS:None]
(hide)
[GWAS:None]
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[GWAS:None]
Frequency: 83.2%
References:1
References:1
(hide)
[GWAS:None]
(hide)
[GWAS:None]
Frequency: 84.1%
References:3
References:3
(hide)
[GWAS:None]
(hide)
[GWAS:None]
Frequency: 85.8%
References:1
References:1
(hide)
[GWAS:None]
(hide)
[GWAS:None]
(hide)
[GWAS:None]
(hide)
[GWAS:None]
Frequency: 88.5%
References:1
References:1
(hide)
[GWAS:None]
(hide)
[GWAS:None]
(hide)
[GWAS:None]
(hide)
[GWAS:None]
(hide)
[GWAS:None]
(hide)
[GWAS:None]
(hide)
[GWAS:None]
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[GWAS:None]
Frequency: 99.1%
References:1
References:1
(hide)
[GWAS:None]
(hide)
[GWAS:None]
(hide)
[PharmGKB:Curated This variant is significantly associated with late-onset Alzheimer disease (LOAD) in a GWAS study with 492 LOAD cases and 498 cognitive controls using Illumina's HumanHap550 beadchip.]
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[GWAS:None]
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[GWAS:None]
(hide)
Gene-nutrient interactions among determinants of folate and one-carbon metabolism on the risk of non-Hodgkin lymphoma: NCI-SEER case-control study.
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[PharmGKB:Curated In a GWAS of 3497 Dutch subjects from the Netherlands Study of Depression and Anxiety or from the Netherlands Twin Registry, this SNP was found to be associated with Smoking Initiation (p = 0.00007324; OR for minor allele A:0.804)]
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Association study of mast cell chymase polymorphisms with atopy. Genetic-epidemiological evidence on genes associated with HDL cholesterol levels: a systematic in-depth review. Power of multifactor dimensionality reduction and penalized logistic regression for detecting gene-gene interaction in a case-control study. Impact of polymorphisms of the genes encoding angiotensin II-forming enzymes on the progression of IgA nephropathy.
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rs2631372 increases susceptibility to Crohn's disease 1.28 times for carriers of the C allele
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Variants of CTGF are associated with hepatic fibrosis in Chinese, Sudanese, and Brazilians infected with schistosomes.
normal
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Testicular germ cell tumor risk I('TGCT'; i.e. testicular cancer risk) was increased 40% per copy of the major allele (C) at rs4324715 and rs6897876 (OR = 1.37, CI: 1.14–1.64; OR = 1.39, CI: 1.16–1.66, respectively), based on a genome-wide scan of 277 primarily Caucasian TGCT cases and 919 controls. Men who have two copies of the common version of the sprouty 4 SPRY4 gene have a 1.5-fold higher risk of testicular cancer than men who have two copies of the less common or minor version of the gene. [doi|10.1038/ng.393]
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G-C-T-C haplotype of rs2340690-rs788016-rs2305560-rs2565163 has odds ratio of 1.91 (CI: 1.26-2.89, p=0.002) for coronary heart disease compared to G-T-T-C, based on a study of 1,000 Han Chinese patients and matched controls. * Note: Haplotype allele assignments may not be in dbSNP orientation.
Magnitude: 0
Frequency: 46.9%
Repute:Good
References:1
Frequency: 46.9%
Repute:Good
References:1
Normal risk for meningioma
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rs4968451, which is in a breast cancer susceptibility gene, was associated with increased risk of meningioma, a common form of brain tumor, in a combination of five studies totaling 631 European patients. 'Meningioma risks associated with hetero- and homozygosity for the minor allele of were 1.61 (95% CI = 1.26 to 2.06) and 2.33 (95% CI = 1.25 to 4.34), respectively, and were thus compatible with a multiplicative model of action.' The risk allele and minor allele is rs4968451(C). Around 30% of Europeans carry one of risk genotypes, i.e. rs4968451(A;C) or (C;C); and perhaps 16% of meningiomas might be associated with this SNP.
Magnitude: 0
Frequency: 75.0%
References:0
Frequency: 75.0%
References:0
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A GCH1 Haplotype Associated with Susceptibility to Vasoocclusive Pain and Impaired Vascular Function in Sickle Cell Anemia
Magnitude: 0
Frequency: 76.1%
Repute:Good
References:1
Frequency: 76.1%
Repute:Good
References:1
Magnitude: 0
Frequency: 76.1%
Repute:Good
References:2
Frequency: 76.1%
Repute:Good
References:2
(hide)
[GWAS:None]
Magnitude: 0
Frequency: 84.1%
Repute:Good
References:1
Frequency: 84.1%
Repute:Good
References:1
(hide)
[PharmGKB:Curated In a GWAS of 3497 Dutch subjects from the Netherlands Study of Depression and Anxiety or from the Netherlands Twin Registry, this SNP was found to be associated with Current Smoking (p = 0.00005649;OR for minor allele T:1.504).]
Magnitude: 0
Frequency: 85.0%
Repute:Good
References:3
Frequency: 85.0%
Repute:Good
References:3
normal
(hide)
rs10754339 is a SNP in the V-set domain containing T cell activation inhibitor 1 VTCN1 gene, which is also known as B7-H4. A study of 500 Chinese Han women with breast cancer (and an equal number of matched controls) concluded that the rs10754339(A;G) genotype and G allele showed a significantly increased risk of breast cancer (odds ratio 1.455, CI: 1.119-1.892, and 1.325, CI: 1.073-1.637, respectively). Additionally, the rs10754339(G;G) genotype was significantly associated with lymph node metastasis and PR status, and the G allele and the (A;G) genotype were respectively associated with lymph node metastasis and ER status.
Magnitude: 0
Frequency: 85.8%
Repute:Good
References:0
Frequency: 85.8%
Repute:Good
References:0
common in complete genomics
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rs10494366, rs4657139 and rs16847548 were significantly associated with adjusted QT interval in whites. relative hazard of SCD associated with each C allele at rs16847548 was 1.31. rs12567209 was also independently associated with SCD in whites (relative hazard 0.57, 95% confidence interval 0.39 to 0.83, P=0.003). No significant associations observed in blacks. Multiple independent genetic factors at NOS1AP modulate the QT interval in a multi-ethnic population. Genetic variation in NOS1AP is associated with sudden cardiac death: evidence from the Rotterdam Study.
Magnitude: 0
Frequency: 85.8%
Repute:Good
References:1
Frequency: 85.8%
Repute:Good
References:1
Magnitude: 0
Frequency: 87.2%
Repute:Good
References:0
Frequency: 87.2%
Repute:Good
References:0
(hide)
[GWAS:None]
Magnitude: 0
Frequency: 90.3%
Repute:Good
References:1
Frequency: 90.3%
Repute:Good
References:1
common in complete genomics
(hide)
[PharmGKB:Curated This variant is associated with end-of-induction minimal risidual disease (MRD) in childhood acute lymphoblastic leukemia (ALL) from 2 independent cohorts (GWAS result). Risk Allele: A, MAF= 0.06, combined P value= 2.63E-05.]
Magnitude: 0
Frequency: 90.3%
Repute:Good
References:0
Frequency: 90.3%
Repute:Good
References:0
(hide)
[GWAS:Cognitive performance]
Magnitude: 0
Frequency: 90.9%
Repute:Good
References:2
Frequency: 90.9%
Repute:Good
References:2
Magnitude: 0
Frequency: 91.2%
Repute:Good
References:1
Frequency: 91.2%
Repute:Good
References:1
normal
(hide)
rs6013029 is a SNP in the CTNNBL1 gene. Found no evidence of early onset obesity or increased body mass index association with this SNP in several populations (~3,000 cases overall) of Central European (German) ancestry. While the older a study of ~1,900 Caucasians turned up associations between several SNPs in the CTNNBL1 gene and increased risk for obesity, of which rs6013029 was statistically the strongest, with an odds ratio of 1.42 for (T;T) homozgyotes compared to (G;G) homozygotes. This SNP achieved experiment-wise p values of 2.69 x 10<sup>-7</sup> for body mass index (BMI) and of 4.99 x 10<sup>-8</sup> for fat mass, respectively. The rs6013029(T) allele confers an average increase in BMI and fat mass of 2.67 kg/m(2) and 5.96 kg, respectively, compared to rs...
(hide)
[GWAS:None]
Magnitude: 0
Frequency: 96.5%
Repute:Good
References:1
Frequency: 96.5%
Repute:Good
References:1
(hide)
[GWAS:None]
Magnitude: 0
Frequency: 96.5%
Repute:Good
References:1
Frequency: 96.5%
Repute:Good
References:1
Magnitude: 0
Frequency: 97.3%
Repute:Good
References:0
Frequency: 97.3%
Repute:Good
References:0
Magnitude: 0
Frequency: 98.2%
Repute:Good
References:2
Frequency: 98.2%
Repute:Good
References:2
common in complete genomics
(hide)
[PharmGKB:Curated Based on an study on 284 Mexican Americans, this variant in the 5' UTR of PSMB4 is significantly associated with major depressive disorder (MDD). The results implicate that the specific UTR variation increases the risks for a T-cell dysfunction in MDD in the studied population.]
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The association of single nucleotide polymorphisms in the 5'-regulatory region of the lumican gene with susceptibility to high myopia in Taiwan. High myopia is not associated with the SNPs in the TGIF, lumican, TGFB1, and HGF genes. The association of haplotype at the lumican gene with high myopia susceptibility in Taiwanese patients. Association of lumican gene with susceptibility to pathological myopia in the northern han ethnic chinese.
common in complete genomics
(hide)
chronic lymphocytic leukemia rs2266690 rs17028658 rs4505265 rs1045485 rs2779251 rs3136687
common in complete genomics
(hide)
[PharmGKB:Curated This variant is associated with end-of-induction minimal risidual disease (MRD) in childhood acute lymphoblastic leukemia (ALL) from 2 independent cohorts (GWAS result). Risk Allele: G, MAF= 0.04, combined P value= 3.73E-04.]
(hide)
[GWAS:None]
common in complete genomics
(hide)
Cytokine SNPs: Comparison of allele frequencies by race and implications for future studies.
461 snps
(hide) Native American
Duffy-positive This genotype is associated with European populations and southwestern Native American populations.
(hide)
rs2814778 is within the DARC gene, which encodes the Duffy blood group antigen . This SNP shows an almost perfectly fixed difference in frequency between Europeans and those with African ancestry. (One exception appears to be a certain population of Czech gypsies, and certain non-Ashkenazi Jewish populations.) Additionally the Namibian San samples of the CEPH-HGDP are, uncharacteristically for Africans, all AA homozygotes for this SNP. The rs2814778 (G) allele is associated with African populations, while rs2814778 (A) is associated with European populations and southwestern Native American populations. rs2814778(G;G) protect against Plasmodium vivax malaria and predicts of white blood cell and neutrophil count 23andMe blog discussion Malaria Resistance (Duffy Antigen) [PharmGKB:Curated A...
common one paper reports increased risk of alcoholism for African-Americans with this genotype.
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This paper found significant association with rs2066702, the SNP that defines ADH1B*3, in African American families. Association was strongest with the ICD-10 definitions of alcoholism, with P=0.046 for PDTsum and 0.029 for PDTaverage; it was also significant for DSM-IV for PDTaverage (P=0.039). The high-risk allele was the C that encodes ADH1B*1, and the low-risk allele encodes ADH1B*3. A review of the (at times conflicting) findings regarding ADH1B genotypes and maternal and fetal alcohol syndromes is available.In some African American] and Native American populations, the ADH1B*3 allele (Arg369Cys in exon 9) is correlated with protection against alcoholism. [PharmGKB:In-Depth This allele has been found in some African American and Native American populations to be correlated with prote...
2 snps
(hide) Neanderthal
less able to detect β-ionone (floral) fragrance
(hide)
rs6591536, also known as N183D or Asn183Asp, is a SNP in the olfactory receptor, family 5, subfamily A, member 1 OR5A1 gene. The rs6591536(A) allele encodes the asparagine (N). Individuals vary in their ability to smell various odors, largely due to variations in their olfactory receptors. Carriers of one or two rs6591536(G) alleles can detect a particular compound, β-ionone, at levels two orders of magnitude lower than rs6591536(A;A) individuals. In fact, this study reports that 96% of the observed phenotypic variation is determined by this single SNP, making it nearly a completely Mendelian trait. People with high or low β-ionone sensitivity are found in all populations, and based on this SNP, variability was seen even in Neanderthal populations. Since rs6591536 determines ^...
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Rs332951 is an intergenic SNP, located most closely to the genes EPHA7 (642932 bps) and MIR4643 (1075353 bp). Based on the draft Neanderthal genome () it is thought the T allele of this SNP may be derived from Neanderthal admixture.
Frequency: 19.5%
References:0
References:0
Frequency: 20.0%
References:0
References:0
(hide)
Genome-wide association identifies ATOH7 as a major gene determining human optic disc size.
Magnitude: 1
Frequency: 20.4%
References:1
Frequency: 20.4%
References:1
Frequency: 25.7%
References:0
References:0
Frequency: 31.9%
References:0
References:0
Frequency: 38.9%
References:0
References:0
Frequency: 41.6%
References:1
References:1
Frequency: 46.4%
References:0
References:0
(hide)
The enabled homolog gene polymorphisms are associated with susceptibility and progression of childhood IgA nephropathy.
Frequency: 53.1%
References:0
References:0
Frequency: 64.6%
References:0
References:0
Frequency: 78.5%
References:0
References:0
Frequency: 81.2%
References:0
References:0
Frequency: 82.3%
References:0
References:0
Frequency: 86.7%
References:1
References:1
Magnitude: 0.1
Frequency: 78.8%
References:0
Frequency: 78.8%
References:0
homo sapiens gene (not Neanderthal) This is the human, homo sapiens version of the gene, not the neanderthal version.
Magnitude: 0
Frequency: 75.9%
Repute:Good
References:0
Frequency: 75.9%
Repute:Good
References:0
Magnitude: 0
Frequency: 77.7%
Repute:Good
References:0
Frequency: 77.7%
Repute:Good
References:0
Magnitude: 0
Frequency: 77.9%
Repute:Good
References:0
Frequency: 77.9%
Repute:Good
References:0
Magnitude: 0
Frequency: 77.9%
Repute:Good
References:0
Frequency: 77.9%
Repute:Good
References:0
Magnitude: 0
Frequency: 77.9%
Repute:Good
References:0
Frequency: 77.9%
Repute:Good
References:0
Magnitude: 0
Frequency: 78.5%
Repute:Good
References:0
Frequency: 78.5%
Repute:Good
References:0
Magnitude: 0
Frequency: 85.8%
Repute:Good
References:0
Frequency: 85.8%
Repute:Good
References:0
Magnitude: 0
Frequency: 88.5%
Repute:Good
References:1
Frequency: 88.5%
Repute:Good
References:1
(hide)
This SNP is located within the DNAJA1 gene. The A allele is suspected to be derived from admixture with Neanderthals in Non-African populations based on the draft Neanderthal Genome ().
Magnitude: 0
Frequency: 88.5%
Repute:Good
References:0
Frequency: 88.5%
Repute:Good
References:0
Magnitude: 0
Frequency: 90.3%
Repute:Good
References:0
Frequency: 90.3%
Repute:Good
References:0
Magnitude: 0
Frequency: 97.3%
Repute:Good
References:0
Frequency: 97.3%
Repute:Good
References:0
Magnitude: 0
Frequency: 98.2%
Repute:Good
References:0
Frequency: 98.2%
Repute:Good
References:0
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:0
Frequency: 100.0%
Repute:Good
References:0
42 snps
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reduced MAOA activity
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rs6323 (R297R / Arg297Arg) is a SNP in the MAOA (monoamine oxidase A) gene. Monoamine oxidase A degrades serotonin, dopamine, epineprine, and norepinephrine. The G allele encodes for the higher activity form of the enzyme. Subjects with major depressive disorder with the highest activity form of the enzyme (G or G/G) had a significantly lower magnitude of placebo response.
Impaired muscle performance. Likely endurance athlete. This is under-represented in elite strength and sprint athletes, consistent with previous reports of impaired muscle performance. However this is more common in endurance athletes. This SNP makes fast-twitch muscle fibers completely unable to produce alpha-actinin-3.
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This SNP, in the ACTN3 gene, encodes a premature stop codon in a muscle protein called alpha-actinin-3. The polymorphism alters position 577 of the alpha-actinin-3 protein. In the (C;C) genotype is often called RR. The truncated (T;T) is often called XX. (T;T) is under-represented in elite strength athletes, consistent with previous reports indicating that alpha-actinin-3 deficiency appears to impair muscle performance. The most common nucleotide at this position, (C), encodes an arginine (amino acid code R), the alternative T allele encodes a stop codon (X). Hence, the SNP is referred to as R577X, with homozygotes being either RR or XX and heterozygotes being RX. XX individuals completely lack the expression of alpha-actinin-3. An earlier report studying a relatively small number of Austr...
3.5x asthma risk in certain populations
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This SNP, in the GSTP1 gene influences asthma risk; the (A) allele encodes the Ile, while the (G) allele encodes the Val. This SNP is also known as GSTP1Val105, or GSTP1 Ile105Val. Despite evidence of antioxidant effects of vitamin E in vitro and in animal studies, large, randomized clinical trials have not substantiated a benefit of vitamin E in reducing inflammation in humans. In healthy control subjects, the effect of α-tocopherol supplementation on the production of inflammatory cytokines appears to be dependent on an individual's genotype. These genotype-specific differences may help explain some of the discordant results in studies that used vitamin E. Persons having the alleles AA or AG had an increase in interleukin-6 (IL-6) upon supplementing alpha-tocopherol (the most common...
Carrier of one CYP1A2*1F allele; Slow Caffeine Metabolizer. One copy of the slow caffeine metaboliser SNP, and one copy of the fast version. This makes you more strongly affected by drinking coffee, as caffeine is broken down slower in the liver. Supposedly this increases the risk of heart attacks, although other studies show caffeine is generally good for the heart. It also makes caffeine more effective at preventing Breast Cancer, Alzheimer's Disease, and Parkinson's disease. Too much caffeine will shrink your breasts.
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rs762551, also known as -164A>C or -163C>A, is a SNP encoding the CYP1A2*1F allele of the CYP1A2 gene. For historic reasons, the rs762551(C) allele is considered the wild-type, even though it is the rarer allele in most populations. The rs762551(A) allele is the 'fast metabolizer' allele known as CYP1A2*1F; the (C) allele is by comparison a slower metabolizer of certain substrates (including caffeine). In terms of genotypes, only rs762551(A;A) individuals are considered fast metabolizers. Individuals who are rs762551(A;C) heterozygotes or rs762551(C;C) homozygotes are both considered slow metabolizers. The CYP1A2 gene encodes a member of the cytochrome p450 family of proteins, which metabolize nutrients and drugs. One well known substrate of CYP1A2 is caffeine; individuals who are ca...
Possible risks. Complex. MTHFR rs1801131 is involved in converting 5-methylfolate (5MTHF) to tetrahydrofolate (THF). Unlike MTHFR C677T, this mutation does not lead to elevated homocysteine levels.
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rs1801131 is a SNP in the MTHFR gene, representing an A>C mutation at mRNA position 1298, resulting in a glu429-to-ala (E429A) substitution (hence this SNP is also known as A1298C or E429A). A diplotype (according to the authors, but perhaps actually a genoset) of rs1801131 and rs1801133 has been linked to increased risk for several types of brain cancer. The highest risk of meningioma was associated with heterozygosity for both MTHFR SNPs (odds ratio 2.11, CI: 1.42-3.12, p=0.002). The corresponding odds ratio for glioma was 1.23 (CI: 0.91-1.66, p=0.02. In general, risks were increased with genotypes associated with reduced MTHFR activity. rs1801131 shows no consistent association with schizophrenia overall in 12 studies totaling 3,000+ patients [PharmGKB:Curated Risk or phenotype-asso...
higher risk for endometrial cancer
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rs4633 is a variant at codon 62 of the COMT gene, however, it does not change the amino acid sequence of the COMT protein. In a study of 150 (Caucasian) cases of endometrial cancer, a significant increase in rs4633(T;T) genotype was observed in patients compared to controls (OR = 2.39, CI: 1.31-4.37, p = 0.004). Furthemore, the frequency of the C-G haplotype of rs4633-rs4680 was significantly higher in controls (p < 0.0001) than in patients. This correlated with lower expression levels of the COMT protein in carriers of these alleles. pubmed 1180576 Schizophrenia Susceptibility Genetic basis for individual variations in pain perception and the development of a chronic pain condition [PharmGKB:Curated On the basis of subjects' pain responsiveness, haplotypes involving rs6269 (A/G), rs46...
Carrier of one CYP2D6 decreased or non-functioning variant. Your body may have a reduced ability to process some medicines. You are a carrier for rs1065852(T;T)
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The wild type (normal) allele at this SNP is (C). The (T) variant indicates the presence of a non-wild type CYP2D6 variant, but it appears in many different variants so it can not be used to determine the presence of any particular variant. The most common variants it appears in are CYP2D6*10 and CYP2D6*4, but these are not the only ones. While this is the defining mutation for CYP2D6*10, it is not possible by itself for this mutation to determine a particular variant. In addition, the CYP2D6*4 variant includes this mutation, but the defining mutation 1846G>A SNP is not available in the common direct to consumer testing services. While it is not possible for this mutation to identify one particular variant, all the variants in which it appears have reduced or no CYP2D6 activity. If two ...
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Yasko Methylation The product the BHMT gene is central to the ‘short cut’ through the methylation cycle, again helping to convert homocysteine to methionine. The activity of this gene product can be affected by stress, by cortisol levels and may play a role in ADD/ADHD by affecting norepinephrine levels. Yasko believes that believes BHMT-02 and BHMT-04 play a role in the gut environment. Yasko also believes that BHMT-08 is related to the impact that psychological stress has on a patient's attention levels.
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Influence of child abuse on adult depression: moderation by the corticotropin-releasing hormone receptor gene. Association of FKBP5 polymorphisms and childhood abuse with risk of posttraumatic stress disorder symptoms in adults. Risk and resilience: genetic and environmental influences on development of the stress response. A comparison of classification methods for predicting Chronic Fatigue Syndrome based on genetic data. The distribution and most recent common ancestor of the 17q21 inversion in humans. Effect of Childhood Trauma on Adult Depression and Neuroendocrine Function: Sex-Specific Moderation by CRH Receptor 1 Gene. Moderation of the association between childhood maltreatment and neuroticism by the corticotropin-releasing hormone receptor 1 gene. Association of CRHR1 and CRHR2 w...
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Polymorphisms affecting gene transcription and mRNA processing in pharmacogenetic candidate genes: detection through allelic expression imbalance in human target tissues. Glucocorticoid receptor gene variant in the 3' untranslated region is associated with multiple measures of blood pressure. Cohort profile: risk patterns and processes for psychopathology emerging during adolescence: the ROOTS project. A comparison of classification methods for predicting Chronic Fatigue Syndrome based on genetic data. Glucocorticoid receptor gene haplotype structure and steroid therapy outcome in IBD patients. Association of FKBP5 gene haplotypes with completed suicide in the Japanese population. Glucocorticoid receptor polymorphism is associated with lithium response in bipolar patients.
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Yasko Methylation Catalyzes the hydrolysis of AdoHcy to adenosine and homocysteine. AdoHcy hydrolysis serves not only to sustain the flux of methionine sulfur toward cysteine, but is believed also to play a critical role in the regulation of biologic methylations. This is one of the SNPs reported by NutraHacker.
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Associated with insulin resistance in men Associated with bone mineral density and thus osteoporosis in a Chinese population. A comparison of classification methods for predicting Chronic Fatigue Syndrome based on genetic data.
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Association between a functional polymorphism in the serotonin transporter gene and diarrhoea predominant irritable bowel syndrome in women. Genetic polymorphisms in monoamine neurotransmitter systems show only weak association with acute post-surgical pain in humans. Gene-gene interaction associated with neural reward sensitivity. Sexually dimorphic effects of four genes (COMT, SLC6A2, MAOA, SLC6A4) in genetic associations of ADHD: a preliminary study. Variants of the serotonin transporter gene and NEO-PI-R Neuroticism: No association in the BLSA and SardiNIA samples. Development and validation of a high-throughput screening method for two polymorphisms in the serotonin transporter gene. Association and gene-gene interaction of SLC6A4 and ITGB3 in autism. Association of tagging single nuc...
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Influence of child abuse on adult depression: moderation by the corticotropin-releasing hormone receptor gene. Association of FKBP5 polymorphisms and childhood abuse with risk of posttraumatic stress disorder symptoms in adults. Psychobiology and molecular genetics of resilience. Risk and resilience: genetic and environmental influences on development of the stress response. A comparison of classification methods for predicting Chronic Fatigue Syndrome based on genetic data. Effect of Childhood Trauma on Adult Depression and Neuroendocrine Function: Sex-Specific Moderation by CRH Receptor 1 Gene. Moderation of the association between childhood maltreatment and neuroticism by the corticotropin-releasing hormone receptor 1 gene. Association of CRHR1 and CRHR2 with major depressive disorder a...
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Associated with lean body mass but not fat body mass in a study of ~1,800 Caucasians
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association with essential hypertension . Functional analysis showed that the C allele of rs2070762 functioned as an enhancer in the absence of binding by unidentified transcriptional repressor(s)
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[OMIM:CYTOCHROME P450, SUBFAMILY I, POLYPEPTIDE 1; CYP1B1]
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Plays a major role in ketone body metabolism. Defects cause a 3-ketothiolase deficiency. Yasko believes it will cause an increase in gut bugs (particularly clostridia) as well as elevated fatty acid metabolites. This is one of the SNPs reported by NutraHacker.
Normal risk for anxiety disorders
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A study of patients with panic disorder or social anxiety disorder, both moderately heritable anxiety disorders, concluded that the rs140701(A) allele was associated with increased risk for both disorders. This SNP was actually part of a tightly linked haplotype A-A-G (for SNPs rs3794808, rs140701 and rs4583306, respectively) that had 1.7x increased risk for panic disorder (CI: 1.2-2.3).
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This is one of the SNPs reported by NutraHacker.
normal
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A study of 733 breast cancer cases for 10 SNPs concluded that the rs1501299(C;C) genotype (in dbSNP orientation) was at increased risk (odds ratio 1.80, CI: 1.14 - 2.85). After categorizing individuals by adiponectin signaling status, this study found that compared with high signalers, intermediate signalers had a 4.16-fold increase in breast cancer risk (CI: 0.49-35.19), and low signalers had a 6.56x higher breast cancer risk (CI: 0.78-54.89, p(trend) = 0.001). Adiponectin signaling status was assigned as follows: rs1501299(G,G) + rs2241766(T,T) = low signaler<br> rs1501299(G,T) + rs2241766(T,T) = low signaler<br> rs1501299(G,G) + rs2241766(G,T) = low signaler<br> rs1501299(T,T) + rs2241766(T,T) = intermediate signaler<br> rs1501299(G,T) + rs2241766(G,T) = intermed...
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ADHD GIT1 is associated with ADHD in humans and ADHD-like behaviors in mice
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Being investigated in Ehlers-Danlos syndrome
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Yasko Methylation The product the BHMT gene is central to the ‘short cut’ through the methylation cycle, again helping to convert homocysteine to methionine. The activity of this gene product can be affected by stress, by cortisol levels and may play a role in ADD/ADHD by affecting norepinephrine levels. Yasko believes that believes BHMT-02 and BHMT-04 play a role in the gut environment. Yasko also believes that BHMT-08 is related to the impact that psychological stress has on a patient's attention levels.
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This is one of the SNPs reported by NutraHacker.
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Associated with bone mineral density and thus osteoporosis in a Chinese population. A comparison of classification methods for predicting Chronic Fatigue Syndrome based on genetic data. Genetic modulation of neural response during working memory in healthy individuals: interaction of glucocorticoid receptor and dopaminergic genes.
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Yasko Methylation The product the BHMT gene is central to the ‘short cut’ through the methylation cycle, again helping to convert homocysteine to methionine. The activity of this gene product can be affected by stress, by cortisol levels and may play a role in ADD/ADHD by affecting norepinephrine levels. Yasko believes that BHMT-02 and BHMT-04 play a role in the gut environment. Yasko also believes that BHMT-08 is related to the impact that psychological stress has on a patient's attention levels.
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Polymorphisms in inflammation-related genes are associated with susceptibility to major depression and antidepressant response. A comparison of classification methods for predicting Chronic Fatigue Syndrome based on genetic data. [PharmGKB:Curated This variant is associated with response to escitalopram and nortriptyline in a study of 760 adult patients with moderate-to-severe depression.]
Intermediate risk of low bone mineral density disorders
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rs1544410, also known as the BsmI polymorphism, is a SNP in the Vitamin D receptor (VDR). Multiple studies examining bone mineral density (BMD) in women have associated the A allele with increased risk of low BMD , , & . Additionally, A meta-analysis of 26 studies estimated a decreased risk of osteoporosis associated with the G;G genotype with an odds ratio of 0.61, 95% CI, 0.40-0.92 . rs1544410 increases susceptibility to Shorter stature for carriers of the A allele [PharmGKB:Curated This variant is associated with etidronate response in Caucasian (Slovenian) postmenopausal women (24 patients), with bb genotype associated with lower increase in bone mineral density (BMD) after bisphosphonate treatments.]
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rs731236 protection from breast cancer (OR=0.80, 95%CI=0.64-0.99; p= 0.047) [PharmGKB:Curated This variant was significantly associated with acquired resistance to clodronate treatment in Caucasian patients with Paget's disease of the bone]
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rs1208 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The risk allele for this SNP is rs1208(G). [PharmGKB:Curated in vitro study; PK: 20-fold reduction in Vmax vs wild type] [OMIM:?]
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This is one of the SNPs reported by NutraHacker.
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This is one of the SNPs reported by NutraHacker.
multiple associations, see details
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rs4680 (Val158Met) is a well studied SNP in the COMT gene. 23andMe blog summarizes them as *rs4680(A) = Worrier. Met, more exploratory, lower COMT enzymatic activity, therefore higher dopamine levels; lower pain threshold, enhanced vulnerability to stress, yet also more efficient at processing information under most conditions *rs4680(G) = Warrior. Val, less exploratory, higher COMT enzymatic activity, therefore lower dopamine levels; higher pain threshold, better stress resiliency, albeit with a modest reduction in executive cognition performance under most conditions Roughly speaking, the predominant wisdom (known colloquially as the warrior/worrier hypothesis; summary at ) posits that people with Val alleles have increased COMT activity and lower prefrontal extracellular dopamine compar...
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[PharmGKB:Non-Curated GWAS results: Genome-wide Association Study of Vitamin B6, Vitamin B12, Folate, and Homocysteine Blood Concentrations. (Initial Sample Size: 2,934 individuals; Replication Sample Size: 686 individuals); (Region: 19q13.33; Reported Gene(s): FUT2; Risk Allele: rs602662-A); (p-value= 3E-20).This variant is associated with Folate pathway vitamins.] [OMIM:VITAMIN B12 PLASMA LEVEL QUANTITATIVE TRAIT LOCUS 1; B12QTL1] [GWAS:Folate pathway vitamins]
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Yasko Methylation Methionine synthase, coded by the MTR gene, has a B12 attached to it. The Methionine synthase takes a methyl group from methyl folate and attaches it to its B12, then it attaches it to a molecule of homocysteine, turning it into methionine, which in turn becomes SAMe. After 1000-2000 times doing this, the B12 gets turned into a useless form, and MTRR turns the B12 back into the useful form so that the molecule of MTR can keep working. The MTRR mutations make this enzyme less active, suggesting a need for more B12.
Frequency: 48.7%
References:3
References:3
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Common variation in the beta-carotene 15,15'-monooxygenase 1 gene affects circulating levels of carotenoids: a genome-wide association study. Single nucleotide polymorphisms upstream from the beta-carotene 15,15'-monoxygenase gene influence provitamin A conversion efficiency in female volunteers. [OMIM:HYPERCAROTENEMIA AND VITAMIN A DEFICIENCY, AUTOSOMAL DOMINANT]
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Parkinson's disease The risk alleles for each SNP identified from conditional logistic regression, rs1721100 C, rs1721082 T and rs1799836 A, are consistent with previous reports. Significant interaction between this MAOB SNP and a FGF20 SNP, rs1721100 was also noticed.
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This is one of the SNPs reported by NutraHacker. Common variation in the beta-carotene 15,15'-monooxygenase 1 gene affects circulating levels of carotenoids: a genome-wide association study. [OMIM:HYPERCAROTENEMIA AND VITAMIN A DEFICIENCY, AUTOSOMAL DOMINANT]
Magnitude: 1
Frequency: 49.2%
Repute:Bad
References:4
Frequency: 49.2%
Repute:Bad
References:4
Reduced conversion of beta-carotene to retinol Associated with Rs7501331 and reduced BCMO1, lower ability to convert beta-carotene to retinyl esters and higher serum beta-carotene levels. See also Rs7501331
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rs12934922 (R267S) and rs7501331 (A379V) double mutant have a reduced catalytic activity of beta-carotene by 57%. Female volunteers carrying the T variant of rs7501331 (379V) had a 32% lower ability to convert Beta-carotene, and those carrying at least one T in both SNPs show a 69% lower ability to convert Beta-carotene into retinyl esters. rs7501331: the frequency of the wild-type C allele and variant T allele was 76 and 24%, respectively; 56% of the population was CC wild-type genotype, and 39% was heterozygote CT with the TT variant present in 5% of the population. rs12934922: the frequency of the wild-type A allele and variant T allele was 58 and 42%, respectively; 38% of the population was AA wild-type genotype, 40% was heterozygote AT, and 22% was TT homozygote
higher beta-carotene levels
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rs6564851(G) associated with higher beta-carotene (p = 1.6 x 10(-24)) and alpha-carotene (p = 0.0001) levels and lower lycopene (0.003), zeaxanthin (p = 1.3 x 10(-5)), and lutein (p = 7.3 x 10(-15)) levels, with effect sizes ranging from 0.10-0.28 SDs per allele. Note that low plasma levels of carotenoids and tocopherols are associated with increased risk of chronic disease and disability, yet dietary intake of these lipid-soluble antioxidant vitamins is only poorly correlated with plasma levels, leading to the hypothesis that it isn't what you eat, it's your SNPs that regulate your carotenoid levels. This is one of the SNPs reported by NutraHacker. [PharmGKB:Non-Curated GWAS results: Common variation in the beta-carotene 15,15'-monooxygenase 1 gene affects circulating levels of carotenoi...
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rs1801280, also known as T341C, is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The allele associated with slow NAT2 metabolization for this SNP is rs1801280(C). Genosets gs154 and gs156 evaluate predicated NAT2 metabolizer phenotype based on rs1041983 and rs1801280. [PharmGKB:Curated in vitro study; PK: 20-fold reduction in Vmax vs wild type] [OMIM:?]
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This is one of the SNPs reported by NutraHacker.
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This is one of the SNPs reported by NutraHacker.
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rs7946, a SNP in the phosphatidylethanolamine N-methyltransferase PEMT gene and also known as +5465G-A, leads to a V175M (valine to methionine at amino acid position 175) substitution in the PEMT protein, and is a loss of function mutation. Caucasians with nonalcoholic fatty liver are more likely to carry the rs7946 (A), with the effect being most pronounced for rs7946(A;A) genotypes. However, rs7946(A) carriers are not more likely to have fatty liver, based on a study of many more patients, including ones of Hispanic and African-American descent. How can this be? One explanation [doi: 10.1096/fj.06-1005ufm] concludes the following: * Caucasians have a different distribution of this SNP than do Hispanics and African Americans; * Having this SNP may be necessary, but is not sufficient, to c...
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a haplotype consisting of rs3027400(G) and rs2072743(C) associated with increased incidence of migraine without aura among a sample of 528 migraine patients (308 without aura, 220 with aura) and 528 sex-matched migraine-free controls
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This is one of the SNPs reported by NutraHacker.
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[PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: The GG (Gly/Gly) genotype was associated with lower risk for colorectal cancer. This risk was further lowered in men with low alcohol intake. Study size: Study population/ethnicity: Patients with colorectal cancer from the Physicians' Health Study (PHS) and the Health Professional Follow-up Study (HPFS). Significance metric(s): OR = 0.59 (95% CI, 0.27-1.27); OR = 0.27 (95% CI, 0.09-0.81)(interaction with alcohol) Type of association: CO]
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This is one of the SNPs reported by NutraHacker.
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This is one of the SNPs reported by NutraHacker.
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577 testicular germ cell tumors cases (254 seminoma, 323 nonseminoma) and 707 controls. inversely associated with nonseminoma: *rs4886605 OR = 0.75 (95% CI = 0.54-1.04) among the heterozygotes and OR = 0.37, 95% CI = 0.12-1.11 among the homozygotes with a p-value for trend = 0.02; *rs2606345 OR = 0.69 (95% CI = 0.51-0.93) among heterozygotes and OR = 0.70 (95% CI = 0.42-1.17) among homozygotes, with a p-value for trend = 0.02.
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identifies a region associated with nicotine dependence in this particular study (1,050 dependents, 879 non-dependent controls, all of European descent), noted as distinct from the loci which rs16969968 defines Cholinergic nicotinic receptor genes implicated in a nicotine dependence association study targeting 348 candidate genes with 3713 SNPs. Variants in nicotinic receptors and risk for nicotine dependence. Systematic biological prioritization after a genome-wide association study: an application to nicotine dependence. Genetic variability in nicotinic acetylcholine receptors and nicotine addiction: converging evidence from human and animal research. Familial aggregation of common sequence variants on 15q24-25.1 in lung cancer. Association of a single nucleotide polymorphism in neuronal...
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This is one of the SNPs reported by NutraHacker.
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[PharmGKB:Curated On the basis of subjects' pain responsiveness, haplotypes involving rs6269 (A/G), rs4633 (C/T), rs4818 (C/G), and rs4680 (G/A) were designated as low (low pain sensitivity (LPS) haplotype; GCGG), average (average pain sensitivity (APS) haplotype; ATCA), or high (high pain sensitivity (HPS) haplotype; ACCG) pain sensitive.]
References:1
also known as F186L, Phe186Leu, c.558C>A, g.32755C>A, g.45833194C>A According to the literature, this is the cause of the CYP1A2*11 homozygote which produces 5% Vmax of the normal enzyme level. However 23andMe data shows that A is more common. in allele CYP1A2*11; drastic reduction in O-deethylation of phenacetin and 7-ethoxyresorufin; has a Vmax of approximately 5% of that of the wild-type and 5-fold lower Km value.
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rs72547513, also known as 558C>A or F186L, is a SNP in the CYP1A2 gene. In a CYP database, it is listed as defining the CYP1A2*11 allele. 23andMe and opensnp show A as more common. dbSNP shows C as the reference, and A as the variant, but no population frequency information is provided. This SNP was originally observed in a Japanese population at a frequency of 0.3%; in an Italian study of 500 healthy individuals, it was not observed. claims that A is the variant, and that it defined the CYP1A2*11 allele with a Vmax approximately 5% of that of the CYP1A2 wild type, and reduced enzymatic activity. Two subsequent theoretical studies provide hypotheses for why this change results in lowered activity.,
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Yasko Methylation Catalyzes the hydrolysis of AdoHcy to adenosine and homocysteine. AdoHcy hydrolysis serves not only to sustain the flux of methionine sulfur toward cysteine, but is believed also to play a critical role in the regulation of biologic methylations.
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Yasko Methylation Catalyzes the hydrolysis of AdoHcy to adenosine and homocysteine. AdoHcy hydrolysis serves not only to sustain the flux of methionine sulfur toward cysteine, but is believed also to play a critical role in the regulation of biologic methylations. This is one of the SNPs reported by NutraHacker.
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This is one of the SNPs reported by NutraHacker.
normal Vitamin B6 blood concentration
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This is one of the SNPs reported by NutraHacker. Genetics and genomics of human aging. [PharmGKB:Non-Curated The C allele of this SNP is associated with lower blood concentration of vitamin B6 (Combined studies of Tuscan Italians ( inCHIANTI:N =1175 and Progetto Nutrizione study:N = 687) found 1.45 ng/mL lower vitamin B6 per copy of C (p = 8.3 x 10 (-18)))] [OMIM:?] [GWAS:Folate pathway vitamins]
normal
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rs1801394, also known as A66G or Ile22Met, is a SNP in the methionine synthase MTRR gene. This gene encodes one of the two enzymes involved in the production of methionine (the other is MTR). The protein encoded by an rs1801394 allele has a lower affinity for MTR () and is inconsistently associated with homocysteine level, although it is a risk factor for neural tube defects () and Down syndrome () in conditions of higher homocysteine. Based on a study of British patients with primary brain tumors, (1,005 glioma cases and 631 meningioma cases), rs1801394(G;G) individuals were at higher risk for meningioma (odds ratio 1.41, CI: 1.02-1.94). In general, genotypes associated with increased 5,10-methylenetetrahydrofolate levels are associated with elevated risk for these types of brain cancer. ...
normal
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Several SNPs in the VKORC1 gene have been linked to warfarin sensitivity, with perhaps the most common being this SNP rs9923231. Note that the orientation as published in scientific articles is often on the opposite strand compared to the orientation in dbSNP, so you will sometimes see it as a G>T snp. It is also known as *-1639G>A with the minus indicating that this is in an upstream promoter *3673 based on its position in GenBank accession number AY587020. *VKORC1*2. The main findings related to the treatment of venous thromboembolism (aka VTE; from hypercoagulability) with the blood thinner warfarin for this SNP are that carriers of the rs9923231(T) allele require significantly reduced doses of warfarin, and are (otherwise) at a higher risk of serious bleeding. Clinical studies de...
normal
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rs1056836, also known as 4326C/G, Val432Leu or L432V, is a SNP in the cytochrome P450 1B1 (CYP1B1) gene. This gene is a member of the CYP1 gene family and one of the major enzymes involved in the hydroxylation of estrogens, a reaction likely to be relevant in hormonal carcinogenesis. [In dbSNP orientation, the (C) allele encodes the Leu; the (G) the Val.] In a study of 153 Hispanic Caucasians with prostate cancer the rs1056836(G;G) genotype showed decreased risk compared to the more common (C;C) genotype (odds ratio = 0.31, p = 0.04, CI: 0.10-0.96). This report cites another study as indicating that rs1056836(C;C) high-risk stage III and IV breast cancer patients receiving dose-intense paclitaxel in combination with doxorubicin and cyclophosphamide experience a longer progression-free surv...
normal
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rs12934922 (R267S) and rs7501331 (A379V) double mutant have a reduced catalytic activity of beta-carotene by 57%. Female volunteers carrying the T variant of rs7501331 (379V) had a 32% lower ability to convert Beta-carotene, and those carrying at least one T in both SNPs show a 69% lower ability to convert Beta-carotene into retinyl esters. rs7501331: the frequency of the wild-type C allele and variant T allele was 76 and 24%, respectively; 56% of the population was CC wild-type genotype, and 39% was heterozygote CT with the TT variant present in 5% of the population. rs12934922: the frequency of the wild-type A allele and variant T allele was 58 and 42%, respectively; 38% of the population was AA wild-type genotype, 40% was heterozygote AT, and 22% was TT homozygote
Common genotype: normal homocysteine levels
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rs1801133 is a SNP that is relatively common and has been studied for (relatively) a long time. Also known as C677T, Ala222Val, and A222V, it encodes a variant in the MTHFR gene, which encodes an enzyme involved in folate metabolism. Homozygous rs1801133(T;T) individuals have ~30% of the expected MTHFR enzyme activity, and rs1801133(C;T) heterozygotes have ~65% activity, compared to the most common genotype, rs1801133(C;C). This reduced activity (i.e. this SNP) has been linked at least once to each of the following disorders (though not necessarily reproducibly): * autism * cancer, including ** gastric cancer ** lung cancer ** head and neck cancer ** renal cancer * cleft lip and cleft palate * coronary artery disease * dementia * depression * hyperhomocysteinemia * migraine * neural tube d...
Magnitude: 0
Frequency: 76.1%
Repute:Good
References:8
Frequency: 76.1%
Repute:Good
References:8
normal
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This position is odd. Under the older reference genome build36, it was on the plus strand; in build37 it is on the minus strand. This makes it very prone to some ambiguous flip confusion in the literature, plus, 23andMe users have self-reported the flipped form. IN addition, instead of the usual SNP listed as having 2 alleles, all 4 alleles are reported in dbSNP, even if this is probably due to the strand changes. dbSNP currently says the normal allele is C, and T is the rare geno which causes a premature stop, early in the gene. We at SNPedia suspect that the A & G alleles are not common enough to have ever been genuinely reported, but for de-novo mutations each allele would be non-synonymous and result in a different amino acid. http://snpedia.blogspot.com/2012/12/snpedias-nightmare-befo...
Magnitude: 0
Frequency: 86.2%
Repute:Good
References:24
Frequency: 86.2%
Repute:Good
References:24
common on affy axiom data
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23andMe blog rs10994336 or (rs4948418) Each T at this SNP increased the odds of developing bipolar disorder by 1.45 times compared to the CC genotype. This is one of the SNPs reported by NutraHacker. [PharmGKB:Curated GWAS Results: Collaborative genome-wide association analysis supports a role for ANK3 and CACNA1C in bipolar disorder (Initial Sample Size: 1,098 cases, 1,267 controls; Replication Sample Size: 4,387 cases, 6,209 controls; Risk Allele: rs10994336-T). This variant is associated with Bipolar disorder.] [OMIM:MAJOR AFFECTIVE DISORDER 8; MAFD8] [GWAS:Bipolar disorder]
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Also known as Ile462Val A4889G CYP1A1*2C Genome amplification of single sperm using multiple displacement amplification. Decision forest analysis of 61 single nucleotide polymorphisms in a case-control study of esophageal cancer; a novel method. Multilocus analysis of SNP and metabolic data within a given pathway. CYP1A1 and CYP1B1 polymorphisms and their association with estradiol and estrogen metabolites in women who are premenopausal and perimenopausal. Dietary phytoestrogen intake is associated with reduced colorectal cancer risk. Associations between smoking, polymorphisms in polycyclic aromatic hydrocarbon (PAH) metabolism and conjugation genes and PAH-DNA adducts in prostate tumors differ by race. Cytochrome P450 1A1 (CYP1A1) polymorphisms and breast cancer risk in Korean women. Cor...
common in complete genomics
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[PharmGKB:Curated Increased risk for smokers to develop gastric cancer, no association for breast cancer.]
common in complete genomics
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[PharmGKB:Curated Homozygotes associated with breast cancer risk, negative association for SIDS.]
80 snps
(hide) Pain
higher risk for endometrial cancer
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rs4633 is a variant at codon 62 of the COMT gene, however, it does not change the amino acid sequence of the COMT protein. In a study of 150 (Caucasian) cases of endometrial cancer, a significant increase in rs4633(T;T) genotype was observed in patients compared to controls (OR = 2.39, CI: 1.31-4.37, p = 0.004). Furthemore, the frequency of the C-G haplotype of rs4633-rs4680 was significantly higher in controls (p < 0.0001) than in patients. This correlated with lower expression levels of the COMT protein in carriers of these alleles. pubmed 1180576 Schizophrenia Susceptibility Genetic basis for individual variations in pain perception and the development of a chronic pain condition [PharmGKB:Curated On the basis of subjects' pain responsiveness, haplotypes involving rs6269 (A/G), rs46...
Magnitude: 1.7
possible low pain sensitivity
suggests you may be able to tolerate more pain than most people. However phased data may be necessary to increase certainty. See also gs232 gs233 gs234 gs235
possible high pain sensitivity
suggests you may be able to tolerate less pain than most people. However phased data may be necessary to increase certainty. See also gs232 gs233 gs234 gs235
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[PharmGKB:Non-Curated GWAS results: Genome-wide association study of acute post-surgical pain in humans. (Initial Sample Size: 60 females, 52 males; Replication Sample Size: NR); (Region: 1p21.3; Reported Gene(s): NR; Risk Allele: rs6693882-?); (p-value= 0.000002).This variant is associated with Pain.] [GWAS:Pain]
Frequency: 45.1%
References:2
References:2
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[PharmGKB:Non-Curated GWAS results: Genome-wide association study of acute post-surgical pain in humans. (Initial Sample Size: 60 females, 52 males; Replication Sample Size: NR); (Region: 11q23.3; Reported Gene(s): NR; Risk Allele: rs17122021-?); (p-value= 0.0000007).This variant is associated with Pain.] [GWAS:Pain]
multiple associations, see details
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rs4680 (Val158Met) is a well studied SNP in the COMT gene. 23andMe blog summarizes them as *rs4680(A) = Worrier. Met, more exploratory, lower COMT enzymatic activity, therefore higher dopamine levels; lower pain threshold, enhanced vulnerability to stress, yet also more efficient at processing information under most conditions *rs4680(G) = Warrior. Val, less exploratory, higher COMT enzymatic activity, therefore lower dopamine levels; higher pain threshold, better stress resiliency, albeit with a modest reduction in executive cognition performance under most conditions Roughly speaking, the predominant wisdom (known colloquially as the warrior/worrier hypothesis; summary at ) posits that people with Val alleles have increased COMT activity and lower prefrontal extracellular dopamine compar...
slightly less drug dependence, decreased effectiveness of analgesics
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Genome-wide association study identifies a potent locus associated with human opioid sensitivity rs2952768(C) was associated with more analgesic requirements ... exhibited less vulnerability to severe methamphetamine or alcohol dependence, fewer eating disorders, and a lower ‘Reward Dependence’ score on a personality questionnaire. The (C;C) genotype was significantly associated with the elevated expression of a neighboring gene, CREB. SNPs in this locus are the most potent genetic factors associated with human opioid sensitivity known to date, affecting both the efficacy of opioid analgesics and liability to severe substance dependence. Our findings provide valuable information for the personalized treatment of pain and drug dependence. [GWAS:Opioid sensitivity]
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[PharmGKB:Non-Curated GWAS results: Genome-wide association study of acute post-surgical pain in humans. (Initial Sample Size: 60 females, 52 males; Replication Sample Size: NR); (Region: 19p12; Reported Gene(s): LOC400680, ZNF429; Risk Allele: rs2562456-?); (p-value= 0.0000000002).This variant is associated with Pain.] [GWAS:Pain]
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[PharmGKB:Curated On the basis of subjects' pain responsiveness, haplotypes involving rs6269 (A/G), rs4633 (C/T), rs4818 (C/G), and rs4680 (G/A) were designated as low (low pain sensitivity (LPS) haplotype; GCGG), average (average pain sensitivity (APS) haplotype; ATCA), or high (high pain sensitivity (HPS) haplotype; ACCG) pain sensitive.]
Magnitude: 0.1
normal pain sensitivity
You probably experience typical sensitivity to pain according to See also gs232, gs234, and gs235
Normal perception of pain
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rs6746030 is a SNP in the sodium channel Nav1.7 SCN9A gene. In five cohorts tested, totaling 1,277 individuals, the rarer rs6746030(A) allele was associated with increased pain (p=0.0001).
3 genosets 8 snps
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Lack of empathy? You have a SNP in the oxytocin receptor which may make you less empathetic than most people. When under stress you may have more difficulty recognizing the emotional state of others which impacts loneliness, parenting, and socializing skills. Some studies have suggested that the A;G genotype is associated with an intermediate level of empathy (compared to the G;G and A;A genotypes), although most report that A;G and A;A individuals have similar levels of empathy and stress handling capabilities.
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rs53576 is a silent G to A change in the oxytocin receptor (OXTR) gene. Studies have demonstrated that individuals with the G allele are more empathetic, feel less lonely, employ more sensitive parenting techniques, and have lower rates of autism (discussed in ) The blog Not Exactly Rocket Science discusses that Americans with (G;G) tend to be more sensitive parents, more empathetic and less lonely than those with an ‘A’. In a Korean population people with (G;G) were less likely to seek support from their peers. Culture, distress, and oxytocin receptor polymorphism (OXTR) interact to influence emotional support seeking. Oxytocin receptor genetic variation relates to empathy and stress reactivity in humans. In brief, people with the G;G genotype were better able to discern the e...
long form of 5-HTTLPR. less sensitive to pain 23andMe reports that this genotype is not reliable on their platform. 23andMe users should ignore this result. happier, less sensitive to pain You consider perpetrating unintentional harm as more acceptable The genotype of this SNP is not meaningful on 23andme v3. *https://www.23andme.com/you/community/thread/6192/
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According to David Hinds of 23andMe on community forums, 'nearly everyone (99.97%) is getting called as CC, and there is no clear heterozygote cluster' ... 'the genotype calls for rs25531 on our platform are not meaningful.' Looking at OpenSNP frequency data, this seems to be universal for direct to consumer genotyping services at this stage. The minor allele (G) of rs25531 is almost always in phase with the long (L) allele of the 5-HTTLPR, which is the most commonly studied variation in this region. The (L) long allele may be associated with lower levels of serotonin. The article and video from 'The Atlantic' suggests that children with the short allele (A), may need and benefit greatly from more maternal support *http://www.theatlantic.com/doc/200912/dobbs-orchid-gene In contrast to earl...
Normal risk of sexual dysfunction when taking SSRI Antidepressants.
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rs6311 (-1438A>G / A-1438G or -1438G>A / G-1438A) is a SNP located upstream (and within the promoter region of) HTR2A. Multiple Regulatory Variants Modulate Expression of 5-Hydroxytryptamine 2A Receptors in Human Cortex. The minor A allele of rs6311 reduces expression of a previously unannotated extension of the 5' untranslated region of HTR2A mRNA. rs6311 together with rs6314 have a modest effect on depression severity, when examined in the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) study. Three (rs643627-rs594242-rs6311: A-C-T), two (rs594242-rs6311: C-T) and a single functional (rs6311: T) marker were protective against suicidal behavior. The complementary markers (rs594242-rs6311: G-C and rs6311: C) were associated with increased risk for non-violent and impu...
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[GWAS:Personality dimensions]
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[PharmGKB:Non-Curated GWAS results: Genome-wide association scan for five major dimensions of personality. (Initial Sample Size: 3,972 individuals; Replication Sample Size: 3,903 individuals); (Region: Xp11.3; Reported Gene(s): FUNDC1; Risk Allele: rs6610953-G); (p-value= 0.000006).This variant is associated with Personality dimensions.] [GWAS:Personality dimensions]
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[GWAS:Personality dimensions]
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[GWAS:Personality dimensions]
normal
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rs1800759 is a SNP in the promoter (regulatory region) of the alcohol dehydrogenase 4 (ADH4) gene. In a study of 500+ patients with either alcohol dependence or drug dependence, rs1800759 was the most significant ADH4 SNP to be associated (in a recessive manner) with increased risk for either condition, at least in Caucasians. In another study, a five-factor model of personality in 243 subjects with substance dependence (175 European Americans [EAs] and 68 African Americans [AAs]), along with 296 healthy control subjects (256 EAs and 40 AAs), was conducted in association with an ADH4 SNP survey. rs1800759(A) alleles and (A;A) genotypes A/A were significantly associated with agreeableness scores.
Frequency: 38.5%
References:1
References:1
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[GWAS:Personality dimensions]
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The G allele of SNAP25 gene SNP rs362584 was associated with increased neurotic traits (combined p value = 0.0000522) in a group of 3972 Sardinians, and two smaller replicative samples from the USA and Netherlands (the replicative samples were not significant by themselves, with the Netherlands sample showing considerably less of a trend).full paper in pdf
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Our findings suggest an influence of the gene in the neural substrate mediating sensorimotor gating and working memory, especially when combined with high anxiety. Genetic associations with schizophrenia: meta-analyses of 12 candidate genes. The neurobiology of D-amino acid oxidase and its involvement in schizophrenia. Persistence criteria for susceptibility genes for schizophrenia: a discussion from an evolutionary viewpoint.
multiple associations, see details
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rs4680 (Val158Met) is a well studied SNP in the COMT gene. 23andMe blog summarizes them as *rs4680(A) = Worrier. Met, more exploratory, lower COMT enzymatic activity, therefore higher dopamine levels; lower pain threshold, enhanced vulnerability to stress, yet also more efficient at processing information under most conditions *rs4680(G) = Warrior. Val, less exploratory, higher COMT enzymatic activity, therefore lower dopamine levels; higher pain threshold, better stress resiliency, albeit with a modest reduction in executive cognition performance under most conditions Roughly speaking, the predominant wisdom (known colloquially as the warrior/worrier hypothesis; summary at ) posits that people with Val alleles have increased COMT activity and lower prefrontal extracellular dopamine compar...
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[GWAS:Personality dimensions]
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[GWAS:Personality]
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[PharmGKB:Non-Curated GWAS results: Genome-wide association scan for five major dimensions of personality. (Initial Sample Size: 3,972 individuals; Replication Sample Size: 3,903 individuals); (Region: 2p22.1; Reported Gene(s): THUMPD2; Risk Allele: rs2540226-T); (p-value= 0.000003).This variant is associated with Personality dimensions.] [GWAS:Personality dimensions]
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The A allele of the CLOCK gene SNP rs6832769 was associated with lessened agreeableness (p = 0.00000871) in a group of 3972 Sardinians. The effect remained significant in the replicative American sample, but failed to achieve significance in the Norwegian sample and third sample (though the combined p value remained significant at 0.000865). full paper in pdf [PharmGKB:Non-Curated GWAS results: Genome-wide association scan for five major dimensions of personality. (Initial Sample Size: 3,972 individuals; Replication Sample Size: 3,903 individuals); (Region: 4q12; Reported Gene(s): CLOCK; Risk Allele: rs6832769-A); (p-value= 0.000002).This variant is associated with Personality dimensions.]
higher risk for RA
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rs6313, also known as T102C, is part of a 4-SNP haplotype in the serotonin 2A receptor gene HTR2A that has been associated with rheumatoid arthritis in a study of 1800 European patients. The risk allele is rs6313(C). The overall risk for the haplotype CTCC of SNPs rs6311-rs1328674-rs6313-rs6314 is 1.68 (CI: 1.20 - 2.34, p = 0.02). Note: the orientation of rs1328674 in dbSNP is opposite that cited by this publication; therefore, with respect to dbSNP, the haplotype of risk as cited above is CACC rather than CTCC. see also gs108 and gs226 Polymorphisms in the serotonin receptor gene HTR2A are associated with quantitative traits in panic disorder. [PharmGKB:Curated Risk or phenotype-associated allele (s): T/T. Phenotype: Patients, with a diagnosis of probable Alzheimer's disease, carryi...
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[PharmGKB:Non-Curated GWAS results: Genome-wide association scan for five major dimensions of personality. (Initial Sample Size: 3,972 individuals; Replication Sample Size: 3,903 individuals); (Region: 19q13.31; Reported Gene(s): ZNF180; Risk Allele: rs644148-G); (p-value= 0.0000009).This variant is associated with Personality dimensions(openness).] [GWAS:Personality dimensions]
normal
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rs1611115 (C-1021T) is a SNP near the dopamine beta-hydroxylase (DBH) gene. per OMIM, the T allele is associated with lower DBH expression in plasma (16 of TT genotype had DBH activity of 4.1, 46 of CT genotype had DBH activity of 25.2, and 112 of CC genotype had DBH activity of 48.1 nmol/min/ml) Association tests related to affective disorders such as ADHD were performed using four independent samples, healthy volunteers (N = 387), patients with affective disorders (N = 182), adult attention deficit hyperactivity disorder (ADHD) patients (N = 407), and patients with personality disorders (N = 637). Personality disorder patients carrying the DBH TT genotype exhibited higher neuroticism and novelty seeking scores as compared to individuals with the (C;C) or (C;T) genotype. Analyses on the l...
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[GWAS:Personality dimensions]
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[GWAS:Personality dimensions]
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[GWAS:Personality]
complex; possible association with anxiety related behaviours
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In mice, the genetic locus best correlated to anxiety-related behaviour contains the 'regulator of G protein signaling 2' gene . In humans, SNPs in the equivalent RGS2 gene have now been studied to see if they are correlated to anxiety related disorders. In the first part of one study, 119 families including children underwent standard lab-based behavioural assessments of behavioural inhibition, defined as a heritable temperamental profile characterized by a tendency to be shy, avoident, and behaviourally restrained in situations that are novel or unfamiliar. Along with some other RGS2 SNPs, carriers of a rs4606(G) allele were 3 fold more likely to exhibit behavioural inhibition (CI: 1.31-6.84, p = 0.0026). In the second part of this study, 744 college undergraduates (228 men, 516 women) w...
Magnitude: 0
References:12
References:12
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Rs35753505 (SNP8NRG221533) is located within the 5'-flanking region of the NRG1 (Neuregulin 1) gene. g2b2mh blog rs35753505(C;C) correlates with frontal brain having to working harder during a working memory task. personality traits - C allele carriers associated with higher (NEO-FFI) scores of neuroticism and lower scores of conscientiousness in a sample of 523 healthy individuals The results suggest that subjects with risk alleles show hyperactivations in areas associated with elaborate episodic memory encoding and retrieval strategies.
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rs1800544 (C-1291G) is a SNP located in the promoter region of ADRA2A (adrenergic receptor alpha 2A). GG genotype carriers had significantly higher consumption of sweet food products (Estonian Children Personality Behavior and Health Study subset, n = 419) GG genotype carriers had significantly higher scores on an assessment of depression, and significantly lower scores on morality and orderliness compared to CC carriers. girls with CC and CG genotypes scored higher than boys with the same genotypes on an assessment of extraversion. boys with GG genotypes, however, scored higher than girls with GG genotypes. GG genotype assoc. w/ higher scores of inattention Food Preference [OMIM:ALPHA-2A-ADRENERGIC RECEPTOR; ADRA2A]
27 snps
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CYP3A5*3 homozygote; CYP3A5 non-expressor Impacts metabolism of tacrolimus, an immunosuppressive drug used in organ transplantation. This is the most common phenotype in caucasian and many other populations. Only in africans is expressing the gene common.
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rs776746, also known as 6986A>G, is a SNP encoding the (nonfunctional) CYP3A5*3 allele of the CYP3A5 gene. CYP3A5*3 has been studied especially in connection with the metabolism of tacrolimus, an immunosuppressive drug used in organ transplantation. The optimal therapeutic dose is in a relatively narrow window, so blood concentration monitoring is recommended. CYP3A5*3 carriers tend to build up higher levels of tacrolimus than CYP3A5*1 carriers, unless their tacrolimus intake is reduced. Risk of testicular germ cell cancer in relation to variation in maternal and offspring cytochrome p450 genes involved in catechol estrogen metabolism. Polymorphisms in the cytochrome P450 genes CYP1A2, CYP1B1, CYP3A4, CYP3A5, CYP11A1, CYP17A1, CYP19A1 and colorectal cancer risk. Prevalence of common dis...
3.5x asthma risk in certain populations
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This SNP, in the GSTP1 gene influences asthma risk; the (A) allele encodes the Ile, while the (G) allele encodes the Val. This SNP is also known as GSTP1Val105, or GSTP1 Ile105Val. Despite evidence of antioxidant effects of vitamin E in vitro and in animal studies, large, randomized clinical trials have not substantiated a benefit of vitamin E in reducing inflammation in humans. In healthy control subjects, the effect of α-tocopherol supplementation on the production of inflammatory cytokines appears to be dependent on an individual's genotype. These genotype-specific differences may help explain some of the discordant results in studies that used vitamin E. Persons having the alleles AA or AG had an increase in interleukin-6 (IL-6) upon supplementing alpha-tocopherol (the most common...
Carrier of one CYP1A2*1F allele; Slow Caffeine Metabolizer. One copy of the slow caffeine metaboliser SNP, and one copy of the fast version. This makes you more strongly affected by drinking coffee, as caffeine is broken down slower in the liver. Supposedly this increases the risk of heart attacks, although other studies show caffeine is generally good for the heart. It also makes caffeine more effective at preventing Breast Cancer, Alzheimer's Disease, and Parkinson's disease. Too much caffeine will shrink your breasts.
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rs762551, also known as -164A>C or -163C>A, is a SNP encoding the CYP1A2*1F allele of the CYP1A2 gene. For historic reasons, the rs762551(C) allele is considered the wild-type, even though it is the rarer allele in most populations. The rs762551(A) allele is the 'fast metabolizer' allele known as CYP1A2*1F; the (C) allele is by comparison a slower metabolizer of certain substrates (including caffeine). In terms of genotypes, only rs762551(A;A) individuals are considered fast metabolizers. Individuals who are rs762551(A;C) heterozygotes or rs762551(C;C) homozygotes are both considered slow metabolizers. The CYP1A2 gene encodes a member of the cytochrome p450 family of proteins, which metabolize nutrients and drugs. One well known substrate of CYP1A2 is caffeine; individuals who are ca...
Slower metaboliser for some drugs
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rs1045642, also known as C3435T, is a SNP located in the ABCB1 gene. It is often studied in conjunction with rs2032582. C3435T has been mentioned by: * A 'Silent' Polymorphism in the MDR1 Gene Changes Substrate Specificity (for example, to verapamil) * (R)-lansoprazole (Prevacid) concentrations are significantly increased in CYP2C19 extensive metabolizers with ABCB1 C3435T C allele. * In a Korean population, plasma concentrations of fexofenadine (Allegra) were 17% lower in 2677AA/3435CC subjects and 47% higher in the 2677TT/3435TT subjects compared to 2677GG/3435CC subjects. * In contrast, in this study no association was observed between the C3435T polymorphism and fexofenadine plasma or urine concentrations in a German Caucasian population. * A meta-analysis including 9 case-control stud...
Carrier of one CYP2D6 decreased or non-functioning variant. Your body may have a reduced ability to process some medicines. You are a carrier for rs1065852(T;T)
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The wild type (normal) allele at this SNP is (C). The (T) variant indicates the presence of a non-wild type CYP2D6 variant, but it appears in many different variants so it can not be used to determine the presence of any particular variant. The most common variants it appears in are CYP2D6*10 and CYP2D6*4, but these are not the only ones. While this is the defining mutation for CYP2D6*10, it is not possible by itself for this mutation to determine a particular variant. In addition, the CYP2D6*4 variant includes this mutation, but the defining mutation 1846G>A SNP is not available in the common direct to consumer testing services. While it is not possible for this mutation to identify one particular variant, all the variants in which it appears have reduced or no CYP2D6 activity. If two ...
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[PharmGKB:In-Depth A study of 124 White patients, which received a high-dose regimen consisting of cyclophosphamide, thiotepa and carboplatin as intravenous infusions, concludes patients homozygous for the GSTP1 C341T allele may have enhanced exposure to thiotepa and tepa.]
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The (C;C) genotype is linked to reduced UGT1A1 activity, and increased Bilirubin, except in people of African origin for whom the T allele is a risk factor for breast cancer. [Genetic polymorphisms of MPO, NQO1, GSTP1, UGT1A6 associated with susceptibility of chronic benzene poisoning]. The influence of metabolic gene polymorphisms on urinary 1-hydroxypyrene concentrations in Chinese coke oven workers. Low-penetrance alleles predisposing to sporadic colorectal cancers: a French case-controlled genetic association study. [Relationship between genetic polymorphisms of phase I and phase II metabolizing enzymes and DNA damage of workers exposed to vinyl chloride monomer]. Serum bilirubin levels on ICU admission are associated with ARDS development and mortality in sepsis. Pazopanib-induced hyp...
Adverse reaction more likely to carbamazepine in epileptic patients
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rs2273697, also known as c1249G>A or p.V471I, is a nonsynonymous polymorphism in the ABCC2 gene. From an initial case-control study of 146 patients with epilepsy, followed by replication (p=0.001) in another 279 patients, the rs2273697(A) allele was associated with neurological adverse drug reactions from taking carbamazepine. Functional studies showed that this SNP selectively reduced carbamazepine transport across the cell membrane. [PharmGKB:Curated Risk or phenotype-associated allele: A. Phenotype: This SNP showed a strong association with the neurological adverse drug reaction caused (ADR) by carbamazepine (P=0.005). The study results indicate that the c.1249A variant is an independent risk factor of carbamazepine CNS ADR. Study size: 146 patients with epilepsy who had been prescr...
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Pharmacokinetics of efavirenz when co-administered with rifampin in TB/HIV co-infected patients: pharmacogenetic effect of CYP2B6 variation. The pharmacokinetics and pharmacogenomics of efavirenz and lopinavir/ritonavir in HIV-infected persons requiring hemodialysis. Polymorphisms of drug-metabolizing enzymes (GST, CYP2B6 and CYP3A) affect the pharmacokinetics of thiotepa and tepa. The impact of cytokines on the expression of drug transporters, cytochrome P450 enzymes and chemokine receptors in human PBMC. Associations between CYP2B6 polymorphisms and pharmacokinetics after a single dose of nevirapine or efavirenz in African americans. CYP2B6 (c.516G-->T) and CYP2A6 (*9B and/or *17) polymorphisms are independent predictors of efavirenz plasma concentrations in HIV-infected patients. CYP...
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rs1208 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The risk allele for this SNP is rs1208(G). [PharmGKB:Curated in vitro study; PK: 20-fold reduction in Vmax vs wild type] [OMIM:?]
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rs2306283 (Asn130Asp/N130D, A388G/388A>G) is a SNP within SLCO1B1 (Solute carrier organic anion transporter family member 1B1). A G at this location denotes the SLCO1B1*1B allele. among 8 healthy volunteers with *1B/*1B genotypes and 16 with the *1A/*1A genotype, *1B/*1B genotype associated with reduced plasma concentrations of repaglinide (but not nateglinide) consistent with increased hepatic uptake by SLCO1B1 (but w/ limited effects on nateglinide pharmacokinetics) news rs2306283 influences statin-related myopathy risk Genotyping panel for assessing response to cancer chemotherapy. Common variants in the SLCO1B3 locus are associated with bilirubin levels and unconjugated hyperbilirubinemia. Pazopanib-induced hyperbilirubinemia is associated with Gilbert's syndrome UGT1A1 polymorphism...
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rs1801280, also known as T341C, is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The allele associated with slow NAT2 metabolization for this SNP is rs1801280(C). Genosets gs154 and gs156 evaluate predicated NAT2 metabolizer phenotype based on rs1041983 and rs1801280. [PharmGKB:Curated in vitro study; PK: 20-fold reduction in Vmax vs wild type] [OMIM:?]
1.6x risk for ICP
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rs3740066, a SNP in the ABCC2 gene, is reported to be associated with a higher risk of developing intrahepatic cholestasis of pregnancy (ICP) based on a study of ~70 Argentinian patients. ICP is associated with increased fetal risks such as premature birth or intrauterine death. The risk allele is rs3740066(A), and the odds ratio for homozygous rs3740066(A;A) mothers is 4.44 (CI: 1.83 - 10.78), and for heterozygous mothers 1.65 (CI: 0.76 - 3.64), compared to rs3740066(G;G) mothers. [PharmGKB:Curated The AUCs of irinotecan, SN-38, SN-38 glucuronide, and APC are influenced by rs3740066, rs2306283, rs35605, rs10276036, and rs717620 .]
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[PharmGKB:Non-Curated PEPT2*1 (350L-409P-509R) showed lower K m for glycyl-sarcosine as compared with PEPT2*2 (350F- 409S-509K) in transfected cells.]
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[PharmGKB:Non-Curated PEPT2*1 (350L-409P-509R) showed lower K m for glycyl-sarcosine as compared with PEPT2*2 (350F- 409S-509K) in transfected cells.]
may require more methadone during heroin withdrawal
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rs1128503 is a SNP in the transporter P-glycoprotein (P-gp) 170, encoded by the ABCB1 (also known as MDR1) gene. Methadone is a substrate of this protein, so variants may affect the efficacy and optimal dosage of this drug as used for treating opiate dependence. A study of 98 methadone-maintaining patients concluded that the higher (>150 mg/day) and lower (< or =150 mg/day) methadone dose groups differed significantly in their rs1128503 status (experiment-wise p = 0.0325). Furthermore, individuals with the 3-locus genotype pattern (T;T)-(T;T)-(T;T) for SNPs rs1045642, rs2032582 and rs1128503, respectively, had an approximately 5-fold chance of requiring the 'higher' methadone dose, while individuals heterozygous for these three SNPs have an approximately 3-fold chance of stabilizing ...
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[PharmGKB:Non-Curated PEPT2*1 (350L-409P-509R) showed lower K m for glycyl-sarcosine as compared with PEPT2*2 (350F- 409S-509K) in transfected cells.]
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Association of the multidrug-resistance-associated protein gene (ABCC2) variants with intrahepatic cholestasis of pregnancy. Polymorphisms of MRP2 (ABCC2) are associated with susceptibility to nonalcoholic fatty liver disease. MRP2 and GSTP1 polymorphisms and chemotherapy response in advanced non-small cell lung cancer. Genetic polymorphisms influence mycophenolate mofetil-related adverse events in pediatric heart transplant patients. ADME pharmacogenetics: investigation of the pharmacokinetics of the antiretroviral agent lopinavir coformulated with ritonavir. Interindividual variability in hepatic expression of the multidrug resistance-associated protein 2 (MRP2/ABCC2): quantification by liquid chromatography/tandem mass spectrometry. A comprehensive study of polymorphisms in ABCB1, ABCC2...
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[PharmGKB:Curated Risk or phenotype-associated allele: SLCO1B3: T334. Phenotype: The metabolic ratio of glucuronidated mycophenolic acid (MPAG) to mycophenolic acid (MPA) showed a very significant decrease in carriers of the SLCO1B3 T334 allele (p = 0.0001). Carriers of at least one SLCO1B3 T334 allele (n = 22) had a 1.42-fold higher (p = 0.0003) MPA AUC(0-12 hours) and a 1.38-fold higher (p = 0.0010) Cmax as compared with carriers of the 334GG genotype (n = 48). Patients carrying 334 TT or TC genotypes (n = 22) had significantly higher MPA AUC(4-9 hours) than patients carrying the CC genotype (n = 48; p = 0.0027). However, they also had higher AUC(0-4 h) (p = 0.0008), resulting in an unchanged AUC(4-9 h)/AUC(0-9 h) ratio (p = 0.4945). In the subgroups of patients cotreated with sirolimus ...
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[PharmGKB:Curated Risk or phenotype-associated allele: SCLO1B3 haplotype formed by 112Ser>Ala (rs4149117, 334T>G) and 223Met>Ile (rs7311358, 699G>A). Phenotype: HEK293 cells transiently expressing the SCLO1B3 334G-699A haplotype or reference haplotype were incubated in the presence of increasing concentrations of mycophenolic acid phenyl-glucuronide (MPAG) for 10 min. The uptake of MPAG according to the SCLO1B3 334G-699A haplotype was markedly lower than in cells expressing the reference sequence 334T-669G. Type of association: GN; FA; PK]
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rs1801030 (Met223Val) is a snp within SULT1A1 (Sulfotransferase 1A1) and defines the SULT1A1*3 allele. [PharmGKB:In-Depth SULT1A1*3 is the second most common SULT1A1 SNP.]
normal
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The (-) form of this SNP, representing a deletion of one nucleotide, causes a frameshift such that the resulting CYP2D6 protein is nonfunctional. The associated allele is also known as CYP2D6*6, and there are several subtypes but they are all nonfunctional. If two copies of this (or similar) changes are inherited, CYP2D6 poor metabolism ('PM') is observed. CYP2D6 poor metabolism may affect the efficacy or degree of side effects of drugs metabolized by CYP2D6, such as dextromorphan, sparteine, nortriptyline, venlafaxine and codeine. Response to serotonin reuptake inhibitors in OCD is not influenced by common CYP2D6 polymorphisms. [PharmGKB:Curated This variant is part of the CYP2D6*6 PM haplotype. Plasma concentrations of metoprolol were shown to be were 4.9-fold higher in the PMs, with gr...
normal
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rs9332131, also known as 818delA, 10601delA or 273Frame shift, is a SNP in the CYP2C9 gene. The rs9332131(-) allele defines the CYP2C9*6 variant, which is inactive. [PharmGKB:Curated Phenotype: In African Americans patients, weekly warfarin dose requirements were lower in those with the CYP2C9*8 allele (34 (30-47) mg; P = 0.023) and the CYP2C9 *2, *3, *5, *6, or *11 allele (33(28-40 mg); P < 0.001) as compared with those with the CYP2C9*1/*1 genotype (43 (35-56) mg). Adding the *5,*6,*8 and *11 alleles to a model containing the *2 and *3 alleles plus the VKORC1 -1639 G>A allele (along with clinical variables) explained 36% vs. 30% of the variability in dose requirements. Study size: 226 . Study population/ethnicity: African-American . Type of association: PD;GN;CO]
normal; no change in warfarin metabolism
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rs1799853 is a SNP in the CYP2C9 gene and is linked to poor warfarin metabolism. Advanced knowledge of this may influence initial warfarin dosing by physicians. Warfarin is monitored through INR (international normalized ratio) and proper dosing is influenced by a variety of factors including warfarin metabolism and diet. rs1799853 is a SNP in the CYP2C9 gene. The rs1799853(T) allele encodes a variant amino acid, cysteine, which has been linked to poor metabolism of warfarin and thus sensitivity . The common nomenclature for this polymorphism is CYP2C9*2 (Cys amino acid, T allele; the SNP is also known as C430T or Cys144Arg). The CYP2C9*2 allele is also associated with higher sensitivity to the anti-epileptic drug phenytoin. The effect of CYP2C9 variants on drug metabolism should not be pr...
normal; no effect on warfarin metabolism
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SNP rs1057910(A), located in the cytochrome p450 CYP2C9 gene, most commonly encodes the amino acid isoleucine at position 359, and the resulting allele is also known as CYP2C9*1. rs1057910(C) encodes a leucine at this same position, and the resulting allele is called CYP2C9*3. This SNP is also known as Ile359Leu or A1075C. The effect of CYP2C9 variants on drug metabolism should not be predicted without also considering CYP2C9*2, defined as the common loss of function variant rs1799853(T) (NM_000771:c.430C>T, NP_000762:p.144R>C) Studies of the effects of these alleles include: * rs1057910(C;C)] genotypes may clear drugs like celecoxib (trade name Celebrex) twice as slowly as rs1057910(A;A) genotypes; the rs1057910(A;C) genotypes are in-between clearance rates. Lower clearance rates wi...
Normal common for Caucasians on the 23andme platform
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rs1799930 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. Also known as G590A. The risk allele for this SNP is rs1799930(A). [PharmGKB:Curated in vitro study; PK: 22-fold reduction in Vmax vs wild type] [OMIM:?]
normal
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influences statin response *rs72559745 (SLCO1B1*1) AA AA *rs56061388 (SLCO1B1*3) TT TT *rs4149056 (SLCO1B1*5) TT TT *rs55901008 (SLCO1B1*6) TT TT rs4149056, also known as 37041T>C or V174A, is a SNP in the SLCO1B1 gene, which encodes the 'organic anion transporting polypeptide 1B1' (OATP1B1) protein. This protein, found primarily in the liver, regulates the uptake of numerous drugs and natural compounds. The rs4149056(C) SNP defines the SLCO1B1*5 allele. The rs4149056(C) allele gives rise to an amino acid change (from valine to alanine at residue 174) which has reduced uptake/transport activity. Therefore, drugs metabolized by OATP1B1 tend to build up to higher circulating concentrations than they would otherwise.. The drugs known (or in some cases, thought) to be transported less well ...
common in clinvar
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Technology to accelerate pangenomic scanning for unknown point mutations in exonic sequences: cycling temperature capillary electrophoresis (CTCE). Genetic variation in the one-carbon transfer pathway and ovarian cancer risk. Strong association of a common dihydropyrimidine dehydrogenase gene polymorphism with fluoropyrimidine-related toxicity in cancer patients. Genetic variation in TYMS in the one-carbon transfer pathway is associated with ovarian carcinoma types in the Ovarian Cancer Association Consortium. [PharmGKB:Curated Patients heterozygous for the C allele of this SNP exhibited increased incidence of medium-severe nausea and vomiting (as defined by WHO criteria) relative to those carrying only the T allele. The patient population consisted of individuals with gastric or colon ca...
Magnitude: 0
Frequency: 75.2%
Repute:Good
References:16
Frequency: 75.2%
Repute:Good
References:16
common on affy axiom data
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CYP2C8 SNP, defining the CYP2C8*3 allele (along with rs11572080). Individuals carrying this SNP may show increased risk of developing acute gastrointestinal bleeding during the use of NSAIDs that are CYP2C8 or CYP2C9 substrates, such as aceclofenac, celecoxib, diclofenac, ibuprofen, indomethazine, lornoxicam, meloxicam, naproxen, piroxicam, tenoxicam and valdecoxib. [PharmGKB:Curated Risk or phenotype-associated allele: G. Phenotype: In woman, the risk of acute myocardial infarction (AMI) tended to be higher for subjects carrying the CYP2C8*3*3 genotype versus *1*1 (OR = 1.9). The CYP2C8*3 variants are 416G>A (rs10509681) and 1196A>G (rs11572080). Tested in all subjects, the risk of AMI was also higher in individuals carrying the CYP2C8*3 allele (*3*3; *1*3 versus*1*1) [1.2 (1.0-1.5...
normal
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rs4244285 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*2 variant. This variant is the most common reason for poor metabolism of compounds like mephenytoin (an anti-convulsant), some antidepressants, the anti-platelet drug Plavix, and some drugs used for ulcer conditions of various types. The risk allele is rs4244285(A). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (trade name Prevacid). In Caucasians, SNPs in CYP2C19 are relatively rare (in contrast to SNPs in CYP2D6), but SNPs in this gene are common in Asians. Ulcer treatment with omeprazole to reduce Helicobacter pyl...
Magnitude: 0
Frequency: 77.1%
Repute:Good
References:17
Frequency: 77.1%
Repute:Good
References:17
common on affy axiom data
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CYP2C8 SNP, defining the CYP2C8*3 allele (along with rs10509681). Individuals carrying this SNP may show increased risk of developing acute gastrointestinal bleeding during the use of NSAIDs that are CYP2C8 or CYP2C9 substrates, such as aceclofenac, celecoxib, diclofenac, ibuprofen, indomethazine, lornoxicam, meloxicam, naproxen, piroxicam, tenoxicam and valdecoxib. [PharmGKB:Curated Risk or phenotype-associated allele: A. Phenotype: This variant was associated with increased risk for neurotoxicity with paclitaxel treatment. Study size: 132. Study population/ethnicity: Patients with Neoplasms receiving paclitaxel; Spain. Significance metric(s): HR = 1.54 (0.96-2.47); p = 0.072. Type of association: PK; TOX.]
normal
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rs2231142, also known as Q141K and C421A, is a SNP in the ABCG2 gene, indicating a missense variant. 'Our data indicate that at least 10% of all gout cases in whites are attributable to this causal variant.' A is the risk allele. A large study totaling 7,699 participants in the Framingham cohort and 4,148 participants in the Rotterdam cohort was conducted, with genome-wide significant SNPs then replicated in 11,000+ Caucasian and ~4,000 African-American individuals who took part in the study of Atherosclerosis Risk in Communities (ARIC). This study calculated an odds ratio of 1.74 for rs2231142 (CI: 1.51-1.99, p = 3.3x10e-15). A genetic score comprised of this SNP plus 2 others may stratify risk for gout. Among non-small cell lung cancer patients treated with gefitinib, there's a 4-5x high...
common in complete genomics
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[PharmGKB:Non-Curated Increased metformin uptake in transfected cells] [GWAS:Blood metabolite levels]
normal
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The rs3758581(A) SNP defines a CYP2C19 allele known as V331I. Analysis of 50 SNPs in CYP2D6, CYP2C19, CYP2C9, CYP3A4 and CYP1A2 by MALDI-TOF mass spectrometry in Chinese Han population.
common in complete genomics
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[PharmGKB:Curated In an 80-patient study, this variant was not associated with plasma concentrations of montelukast or with response to treatment with montelukast.]
common in complete genomics
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[PharmGKB:Curated Risk or phenotype-associated allele: T. Phenotype: CYP2B6*2 genotype in the transplant recipient was associated with hemorrhagic cystitis. Study size:107 . Study population/ethnicity: Donors and patients with leukemia after HLA-identical hematopoietic stem cell transplantation, France. Significance metric(s): p = 0.03. Type of association: TOX]
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Also known as Ile462Val A4889G CYP1A1*2C Genome amplification of single sperm using multiple displacement amplification. Decision forest analysis of 61 single nucleotide polymorphisms in a case-control study of esophageal cancer; a novel method. Multilocus analysis of SNP and metabolic data within a given pathway. CYP1A1 and CYP1B1 polymorphisms and their association with estradiol and estrogen metabolites in women who are premenopausal and perimenopausal. Dietary phytoestrogen intake is associated with reduced colorectal cancer risk. Associations between smoking, polymorphisms in polycyclic aromatic hydrocarbon (PAH) metabolism and conjugation genes and PAH-DNA adducts in prostate tumors differ by race. Cytochrome P450 1A1 (CYP1A1) polymorphisms and breast cancer risk in Korean women. Cor...
common in complete genomics
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[PharmGKB:Curated Increased risk for smokers to develop gastric cancer, no association for breast cancer.]
common in complete genomics
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[PharmGKB:Curated This variant is in exon 1b of ABCB1 and may be associated with tacrolimus pharmacokinetics in renal transplant recipients. It was also associated with lower ABCB1 mRNA expression and possibly being an useful invasive marker predicting poorly-differentiated colorectal adenocarcinomas and thereby the poor prognosis of the Japanese patients in the study.]
common in clinvar
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rs1142345 is a SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The risk allele for this SNP is rs1142345(G), and when it is the only variant in the TPMT gene, it encodes the TPMT*3C allele. While still rare, it is more common in African-Americans (2.4% of all alleles) than in Caucasians. Note that if the same allele also carries the rs1800460(A) SNP, the allele is actually a TPMT*3A allele (OMIM). The medicine 6-Mercaptopurine is metabolized by TPMT. Individual differences in TPMT activity associated with this SNP are now used to determine appropriate dosage range and interval for treatment. 23an...
common in complete genomics
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NAT2 slow acetylation, GSTM1 null genotype, and risk of bladder cancer: results from the Spanish Bladder Cancer Study and meta-analyses. Genetic variation in N-acetyltransferase 1 (NAT1) and 2 (NAT2) and risk of non-Hodgkin lymphoma.
common in clinvar
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rs1799931 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The risk allele for this SNP is rs1799931(A). [PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: The NAT2:rs1799931 G variant was associated with toxicity in response to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.003 Type of association: CO; TOX] [OMIM:?]
common in complete genomics
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rs1800584 is a rare SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The rs1800584(A) SNP defines the TPMT*4A allele (OMIM). wikipedia thiopurine drugs metabolized by TPMT include azathioprine, mercaptopurine, and thioguanine [PharmGKB:In-Depth This splicing variant results in very low TPMT activity and risk for hematologic toxicity as a result of treatment with thiopurines.]
normal
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rs9332130, also known as 815A>G, 10598A>G or E272G, is a SNP in the CYP2C9 gene. The rs9332130(G) allele defines the CYP2C9*10 variant.
normal
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rs2256871, also known as 752A>G, 10535A>G or H251R, is a SNP in the CYP2C9 gene. The rs2256871(C) allele defines the CYP2C9*9 variant.
Magnitude: 0
Frequency: 99.1%
Repute:Good
References:1
Frequency: 99.1%
Repute:Good
References:1
common in complete genomics
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CYP2B6 (c.516G-->T) and CYP2A6 (*9B and/or *17) polymorphisms are independent predictors of efavirenz plasma concentrations in HIV-infected patients. [PharmGKB:In-Depth This variant decreases enzyme activity and affects metabolism of coumarin and nicotine; part of the CYP2A6*17 haplotype.]
common in complete genomics
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23andMe reports that the A allele of rs3918290 is associated with the rare recessive disorder dihydropyrimidine dehydrogenase deficiency (DPD), also known as hereditary thymine-uraciluria or familial pyrimidinemia. Note that the terms used in the literature for this gene can be confusing, since the gene is in reverse orientation to the chromosome strand on the reference genome. pharmgkb - defines *2A allele, which has a significantly higher chance of 5-fluorouracil toxicity Fluorouracil Toxicity [PharmGKB:In-Depth Heterozygosity for the A allele of this SNP is associated with mucositis and leukopenia drug toxicity in cancer patients treated with fluorouracil. Heterozygous males were more likely than heterozygous females to develop severe toxicity. In this study, no A/A homozygotes were ob...
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:9
Frequency: 100.0%
Repute:Good
References:9
normal
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rs10264272, also known as 14690G>A, is a SNP in the CYP3A5 gene. indicates that this corresponds with CYP3A5*6, however, this seems doubtful. CYP3A5 allele nomenclature found at http://www.cypalleles.ki.se/cyp3a5.htm indicates that CYP3A5*6 (also known as 14690G>A) is a splicing defect resulting in essentially no activity in the gene. This does not correspond with dbSNP, which indicates that is a nucleotide substition (624G-A) which only results in a 'silent' substitution of AAG (Lysine) to AAA (Lysine). [PharmGKB:In-Depth Nonfunctional allele present predominantly in the African American population.]
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:2
Frequency: 100.0%
Repute:Good
References:2
normal
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rs12720461 is a SNP in the CYP1A2 gene. The rs12720461(T) allele defines the CYP1A2*1K_-729C>T variant. [PharmGKB:Curated Likely disrupts transcription factor binding, leading to reduced function.]
normal
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Something seems wrong between dbSNP and the results from 23andMe and FTDNA. See Talk:Rs4148323 for more information. rs4148323, a SNP also known as 211G>A or G71R, occurs in the UGT1A1 gene, and defines the UGT1A1*6 allele. This allele is associated with Gilbert's syndrome among Asians, Crigler-Najjar syndrome type II (CN-II), and transient familial neonatal hyperbilirubinemia. rs4148323(A) in exon 1 of the UGT1A1 gene is associated with hyperbilirubinemia. rs4148323 and several other nearby SNPs help predict serum total bilirubin levels, based on a study of 750 Japanese. [PharmGKB:Curated *6 is the most common UGT1A1 coding variant found in Asians. It may result in reduced capacity to metabolize irinotecan and hence irinotecan toxicity.] [OMIM:UDP-GLYCOSYLTRANSFERASE 1 FAMILY, POLYPEP...
common in complete genomics
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[PharmGKB:Non-Curated Increased sensitivity to inhibition by TBA in oocytes]
normal
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rs9332239, also known as 1465C>T, 50338C>T or P489S, is a SNP in the CYP2C9 gene. The rs9332239(T) allele defines the CYP2C9*12 variant. According to a 23andMe discussion This is one of the SNPs which were re-analyzed April 2009. Customers with older data may wish to redownload. SNPs effected rs4420638, rs34276300, rs3091244, rs34601266, rs2033003, rs7900194, rs9332239, rs28371685, rs1229984, and rs28399504.
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
common in complete genomics
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[PharmGKB:Curated Reduced metformin and MPP+ uptake in transfected cells]
normal
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rs1800460 is a SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The risk allele for this SNP is rs1800460(A), and when it is the only variation in the TPMT gene, it encodes the TPMT*3B allele. While still rare, it is more common in Caucasians (4.5% of all alleles) than in African-Americans (0.8%). Note that if the same allele also carries the rs1142345(G) SNP, the allele is actually a TPMT*3A allele (OMIM). The medicine 6-Mercaptopurine is metabolized by TPMT. Individual differences in TPMT activity associated with this SNP are now used to determine appropriate dosage range and interval for treatm...
Magnitude: 0
Repute:Good
References:5
Repute:Good
References:5
normal
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rs28371685, also known as 1003C>T, 42542C>T or R335W is a SNP in the CYP2C9 gene. The rs28371685(T) allele defines the CYP2C9*11 variant, which has decreased activity. According to a 23andMe discussion This is one of the SNPs which were re-analyzed April 2009. Customers with older data may wish to redownload. SNPs effected rs4420638, rs34276300, rs3091244, rs34601266, rs2033003, rs7900194, rs9332239, rs28371685, rs1229984, and rs28399504. [PharmGKB:Curated Phenotype: In African Americans patients, weekly warfarin dose requirements were lower in those with the CYP2C9*8 allele (34 (30-47) mg; P = 0.023) and the CYP2C9 *2, *3, *5, *6, or *11 allele (33(28-40 mg); P < 0.001) as compared with those with the CYP2C9*1/*1 genotype (43 (35-56) mg). Adding the *5,*6,*8 and *11 alleles to a...
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
normal
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rs28371706, also known as 1023C>T or T107I, is a SNP in the CYP2D6 gene. The rs28371706(T) allele is found in several CYP2D6 variants: * CYP2D6*17 decreased activity variant * CYP2D6*40 non-functioning variant * CYP2D6*58 variant * CYP2D6*64 variant [PharmGKB:In-Depth Variant was identified as being part of the reduced function haplotype CYP2D6*17.]
Magnitude: 0
Repute:Good
References:5
Repute:Good
References:5
normal
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rs28371725, also known as 2988G>A, is a SNP in the CYP2D6 gene. The rs28371725(A) allele defines the CYP2D6*41 variant, which has decreased activity. 23andMe also has SNP i4001476 at the same position. [PharmGKB:In-Depth This variant is part of the CYP2D6*41 IM haplotype. Plasma concentrations of metoprolol were shown to be were 4.9-fold higher in the PMs, with greater reductions in heart rate, diastolic blood pressure, and mean arterial pressure in PMs than in non-PMs.]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
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[PharmGKB:In-Depth This variant is part of the *10 haplotype and affects nicotine metabolism.]
Magnitude: 0
Repute:Good
References:11
Repute:Good
References:11
common in complete genomics
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[PharmGKB:In-Depth Risk or phenotype-associated allele: TC. Phenotype: This variant is statistically correlated with the mean of maximum transaminase values (ALT) in patients from Mozambique, with ALT mean value of 91.68 U/l for TT, and 221.45 U/l for TC genotypes (p < 0.001). Study size: 156. Study population/ethnicity: HIV infected patients from Mozambique. Significance metric(s): p< 0.001. Type of association: GN; CO]
Magnitude: 0
Repute:Good
References:7
Repute:Good
References:7
normal
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rs28399504 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*4 variant. This variant has been linked to poor metabolism of compounds like mephenytoin. It is also known as M1V or Met1Val. The risk allele is rs28399504(G). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (Prevacid). According to a 23andMe discussion This is one of the SNPs which were re-analyzed April 2009. Customers with older data may wish to redownload. SNPs effected rs4420638, rs34276300, rs3091244, rs34601266, rs2033003, rs7900194, rs9332239, rs28371685, rs1229984, and rs28399504. Clopidogrel Efficacy [Pharm...
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
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Suspect: Variation suspected to be false positive due to artifacts of the presence of a paralogous sequence in the genome (Musumeci et al. 2010) (Sudmant et al. 2010) or evidence suggested sequencing error or computation artifacts. [PharmGKB:Curated The CYP2B6:1132C>T variant results in a truncated protein and high plasma levels of efavirenz in patients.]
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
normal
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rs41279854, also known as 29748T>C or F446S, is a SNP in the CYP3A5 gene. The rs41279854(G) allele defines the CYP3A5*10 variant, which is nonfunctional.
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
normal
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Defines the CYP2C19 variant known as CYP2C19*8. Carriers of the rs41291556(C) allele may have decreased activity and poor metabolizer (PM) phenotype. This variant is associated with a dramatic (approximately 90% and 70%) reduction in the metabolism of S-mephenytoin and tolbutamide in vitro. Clopidogrel Efficacy [PharmGKB:Curated This variant is the defining SNP for CYP2C19*8 and leads to decreased activity and poor metabolizer (PM) phenotype.This variant is associated with a dramatic (approximately 90% and 70%) reduction in the metabolism of S-mephenytoin and tolbutamide in vitro.]
normal
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rs4986893 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*3 variant. This variant has been linked to poor metabolism of compounds like mephenytoin as well as proguanil, and it therefore has implications for malaria prophylaxis. The risk allele is rs4986893(A). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (Prevacid). Clopidogrel Efficacy [PharmGKB:Curated In contrast to other PPIs, esomeprazole-induced healing of GERD appears to be unrelated to the CYP2C19*3 variant.] [OMIM:MEPHENYTOIN, POOR METABOLISM OF]
normal
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rs5030862, also known as 124G>A or G42R, is a SNP in the CYP2D6 gene. The rs5030862(A) allele defines the CYP2D6*12 variant, which is inactive.
normal
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rs5030867, also known as 2935A>C or H324P, is a SNP in the CYP2D6 gene. The rs5030867(C) allele defines the CYP2D6*7 variant, which is inactive.
common in complete genomics
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[PharmGKB:In-Depth This variant affects heat stability and affects nicotine metabolism; part of the CYP2A6*7 and CYP2A6*10 haplotypes.]
normal
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rs7900194, also known as 449G>A, 3627G>A or R150H, is a SNP in the CYP2C9 gene. The rs7900194(A) allele defines the CYP2C9*8 variant, which has decreased activity. According to a 23andMe discussion This is one of the SNPs which were re-analyzed April 2009. Customers with older data may wish to redownload. SNPs effected rs4420638, rs34276300, rs3091244, rs34601266, rs2033003, rs7900194, rs9332239, rs28371685, rs1229984, and rs28399504. [PharmGKB:Curated Phenotype: In African Americans patients, weekly warfarin dose requirements were lower in those with the CYP2C9*8 allele (34 (30-47) mg; P = 0.023) and the CYP2C9 *2, *3, *5, *6, or *11 allele (33(28-40 mg); P < 0.001) as compared with those with the CYP2C9*1/*1 genotype (43 (35-56) mg). Adding the *5,*6,*8 and *11 alleles to a mod...
common in complete genomics
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[PharmGKB:Curated Alleles positive for this variant are designated CYP2C8*4. In in vitro experiments, the paclitaxel 6 alpha-hydroxylase acivity associated with CYP2C8*4 appeared lower than the wildtpe but the difference was not significant.]
common in clinvar
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minor form is a slow metaboliser according to pharmgkb [PharmGKB:In-Depth This variant results in enzyme inactivity and is considered to be part of the %22slow metabolizer%22 group; part of the CYP2A6*2 haplotype.] [OMIM:?] [GWAS:Smoking behavior]
common in complete genomics
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[PharmGKB:Curated The variant is part of the CYP2C8*2 allele. In an in vitro study, the CYP2C8*2 allele exhibited a two-fold lower clearance for paclitaxel than the wildtype.]
normal for 23andMe appears common for 23andMe users
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rs1800462, also known as A80P, is a rare SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The risk allele for this SNP (in orientation to the dbSNP entry) is rs1800462(C), and it encodes the TPMT*2 allele. It may occur at a frequency of 1 in 200 alleles among Caucasians. wikipedia thiopurine drugs metabolized by TPMT include azathioprine, mercaptopurine, and thioguanine [PharmGKB:In-Depth The TPMT:238G>C SNP was cloned from a patient with severe mercaptopurine toxicity. It results in a non-synonymous protein change TPMT:Ala80Pro that has a 100-fold reduction in catalytic activity compared to w...
normal common for Caucasians on the 23andme platform
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rs28371686, also known as 1080C>G, 42619C>G or D360E, is a SNP in the CYP2C9 gene. The rs28371686(G) allele defines the CYP2C9*5 variant, which appears to have decreased activity. [PharmGKB:Curated Phenotype: In African Americans patients, weekly warfarin dose requirements were lower in those with the CYP2C9*8 allele (34 (30-47) mg; P = 0.023) and the CYP2C9 *2, *3, *5, *6, or *11 allele (33(28-40 mg); P < 0.001) as compared with those with the CYP2C9*1/*1 genotype (43 (35-56) mg). Adding the *5,*6,*8 and *11 alleles to a model containing the *2 and *3 alleles plus the VKORC1 -1639 G>A allele (along with clinical variables) explained 36% vs. 30% of the variability in dose requirements. Study size: 226 . Study population/ethnicity: African-American . Type of association: PD;GN;...
common in complete genomics
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[PharmGKB:Non-Curated Reduced metformin and MPP+ uptake in transfected cells]
80 snps
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CYP3A5*3 homozygote; CYP3A5 non-expressor Impacts metabolism of tacrolimus, an immunosuppressive drug used in organ transplantation. This is the most common phenotype in caucasian and many other populations. Only in africans is expressing the gene common.
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rs776746, also known as 6986A>G, is a SNP encoding the (nonfunctional) CYP3A5*3 allele of the CYP3A5 gene. CYP3A5*3 has been studied especially in connection with the metabolism of tacrolimus, an immunosuppressive drug used in organ transplantation. The optimal therapeutic dose is in a relatively narrow window, so blood concentration monitoring is recommended. CYP3A5*3 carriers tend to build up higher levels of tacrolimus than CYP3A5*1 carriers, unless their tacrolimus intake is reduced. Risk of testicular germ cell cancer in relation to variation in maternal and offspring cytochrome p450 genes involved in catechol estrogen metabolism. Polymorphisms in the cytochrome P450 genes CYP1A2, CYP1B1, CYP3A4, CYP3A5, CYP11A1, CYP17A1, CYP19A1 and colorectal cancer risk. Prevalence of common dis...
Magnitude: 2.5
Repute:Bad
References:2
Repute:Bad
References:2
CYP3A5*7 homozygote; nonexpressor for CYP3A5
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rs41303343, also known as 27131_27132insT, is a SNP in the CYP3A5 gene. The rs41303343(T) allele defines the CYP3A5*7 variant, which is nonfunctional.
3.5x asthma risk in certain populations
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This SNP, in the GSTP1 gene influences asthma risk; the (A) allele encodes the Ile, while the (G) allele encodes the Val. This SNP is also known as GSTP1Val105, or GSTP1 Ile105Val. Despite evidence of antioxidant effects of vitamin E in vitro and in animal studies, large, randomized clinical trials have not substantiated a benefit of vitamin E in reducing inflammation in humans. In healthy control subjects, the effect of α-tocopherol supplementation on the production of inflammatory cytokines appears to be dependent on an individual's genotype. These genotype-specific differences may help explain some of the discordant results in studies that used vitamin E. Persons having the alleles AA or AG had an increase in interleukin-6 (IL-6) upon supplementing alpha-tocopherol (the most common...
Carrier of one CYP1A2*1F allele; Slow Caffeine Metabolizer. One copy of the slow caffeine metaboliser SNP, and one copy of the fast version. This makes you more strongly affected by drinking coffee, as caffeine is broken down slower in the liver. Supposedly this increases the risk of heart attacks, although other studies show caffeine is generally good for the heart. It also makes caffeine more effective at preventing Breast Cancer, Alzheimer's Disease, and Parkinson's disease. Too much caffeine will shrink your breasts.
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rs762551, also known as -164A>C or -163C>A, is a SNP encoding the CYP1A2*1F allele of the CYP1A2 gene. For historic reasons, the rs762551(C) allele is considered the wild-type, even though it is the rarer allele in most populations. The rs762551(A) allele is the 'fast metabolizer' allele known as CYP1A2*1F; the (C) allele is by comparison a slower metabolizer of certain substrates (including caffeine). In terms of genotypes, only rs762551(A;A) individuals are considered fast metabolizers. Individuals who are rs762551(A;C) heterozygotes or rs762551(C;C) homozygotes are both considered slow metabolizers. The CYP1A2 gene encodes a member of the cytochrome p450 family of proteins, which metabolize nutrients and drugs. One well known substrate of CYP1A2 is caffeine; individuals who are ca...
warfarin sensitivity (~2.5 mg/day)
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rs8050894, is located on chromosome 16 in the gene VKORC1. VKORC1 is the primary target of the drug warfarin (Coumadin), a commonly used oral anticoagulant. rs8050894 is one of several polymorphisms found in VKORC1 that is associated with specific warfarin doses (). Other polymorphisms in VKORC1 (rs7196161, rs9923231, rs9934438, rs2359612) are equally predictive of warfarin dose requirement in both European and Asian-descent individuals. Other polymorphisms found in the gene cytochrome P450 2C9 (CYP2C9) influence the metabolism of warfarin and have a smaller effect on warfarin dose. These polymorphisms are rs1799853 (CYP2C9*2) and rs1057910 (CYP2C9*3). In several hundred Europeans, no association was found between rs8050894 and risk for ischemic stroke. Genetic-based dosing in orthopedic p...
Magnitude: 2
Frequency: 43.1%
References:13
Frequency: 43.1%
References:13
CYP2C19*17 ultra fast metabolizer; drug metabolism effects; also 0.77x decreased breast cancer risk
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rs12248560(T) defines the CYP2C19*17 allele, an ultra fast metabolizer phenotype of the CYP2C19 gene. CYP2C19*17 is likely to lead to less effective drug treatment by, for example, proton pump inhibitors (such as omeprazole) and antidepressants. On the other hand, cancer patients who are CYP2C19*17 carriers are more likely to benefit from tamoxifen treatment, presumably because they break it down more rapidly into the antiestrogenic metabolites endoxifen and 4-hydroxytamoxifen. A study of 1,000+ breast cancer patients showed a 0.77x decreased risk of breast cancer for carriers of a CYP2C19*17 allele (CI: 0.65-0.93, p = 0.005). Analysis of a subgroup of such carriers who were using hormone therapy for ten years or longer showed an even stronger effect (odds ratio 0.57, CI: 0.39-0.83, p = 0....
higher risk for endometrial cancer
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rs4633 is a variant at codon 62 of the COMT gene, however, it does not change the amino acid sequence of the COMT protein. In a study of 150 (Caucasian) cases of endometrial cancer, a significant increase in rs4633(T;T) genotype was observed in patients compared to controls (OR = 2.39, CI: 1.31-4.37, p = 0.004). Furthemore, the frequency of the C-G haplotype of rs4633-rs4680 was significantly higher in controls (p < 0.0001) than in patients. This correlated with lower expression levels of the COMT protein in carriers of these alleles. pubmed 1180576 Schizophrenia Susceptibility Genetic basis for individual variations in pain perception and the development of a chronic pain condition [PharmGKB:Curated On the basis of subjects' pain responsiveness, haplotypes involving rs6269 (A/G), rs46...
somewhat less likely to respond to certain antidepressants
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rs2235015 is a SNP in the ABCB1 gene (also known as the MDR1 gene), which encodes a protein that transports certain molecules across the blood-brain barrier. SNPs in ABCB1 may thus influence the intracerebral concentrations of certain drugs and thus their efficacy or potential for adverse side effects. rs2032583 is near 9 SNPs found within a tight linkage block (r<sup>2</sup> >= 0.8 ) such that the minor allele at any one of them predicts (with ~80%+ accuracy) that the other SNPs will also be the minor allele. The list of the 9 SNPs is shown below. rs2235015 has an r<sup>2</sup> value of >0.5 with this group. When treated for depression with substrates of the protein encoded by ABCB1, carriers of one or two minor alleles at these ABCB1 SNPs have been reported ...
Slower metaboliser for some drugs
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rs1045642, also known as C3435T, is a SNP located in the ABCB1 gene. It is often studied in conjunction with rs2032582. C3435T has been mentioned by: * A 'Silent' Polymorphism in the MDR1 Gene Changes Substrate Specificity (for example, to verapamil) * (R)-lansoprazole (Prevacid) concentrations are significantly increased in CYP2C19 extensive metabolizers with ABCB1 C3435T C allele. * In a Korean population, plasma concentrations of fexofenadine (Allegra) were 17% lower in 2677AA/3435CC subjects and 47% higher in the 2677TT/3435TT subjects compared to 2677GG/3435CC subjects. * In contrast, in this study no association was observed between the C3435T polymorphism and fexofenadine plasma or urine concentrations in a German Caucasian population. * A meta-analysis including 9 case-control stud...
2.1x increased risk of Crohn's disease
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rs1050152, a SNP in the SLC22A4 gene known as L503F, has been associated with an autoimmune disease, in this case, Crohn's disease, odds ratio = 2.1 (CI = 1.31–3.39, p = 0.002), based on a study of 203 cases and 200 controls. The risk allele is rs1050152(T). A nearby SNP (rs2631367) in the promoter region of the SLC22A5 gene defines a haplotype along with rs3792876, with odds ratio reported as similar for either SNP or the haplotype. Referring to the TC risk haplotype, the population risk attributable to heterozygotes was 19%, and for homozygous haplotype carriers, 27%. [PharmGKB:Non-Curated Higher gabapentin exposure and lower renal clearance/tubular secretion in individuals carrying this variant] [OMIM:?]
lower warfarin dosing
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rs2108622 is a SNP in the cytochrome P450, family 4, subfamily F, polypeptide 2 CYP4F2 gene. In the males rs2108622(G) was significantly higher in cerebral infarction patients (P = 0.025) A study of Italian patients concluded that rs2108622(T;T) patients require 5.49 mg/day of warfarin versus 2.93 mg/day for (C;C) patients. Analysis of variance indicates that about 7% of mean weekly warfarin dose variance is explained by CYP4F2 genotype. A study of 370 Brazilian ('admixed') patients concludes that prospective CYP4F2 genotyping is of little value to these patients, presumably due to ethnic-based differences. [PharmGKB:Curated Risk or phenotype-associated allele: no allelic association. Phenotype: Improved pharmacogenetic algorithm-based warfarin dosing. Study size: 370. Study population/et...
7x less likely to respond to certain antidepressants
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rs2235040 is a SNP in the ABCB1 gene (also known as the MDR1 gene), which encodes a protein that transports certain molecules across the blood-brain barrier. SNPs in ABCB1 may thus influence the intracerebral concentrations of certain drugs and thus their efficacy or potential for adverse side effects. rs2235040 is one of 9 SNPs found within a tight linkage block (r<sup>2</sup> >= 0.8 ) such that the minor allele at any one of them predicts (with ~80%+ accuracy) that the other SNPs will also be the minor allele. The list of the 9 SNPs is shown below. When treated for depression with substrates of the protein encoded by ABCB1, carriers of one or two minor alleles at these ABCB1 SNPs have been reported to respond better than non-carriers. The antidepressant drugs that are know...
Alcohol Flush: Normal, doesn't flush. Normal hangovers. Normal risk of Alcoholism. Normal risk of Esophageal Cancer. Disulfiram is effective for alcoholism. Two working copies of Aldehyde Dehydrogenase (ALDH2) mean you won't turn bright red when you drink alcohol, unlike most Asians. After your body turns alcohol into the dangerous acetaldehyde, this gene quickly turns the acetaldehyde into vinegar. It also stops the acetaldehyde in cigarettes from causing Esophageal Cancer. It reduces hangovers compared to Asians, but less hangovers and flushing obviously increases the risk of alcoholism. Alcoholism can be treated effectively with the drug Disulfiram (Antabuse) which would stop this gene from working and cause the Asian flush in non-Asians. PMC2659709 [http://www.ncbi.nlm.nih.gov/pmc/art...
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rs671 is a classic SNP, well known in a sense through the phenomena known as the 'alcohol flush', also known as the 'Asian Flush' or 'Asian blush', in which certain individuals, often of Asian descent, have their face, neck and sometimes shoulders turn red after drinking alcohol. The rs671(A) allele of the ALDH2 gene is the culprit, in that it encodes a form of the aldehyde dehydrogenase 2 protein that is defective at metabolizing alcohol. This allele is known as the ALDH*2 form, and individuals possessing either one or two copies of it show alcohol-related sensitivity responses including facial flushing, and severe hangovers (and hence they are usually not regular drinkers). Perhaps not surprisingly they appear to suffer less from alcoholism and alcohol-related liver disease. Disulfiram (...
Carrier of one CYP2D6 decreased or non-functioning variant. Your body may have a reduced ability to process some medicines. You are a carrier for rs1065852(T;T)
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The wild type (normal) allele at this SNP is (C). The (T) variant indicates the presence of a non-wild type CYP2D6 variant, but it appears in many different variants so it can not be used to determine the presence of any particular variant. The most common variants it appears in are CYP2D6*10 and CYP2D6*4, but these are not the only ones. While this is the defining mutation for CYP2D6*10, it is not possible by itself for this mutation to determine a particular variant. In addition, the CYP2D6*4 variant includes this mutation, but the defining mutation 1846G>A SNP is not available in the common direct to consumer testing services. While it is not possible for this mutation to identify one particular variant, all the variants in which it appears have reduced or no CYP2D6 activity. If two ...
Homozygous for CYP2D6 variants (non-CYP2D6*1)
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rs1135840, also known as 4180G>C or S486T, is a SNP in the CYP2D6 gene. The wild type (normal) allele at this SNP is (G). The (C) variant indicates the presence of a non-wild type CYP2D6 variant, but it appears in many different variants so it can not be used to determine the presence of any particular variant. Please be careful when interpreting results for this SNP as it is in dbSNP and SNPedia in minus orientation where the risk allele is C, but test results are usually in plus orientation where the risk allele is G. This SNP has an ambiguous flip which can make this very confusing. Polymorphisms affecting gene transcription and mRNA processing in pharmacogenetic candidate genes: detection through allelic expression imbalance in human target tissues. [PharmGKB:Curated Risk or phenot...
carrier of one CYP1A2*1K_-739T>G allele
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rs2069526 is a SNP in the CYP1A2 gene. The rs2069526(T) allele defines the CYP1A2*1K_-739T>G variant. [PharmGKB:Curated Present in reduced function haplotype, unlikely to be causative.]
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[GWAS:Cataracts in type 2 diabetes]
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[PharmGKB:Curated Risk or phenotype-associated allele: None. Phenotype: Variants identified in a screen of 13 genes involved in the gemcitabine drug metabolic pathway. For the non-synonymous CDA:79A>C (K27Q) SNP, the C allele (27Gln) was at frequency 0.36 and 0.04 in Europeans and Africans, respectively. There was a significant difference between ethnic groups in genotype frequency distribution (p < 0.001) Study size: 180. Study population/ethnicity: Healthy, unrelated blood donors of European (n = 95) and African (n = 85) descent. Significance metric(s): p < 0.001. Type of association: GN.]
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[PharmGKB:Non-Curated altered kinetics of gemcitabine in transfected cells]
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[PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: The PPAR delta SNP rs6922548 A>G was associated with positive clincial response (partial or complete response) to treatment. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.0011 Type of association: PD; CO]
CYP1A2_1545T>C homozygote
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rs2470890 is a SNP in the CYP1A2 gene. The rs2470890(C) allele defines the CYP1A2_1545T>C variant. Low-penetrance alleles predisposing to sporadic colorectal cancers: a French case-controlled genetic association study. [PharmGKB:Curated Weakly associated with tardive dyskinesia and schizophrenia.]
carrier of one CYP2E1*7_-71G>T allele
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rs6413420 is a SNP in the CYP2E1 gene. The rs6413420(T) allele defines the CYP2E1*7_-71G>T variant.
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Polymorphisms affecting gene transcription and mRNA processing in pharmacogenetic candidate genes: detection through allelic expression imbalance in human target tissues. Glucocorticoid receptor gene variant in the 3' untranslated region is associated with multiple measures of blood pressure. Cohort profile: risk patterns and processes for psychopathology emerging during adolescence: the ROOTS project. A comparison of classification methods for predicting Chronic Fatigue Syndrome based on genetic data. Glucocorticoid receptor gene haplotype structure and steroid therapy outcome in IBD patients. Association of FKBP5 gene haplotypes with completed suicide in the Japanese population. Glucocorticoid receptor polymorphism is associated with lithium response in bipolar patients.
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[PharmGKB:Curated Risk or phenotype-associated allele: C Phenotype: The CHST3:rs4148943 C variant was associated with positive clincial response (partial or complete response) to treatment. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.0001 Type of association: PD; CO]
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[PharmGKB:In-Depth A study of 124 White patients, which received a high-dose regimen consisting of cyclophosphamide, thiotepa and carboplatin as intravenous infusions, concludes patients homozygous for the GSTP1 C341T allele may have enhanced exposure to thiotepa and tepa.]
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[PharmGKB:Curated Risk or phenotype-associated allele: A Phenotype: The CHST3:rs1871450 A variant was associated with positive clincial response (partial or complete response) to treatment and toxicity to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.048 (response); p = 0.006 (TOX) Type of association: PD; CO; TOX]
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[PharmGKB:Curated Risk or phenotype-associated allele: C Phenotype: The CHST3:rs4148945 C variant was associated with positive clincial response (partial or complete response) to treatment and toxicity to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.011 (response); p = 0.010 (TOX) Type of association: PD; CO; TOX]
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[PharmGKB:Curated Risk or phenotype-associated allele: A Phenotype: The CHST3:rs4148950 A variant was associated with positive clincial response (partial or complete response) to treatment and toxicity to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s):p = 0.024 (response); p = 0.006 (TOX) Type of association: PD; CO; TOX]
carrier of one CYP2E1_10463T>C(F421F) allele
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rs2515641 is a SNP in the CYP2E1 gene. The rs2515641(T) allele defines the CYP2E1_10463T>C(F421F) variant.
carrier of one CYP2E1*7_-333T>A allele
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rs2070673 is a SNP in the CYP2E1 gene. The rs2070673(A) allele defines the CYP2E1*7_-333T>A variant.
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[OMIM:CYTOCHROME P450, SUBFAMILY I, POLYPEPTIDE 1; CYP1B1]
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non sig. gwas, hit (p = 3 x 10^-6) for paired associates learning (PAL) total errors at 6 patterns in the CANTAB (Cambridge Neuropsychological Test Automated Battery [GWAS:Cognitive performance]
Frequency: 31.0%
References:6
References:6
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[PharmGKB:Curated Subjects homozygous for this genotype showed decreased response to fluvastatin]
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The (C;C) genotype is linked to reduced UGT1A1 activity, and increased Bilirubin, except in people of African origin for whom the T allele is a risk factor for breast cancer. [Genetic polymorphisms of MPO, NQO1, GSTP1, UGT1A6 associated with susceptibility of chronic benzene poisoning]. The influence of metabolic gene polymorphisms on urinary 1-hydroxypyrene concentrations in Chinese coke oven workers. Low-penetrance alleles predisposing to sporadic colorectal cancers: a French case-controlled genetic association study. [Relationship between genetic polymorphisms of phase I and phase II metabolizing enzymes and DNA damage of workers exposed to vinyl chloride monomer]. Serum bilirubin levels on ICU admission are associated with ARDS development and mortality in sepsis. Pazopanib-induced hyp...
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[PharmGKB:Curated UGT1A7:-57T>G increases risk of anemia in irinotecan-treated patients.]
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[PharmGKB:Curated Risk or phenotype-associated allele: G. Phenotype: There was a trend toward an association between the CBR3 V244M polymorphism and the risk of CHF. Study size: 145. Study population/ethnicity: Nested case-control study was conducted within a cohort of 1979 patients enrolled in the Childhood Cancer Survivor Study who received treatment with anthracyclines and had available DNA. Significance metric(s): OR = 8.16, p = 0.056 (G/G vs A/A); OR = 5.44, p = 0.092 (G/A vs A/A). Type of association: CO; TOX; ADR.]
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rs272893 and rs273900 are associated with Crohn's disease (OR 2.16; 95% CI 1.21-3.59 and OR 2.40; 95% CI 1.43-4.05)
Frequency: 37.2%
References:1
References:1
Frequency: 38.1%
References:7
References:7
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[PharmGKB:Curated This SNP is the tagging SNP for VKORC1*4.]
Adverse reaction more likely to carbamazepine in epileptic patients
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rs2273697, also known as c1249G>A or p.V471I, is a nonsynonymous polymorphism in the ABCC2 gene. From an initial case-control study of 146 patients with epilepsy, followed by replication (p=0.001) in another 279 patients, the rs2273697(A) allele was associated with neurological adverse drug reactions from taking carbamazepine. Functional studies showed that this SNP selectively reduced carbamazepine transport across the cell membrane. [PharmGKB:Curated Risk or phenotype-associated allele: A. Phenotype: This SNP showed a strong association with the neurological adverse drug reaction caused (ADR) by carbamazepine (P=0.005). The study results indicate that the c.1249A variant is an independent risk factor of carbamazepine CNS ADR. Study size: 146 patients with epilepsy who had been prescr...
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rs4646(A) allele carriers with breast cancer being treated with letrozole are reported to do worse than rs4646(C;C) patients, based on a study of (only) 95 women. [PharmGKB:Curated A study in 67 patients with hormone receptor-positive metastatic breast cancer treated with letrozole, the presence of this SNP in the 3' untranslated region of the CYP19A1 gene is associated with improved treatment efficacy.]
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[PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: The PPAR delta SNP rs1883322 A>G was associated with positive clincial response (partial or complete response) to treatment. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.0061 Type of association: PD; CO]
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[PharmGKB:Curated This SNP is the tagging SNP for VKORC1*2.]
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Pharmacokinetics of efavirenz when co-administered with rifampin in TB/HIV co-infected patients: pharmacogenetic effect of CYP2B6 variation. The pharmacokinetics and pharmacogenomics of efavirenz and lopinavir/ritonavir in HIV-infected persons requiring hemodialysis. Polymorphisms of drug-metabolizing enzymes (GST, CYP2B6 and CYP3A) affect the pharmacokinetics of thiotepa and tepa. The impact of cytokines on the expression of drug transporters, cytochrome P450 enzymes and chemokine receptors in human PBMC. Associations between CYP2B6 polymorphisms and pharmacokinetics after a single dose of nevirapine or efavirenz in African americans. CYP2B6 (c.516G-->T) and CYP2A6 (*9B and/or *17) polymorphisms are independent predictors of efavirenz plasma concentrations in HIV-infected patients. CYP...
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CYP17 genotype is associated with short menstrual cycles, early oral contraceptive use and BRCA mutation status in young healthy women. Polymorphisms in the cytochrome P450 genes CYP1A2, CYP1B1, CYP3A4, CYP3A5, CYP11A1, CYP17A1, CYP19A1 and colorectal cancer risk. The rs743572 common variant in the promoter of CYP17A1 is not associated with prostate cancer risk or circulating hormonal levels. CYP17 genetic variation and risk of breast and prostate cancer from the National Cancer Institute Breast and Prostate Cancer Cohort Consortium (BPC3). Genetic polymorphisms in CYP17, CYP3A4, CYP19A1, SRD5A2, IGF-1, and IGFBP-3 and prostate cancer risk in African-American men: the Flint Men's Health Study. Genetic variation in CYP17 and endometrial cancer risk. Variants in hormone biosynthesis genes an...
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Associations between CYP2B6 polymorphisms and pharmacokinetics after a single dose of nevirapine or efavirenz in African americans. Univariate/multivariate genome-wide association scans using data from families and unrelated samples. CYP2B6 variants and plasma efavirenz concentrations during antiretroviral therapy in Port-au-Prince, Haiti. Tests of association for quantitative traits in nuclear families using principal components to correct for population stratification. Family-based bivariate association tests for quantitative traits. A comparative study of three methods for detecting association of quantitative traits in samples of related subjects. Family-based genome-wide association study for simulated data of Framingham Heart Study. The Genetic Analysis Workshop 16 Problem 3: simulat...
increases susceptibility to postmenopausal osteoporosis
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rs1062033 increases susceptibility to Osteoporosis, postmenopausal for carriers of the G allele Common variations in estrogen-related genes are associated with severe large-joint osteoarthritis: a multicenter genetic and functional study. [OMIM:CYTOCHROME P450, FAMILY 19, SUBFAMILY A, POLYPEPTIDE 1; CYP19A1]
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[GWAS:HDL cholesterol]
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[GWAS:None]
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Linkage disequilibrium blocks, haplotype structure, and htSNPs of human CYP7A1 gene. Cholesterol 7alpha-hydrolase (CYP7A1) c.-278A>C promoter polymorphism in gallstone disease patients. CYP7A1 (-204 A>C; rs3808607 and -469 T>C; rs3824260) promoter polymorphisms and risk of gallbladder cancer in North Indian population. Promoter variant -204A > C of the cholesterol 7alpha-hydroxylase gene: association with response to plant sterols in humans and increased transcriptional activity in transfected HepG2 cells.
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[OMIM:?]
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rs1208 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The risk allele for this SNP is rs1208(G). [PharmGKB:Curated in vitro study; PK: 20-fold reduction in Vmax vs wild type] [OMIM:?]
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[PharmGKB:Curated Risk or phenotype-associated allele: None. Phenotype: Variants identified in a screen of 13 genes involved in the gemcitabine drug metabolic pathway. For the non-synonymous SLC28A2:283A>C (R75S) SNP, the C (75Ser) allele was at frequency was 0.34 and 0.08 in Europeans and Africans, respectively. There was a significant difference between ethnic groups in genotype frequency distribution (p < 0.001). Study size: 187. Study population/ethnicity: Healthy, unrelated blood donors of European (n = 95) and African (n = 92) descent. Significance metric(s): p < 0.001. Type of association: GN.]
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rs1051740, also known as Tyr113His, is a SNP in the microsomal epoxide hydrolase EPHX1 gene. severe hypersensitivity syndrome, triggered by carbamazepine in the presence of a concomitant active human herpes virus (HHV) 6 and 7 infection with the allele HLA-A*3101 and rs1051740(C;C) [PharmGKB:Curated Risk or phenotype-associated allele: T. Phenotype: In a logistic regression model adjusted for history of phenytoin use during the first trimester and maternal epilepsy, the maternal EPHX1 113 H (rs1051740 T/C) allele was associated with craniofacial abnormalities in the child. Study size: 157 pregnancies. Study population/ethnicity: phenytoin use during the first trimester and maternal epilepsy. metric(s): per rare allele OR: 2.43, 95% confidence interval (CI): 1.16-5.10, P=0.02. Type of asso...
multiple associations, see details
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rs4680 (Val158Met) is a well studied SNP in the COMT gene. 23andMe blog summarizes them as *rs4680(A) = Worrier. Met, more exploratory, lower COMT enzymatic activity, therefore higher dopamine levels; lower pain threshold, enhanced vulnerability to stress, yet also more efficient at processing information under most conditions *rs4680(G) = Warrior. Val, less exploratory, higher COMT enzymatic activity, therefore lower dopamine levels; higher pain threshold, better stress resiliency, albeit with a modest reduction in executive cognition performance under most conditions Roughly speaking, the predominant wisdom (known colloquially as the warrior/worrier hypothesis; summary at ) posits that people with Val alleles have increased COMT activity and lower prefrontal extracellular dopamine compar...
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rs1799929 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The risk allele for this SNP is rs1799929(T). When this SNP is indicative of carrying a NAT2*5A allele, the following may be relevant: A study (based on only 42 patients) found that women with the NAT2*5A slow genotype (which presumably means rs1799929(T;T)) had a significantly higher risk of cervical cancer compared with individuals with the NAT2*5A fast genotype (i.e. carriers of only one rs1799929(T) allele), with a reported odds ratio of 7.469 (CI: 1.6-33.3, p=0.008). [PharmGKB:Curated in vitro study; PK: 20-fold reduction...
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rs2306283 (Asn130Asp/N130D, A388G/388A>G) is a SNP within SLCO1B1 (Solute carrier organic anion transporter family member 1B1). A G at this location denotes the SLCO1B1*1B allele. among 8 healthy volunteers with *1B/*1B genotypes and 16 with the *1A/*1A genotype, *1B/*1B genotype associated with reduced plasma concentrations of repaglinide (but not nateglinide) consistent with increased hepatic uptake by SLCO1B1 (but w/ limited effects on nateglinide pharmacokinetics) news rs2306283 influences statin-related myopathy risk Genotyping panel for assessing response to cancer chemotherapy. Common variants in the SLCO1B3 locus are associated with bilirubin levels and unconjugated hyperbilirubinemia. Pazopanib-induced hyperbilirubinemia is associated with Gilbert's syndrome UGT1A1 polymorphism...
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rs700518 is a SNP potentially linked in a gender-specific manner to hypertension [OMIM:CYTOCHROME P450, FAMILY 19, SUBFAMILY A, POLYPEPTIDE 1; CYP19A1]
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rs10046 is a SNP potentially linked in a gender-specific manner to hypertension rs10046(C;C) associated with miscarriages (P = 0.017) Polymorphisms associated with circulating sex hormone levels in postmenopausal women. Multilocus analysis of SNP and metabolic data within a given pathway. Polymorphisms in the cytochrome P450 genes CYP1A2, CYP1B1, CYP3A4, CYP3A5, CYP11A1, CYP17A1, CYP19A1 and colorectal cancer risk. Sex and body mass index specific regulation of blood pressure by CYP19A1 gene variants. Genome-wide association with bone mass and geometry in the Framingham Heart Study. Single nucleotide polymorphisms of the aromatase gene (CYP19A1), HER2/neu status, and prognosis in breast cancer patients. Association between single-nucleotide polymorphisms in hormone metabolism and DNA repai...
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[PharmGKB:In-Depth May be associated with a higher warfarin dose phenotype]
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Parkinson's disease The risk alleles for each SNP identified from conditional logistic regression, rs1721100 C, rs1721082 T and rs1799836 A, are consistent with previous reports. Significant interaction between this MAOB SNP and a FGF20 SNP, rs1721100 was also noticed.
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Mutation analysis and the correlation between genotype and phenotype of Arg778Leu mutation in chinese patients with Wilson disease.
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rs1801280, also known as T341C, is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The allele associated with slow NAT2 metabolization for this SNP is rs1801280(C). Genosets gs154 and gs156 evaluate predicated NAT2 metabolizer phenotype based on rs1041983 and rs1801280. [PharmGKB:Curated in vitro study; PK: 20-fold reduction in Vmax vs wild type] [OMIM:?]
1.6x risk for ICP
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rs3740066, a SNP in the ABCC2 gene, is reported to be associated with a higher risk of developing intrahepatic cholestasis of pregnancy (ICP) based on a study of ~70 Argentinian patients. ICP is associated with increased fetal risks such as premature birth or intrauterine death. The risk allele is rs3740066(A), and the odds ratio for homozygous rs3740066(A;A) mothers is 4.44 (CI: 1.83 - 10.78), and for heterozygous mothers 1.65 (CI: 0.76 - 3.64), compared to rs3740066(G;G) mothers. [PharmGKB:Curated The AUCs of irinotecan, SN-38, SN-38 glucuronide, and APC are influenced by rs3740066, rs2306283, rs35605, rs10276036, and rs717620 .]
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[GWAS:Blood metabolite levels]
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[PharmGKB:Curated Risk or phenotype-associated allele: None. Phenotype: Variants identified in a screen of 13 genes involved in the gemcitabine drug metabolic pathway. For the non-synonymous SLC28A1:1576T>C (N521D) SNP, the C (521Asp) allele was at frequency was 0.47 and 0.00 in Europeans and Africans, respectively. There was a significant difference between ethnic groups in genotype frequency distribution (p < 0.001). Study size: 185. Study population/ethnicity: Healthy, unrelated blood donors of European (n = 94) and African (n = 91) descent. Significance metric(s): p < 0.001. Type of association: GN.]
Frequency: 52.3%
References:6
References:6
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Clinically relevant UGT1A10 variant. [PharmGKB:Curated *93 is a common variant of UGT1A1 in Caucasian and African-American populations. It is located in the Phenobarbital Response Enhancer Module (an upstream regulatory sequence) and may be important in predicting irinotecan response.]
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[PharmGKB:Curated Risk or phenotype-associated allele: A. Phenotype: CBR3 11G>A variant was associated with lower doxorubicinol AUC, lower CBR3 expression in breast tumor tissue, greater tumor reduction, and greater percentage reduction of leukocyte and platelet counts at nadir. Study size: 101 Study population/ethnicity: Asian; patients with Breast Neoplasms; Chinese; Malay; Indian Significance metric(s): p = 0.009 (AUC); p = 0.001 (expression); p = 0.015 (tumor reduction); p = 0.03 (leukocyte and platelet counts). Type of association: PK; TOX]
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[PharmGKB:Non-Curated PEPT2*1 (350L-409P-509R) showed lower K m for glycyl-sarcosine as compared with PEPT2*2 (350F- 409S-509K) in transfected cells.]
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[PharmGKB:Non-Curated PEPT2*1 (350L-409P-509R) showed lower K m for glycyl-sarcosine as compared with PEPT2*2 (350F- 409S-509K) in transfected cells.]
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common trait being optimism [GWAS:Common traits (Other)]
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rs1051266 (Arg27Cys, 80G>A) is a snp within SLC19A1 (Solute carrier family 19 (folate transporter), member 1). Cys (A) allele associated with reduced plasma folate women with GA and AA genotypes had higher red blood cell folate concentrations, not significantly associated with serum folate or homocysteine levels methotrexate (antifolate drug) uptake lowest in individuals with GG genotype than those with GA or AA genotypes [PharmGKB:Curated Risk or phenotype-associated allele: SLC19A1 80GG (27Arg/Arg) and GA (27His/Arg)>AA (27His/His) genotypes. Phenotype: A composite pharmacogenetic index (additive from zero to five) was calculated using the following values: ATIC 347CC or TSER*3/*3 or SLC19A1 80GG or SLC19A1 80GA genotypes were valued as 0, ATIC 347CG or TSER*2/*3 or SLC19A1 80AA g...
Frequency: 56.6%
References:3
References:3
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[PharmGKB:Non-Curated The AUCs of irinotecan, SN-38, SN-38 glucuronide, and APC are influenced by rs3740066, rs2306283, rs35605, rs10276036, and rs717620 .]
may require more methadone during heroin withdrawal
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rs1128503 is a SNP in the transporter P-glycoprotein (P-gp) 170, encoded by the ABCB1 (also known as MDR1) gene. Methadone is a substrate of this protein, so variants may affect the efficacy and optimal dosage of this drug as used for treating opiate dependence. A study of 98 methadone-maintaining patients concluded that the higher (>150 mg/day) and lower (< or =150 mg/day) methadone dose groups differed significantly in their rs1128503 status (experiment-wise p = 0.0325). Furthermore, individuals with the 3-locus genotype pattern (T;T)-(T;T)-(T;T) for SNPs rs1045642, rs2032582 and rs1128503, respectively, had an approximately 5-fold chance of requiring the 'higher' methadone dose, while individuals heterozygous for these three SNPs have an approximately 3-fold chance of stabilizing ...
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[PharmGKB:Non-Curated PEPT2*1 (350L-409P-509R) showed lower K m for glycyl-sarcosine as compared with PEPT2*2 (350F- 409S-509K) in transfected cells.]
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Association of the multidrug-resistance-associated protein gene (ABCC2) variants with intrahepatic cholestasis of pregnancy. Polymorphisms of MRP2 (ABCC2) are associated with susceptibility to nonalcoholic fatty liver disease. MRP2 and GSTP1 polymorphisms and chemotherapy response in advanced non-small cell lung cancer. Genetic polymorphisms influence mycophenolate mofetil-related adverse events in pediatric heart transplant patients. ADME pharmacogenetics: investigation of the pharmacokinetics of the antiretroviral agent lopinavir coformulated with ritonavir. Interindividual variability in hepatic expression of the multidrug resistance-associated protein 2 (MRP2/ABCC2): quantification by liquid chromatography/tandem mass spectrometry. A comprehensive study of polymorphisms in ABCB1, ABCC2...
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[PharmGKB:Curated Risk or phenotype-associated allele: T Phenotype: The SLC10A2:rs2301159 T variant was associated with toxicity in response to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.01 Type of association: CO; TOX]
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[PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: The SPG7:rs12960 G variant was associated with toxicity in response to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.004 Type of association: CO; TOX]
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[PharmGKB:Curated Risk or phenotype-associated allele: SLCO1B3: T334. Phenotype: The metabolic ratio of glucuronidated mycophenolic acid (MPAG) to mycophenolic acid (MPA) showed a very significant decrease in carriers of the SLCO1B3 T334 allele (p = 0.0001). Carriers of at least one SLCO1B3 T334 allele (n = 22) had a 1.42-fold higher (p = 0.0003) MPA AUC(0-12 hours) and a 1.38-fold higher (p = 0.0010) Cmax as compared with carriers of the 334GG genotype (n = 48). Patients carrying 334 TT or TC genotypes (n = 22) had significantly higher MPA AUC(4-9 hours) than patients carrying the CC genotype (n = 48; p = 0.0027). However, they also had higher AUC(0-4 h) (p = 0.0008), resulting in an unchanged AUC(4-9 h)/AUC(0-9 h) ratio (p = 0.4945). In the subgroups of patients cotreated with sirolimus ...
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[PharmGKB:Curated Risk or phenotype-associated allele: SCLO1B3 haplotype formed by 112Ser>Ala (rs4149117, 334T>G) and 223Met>Ile (rs7311358, 699G>A). Phenotype: HEK293 cells transiently expressing the SCLO1B3 334G-699A haplotype or reference haplotype were incubated in the presence of increasing concentrations of mycophenolic acid phenyl-glucuronide (MPAG) for 10 min. The uptake of MPAG according to the SCLO1B3 334G-699A haplotype was markedly lower than in cells expressing the reference sequence 334T-669G. Type of association: GN; FA; PK]
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[GWAS:None]
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[PharmGKB:Curated Risk or phenotype-associated allele: None. Phenotype: Variants identified in a screen of 13 genes involved in the gemcitabine drug metabolic pathway. For the SLC28A1:1383C>T SNP, the T allele was at frequency was 0.08 and 0.05 in Europeans and Africans, respectively. There was no significant difference between ethnic groups in genotype frequency distribution (p > 0.05). Study size: 185. Study population/ethnicity: Healthy, unrelated blood donors of European (n = 91) and African (n = 94) descent. Significance metric(s): Not significant, p > 0.05. Type of association: GN.]
Frequency: 81.2%
References:4
References:4
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Role of the PXR gene locus in inflammatory bowel diseases. Polymorphisms in NF-kappaB, PXR, LXR, PPARgamma and risk of inflammatory bowel disease. Pregnane X receptor (PXR/NR1I2) gene haplotypes modulate susceptibility to inflammatory bowel disease. Variants of the human NR1I2 (PXR) locus in chronic periodontitis.
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rs1801030 (Met223Val) is a snp within SULT1A1 (Sulfotransferase 1A1) and defines the SULT1A1*3 allele. [PharmGKB:In-Depth SULT1A1*3 is the second most common SULT1A1 SNP.]
References:2
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This SNP is part of the HNMT gene known as C939T (or 939A>G) that regulates histamine. According to the lack of a C allele for this gene indicates an increase in ADHD behavior for children age 3 and 8/9 when they have been exposed to certain food additives: sunset yellow, carmoisine, tartrazine, ponceau 4R, quinoline yellow, allura red AC and sodium benzoate
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[PharmGKB:Curated In a study of ovarian cancer patients (n=104) receiving a cisplatin-cyclophosphamide regimen, the AGG/AGG genotype (insertion) of GSTM3 intron 6 insertion/deletion was associated with decreased incidence of thrombocytopenia, anemia and neuropathy.]
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rs2279343, also known as Lys262Arg, is a SNP within the CYP2B6 gene. variants including the Arg allele include CYP2B6*4, CYP2B6*6, and CYP2B6*7 Pharmacokinetics of efavirenz when co-administered with rifampin in TB/HIV co-infected patients: pharmacogenetic effect of CYP2B6 variation. Polymorphisms of drug-metabolizing enzymes (GST, CYP2B6 and CYP3A) affect the pharmacokinetics of thiotepa and tepa. Associations between CYP2B6 polymorphisms and pharmacokinetics after a single dose of nevirapine or efavirenz in African americans. CYP2B6 variants and plasma efavirenz concentrations during antiretroviral therapy in Port-au-Prince, Haiti. Cyclophosphamide-metabolizing enzyme polymorphisms and survival outcomes after adjuvant chemotherapy for node-positive breast cancer: a retrospective cohort s...
References:3
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rs28360521 is a SNP in the vicinity of the CYP2D6 gene. Little is known of the significance of either allele.
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
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rs28399444 is a truncated non-functioning variant of CYP2A6 known as CYP2A6*20 [PharmGKB:In-Depth This variant results in a truncated protein and no enzyme activity; part of the CYP2A6*20 haplotype.]
References:1
effects of higher bilirubin; irinotecan toxicity; tranilast toxicity http://web.me.com/russbaltman/Site/PharmGKBlog/Entries/2010/10/24_Updated_Irinotecan_Label.html
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Although the insertion is supposed to be the minor allele, the majority of FTDNA v2 and 23andMe v2 results show II as the result, so use caution when interpreting this result. rs34815109 is one of four SNPs all describing an insertion/deletion polymorphism in the promoter region of the UGT1A1 gene. This gene encodes a protein that modifies hepatic bilirubin in order to allow it to be excreted. SNPs that reduce the activity of the UGT1A1 gene therefore tend to increase serum bilirubin levels. The rs34815109(TA) allele represents the insertion variant, which actually adds a seventh (TA) pair to what is already a string of six (TA) pairs; this reduces the activity to 30% of normal, and is thus the risk allele. The risk allele is commonly referred to as the UGT1A1*28 allele, and it is homozygo...
References:1
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[PharmGKB:Curated Associated with significantly lower AUC ratio of SN38G/SN38, high incidence of severe diarrhea, but not tumor response.]
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Cytochrome P450 2C8 pharmacogenetics: a review of clinical studies. [PharmGKB:Curated The allelic variant is designated as CYP2C8*12 allele.]
normal
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The (-) form of this SNP, representing a deletion of one nucleotide, causes a frameshift such that the resulting CYP2D6 protein is nonfunctional. The associated allele is also known as CYP2D6*6, and there are several subtypes but they are all nonfunctional. If two copies of this (or similar) changes are inherited, CYP2D6 poor metabolism ('PM') is observed. CYP2D6 poor metabolism may affect the efficacy or degree of side effects of drugs metabolized by CYP2D6, such as dextromorphan, sparteine, nortriptyline, venlafaxine and codeine. Response to serotonin reuptake inhibitors in OCD is not influenced by common CYP2D6 polymorphisms. [PharmGKB:Curated This variant is part of the CYP2D6*6 PM haplotype. Plasma concentrations of metoprolol were shown to be were 4.9-fold higher in the PMs, with gr...
normal
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The rs5787121(-) (i.e. deletion) SNP defines the CYP2C19 allele known as G439- or 90052delG.
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association of the rs7483 SNP with late-onset Alzheimer's disease
normal
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rs9332131, also known as 818delA, 10601delA or 273Frame shift, is a SNP in the CYP2C9 gene. The rs9332131(-) allele defines the CYP2C9*6 variant, which is inactive. [PharmGKB:Curated Phenotype: In African Americans patients, weekly warfarin dose requirements were lower in those with the CYP2C9*8 allele (34 (30-47) mg; P = 0.023) and the CYP2C9 *2, *3, *5, *6, or *11 allele (33(28-40 mg); P < 0.001) as compared with those with the CYP2C9*1/*1 genotype (43 (35-56) mg). Adding the *5,*6,*8 and *11 alleles to a model containing the *2 and *3 alleles plus the VKORC1 -1639 G>A allele (along with clinical variables) explained 36% vs. 30% of the variability in dose requirements. Study size: 226 . Study population/ethnicity: African-American . Type of association: PD;GN;CO]
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Identification of a haplotype block in the 5q31 cytokine gene cluster associated with the susceptibility to severe malaria.
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rs212090(A;T) (T;T) increased cancer susceptibility (OR, 1.37; 95% CI, 1.03-1.83)
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[PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: The SULT1C2: rs1402467 G variant was associated with positive clincial response (partial or complete response) to treatment. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.0083 Type of association: PD; CO]
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X-inactivation in female human embryonic stem cells is in a nonrandom pattern and prone to epigenetic alterations. [PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: The ATP7A:rs2227291 G variant was associated with toxicity in response to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.006 Type of association: CO; TOX]
normal; no change in warfarin metabolism
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rs1799853 is a SNP in the CYP2C9 gene and is linked to poor warfarin metabolism. Advanced knowledge of this may influence initial warfarin dosing by physicians. Warfarin is monitored through INR (international normalized ratio) and proper dosing is influenced by a variety of factors including warfarin metabolism and diet. rs1799853 is a SNP in the CYP2C9 gene. The rs1799853(T) allele encodes a variant amino acid, cysteine, which has been linked to poor metabolism of warfarin and thus sensitivity . The common nomenclature for this polymorphism is CYP2C9*2 (Cys amino acid, T allele; the SNP is also known as C430T or Cys144Arg). The CYP2C9*2 allele is also associated with higher sensitivity to the anti-epileptic drug phenytoin. The effect of CYP2C9 variants on drug metabolism should not be pr...
normal; no effect on warfarin metabolism
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SNP rs1057910(A), located in the cytochrome p450 CYP2C9 gene, most commonly encodes the amino acid isoleucine at position 359, and the resulting allele is also known as CYP2C9*1. rs1057910(C) encodes a leucine at this same position, and the resulting allele is called CYP2C9*3. This SNP is also known as Ile359Leu or A1075C. The effect of CYP2C9 variants on drug metabolism should not be predicted without also considering CYP2C9*2, defined as the common loss of function variant rs1799853(T) (NM_000771:c.430C>T, NP_000762:p.144R>C) Studies of the effects of these alleles include: * rs1057910(C;C)] genotypes may clear drugs like celecoxib (trade name Celebrex) twice as slowly as rs1057910(A;A) genotypes; the rs1057910(A;C) genotypes are in-between clearance rates. Lower clearance rates wi...
a common variant
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The wild type (normal) allele at this SNP is (G). The (A) variant indicates the presence of a non-wild type CYP2D6 variant, but it appears in many different variants so it can not be used to determine the presence of any particular variant. Inheriting a normal number of copies of this allele results in CYP2D6 function that is indistinguishable from wild-type (normal) activity. However, this variant has been seen present in higher copy numbers, and in these cases, can result in the ultrafast metabolizer phenotype . [PharmGKB:In-Depth Risk or phenotype-associated allele: T. Phenotype: The CYP2D6*2A haplotype was associated with lower incidence of breast cancer on tamoxifen compared to placebo in a prevention study. The CYP2D6*2A allele may be associated with increased efficacy of tamoxifen....
common
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rs1080983 is a SNP near the 5' end of the CYP2D6 gene. Little is known of the significance of either allele.
normal fat metabolism; common in clinvar
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rs1801282, also known as Pro12Ala, is a common SNP in the peroxisome proliferator-activated receptor PPARG gene. The more common (C) allele (in dbSNP orientation) encodes the 'Pro' amino acid at this SNP position. rs1801282 has been reported to be associated with metabolic syndrome, but other studies have not been able to replicate any strong or significant effect. The association between type-2 diabetes and SNP rs1801282 is mentioned as being replicated in rs1801282 and risk of cognitive decline in elders? Maybe with diabetes. A ten-year study of 679 male patients with symptomatic coronary artery disease found that rs1801282(G) carriers had a much lower (10 year) cardiovascular risk, with the hazard ratio estimated to be 0.10 (CI: 0.01-0.70, p = 0.02) for ischemic heart disease and 0.24 f...
normal
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Several SNPs in the VKORC1 gene have been linked to warfarin sensitivity, with perhaps the most common being this SNP rs9923231. Note that the orientation as published in scientific articles is often on the opposite strand compared to the orientation in dbSNP, so you will sometimes see it as a G>T snp. It is also known as *-1639G>A with the minus indicating that this is in an upstream promoter *3673 based on its position in GenBank accession number AY587020. *VKORC1*2. The main findings related to the treatment of venous thromboembolism (aka VTE; from hypercoagulability) with the blood thinner warfarin for this SNP are that carriers of the rs9923231(T) allele require significantly reduced doses of warfarin, and are (otherwise) at a higher risk of serious bleeding. Clinical studies de...
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risk of aortic calcification was calculated, adjusted for potential confounders. The T allele frequency of the VKORC1 1173C>T polymorphism was 38.8%. 1185 (37.2%) persons were homozygous CC, 1529 (48,0%) were heterozygous CT and 473 (14.8%) were homozygous TT. Persons with at least one T-allele had a statistically significant 19% (95% CI 2 to 40%) risk increase of calcification of the aortic far wall compared to CC homozygous persons [PharmGKB:Curated Double homozygous VKORC1 1173T/T, CYP4F2 433Val/Val (n = 5) showed the highest INR (3.1; 2.0-4.7) and required the lowest acenocoumarol dose (11 ± 3 mg/week) The addition of the V433M genotype to the VKORC1 genotype raised the R2 from 8% to 14% for INR, and from 12% to 19% for acenocoumarol dose requirements.] [OMIM:VITAMIN K EPOXIDE...
normal
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rs1056836, also known as 4326C/G, Val432Leu or L432V, is a SNP in the cytochrome P450 1B1 (CYP1B1) gene. This gene is a member of the CYP1 gene family and one of the major enzymes involved in the hydroxylation of estrogens, a reaction likely to be relevant in hormonal carcinogenesis. [In dbSNP orientation, the (C) allele encodes the Leu; the (G) the Val.] In a study of 153 Hispanic Caucasians with prostate cancer the rs1056836(G;G) genotype showed decreased risk compared to the more common (C;C) genotype (odds ratio = 0.31, p = 0.04, CI: 0.10-0.96). This report cites another study as indicating that rs1056836(C;C) high-risk stage III and IV breast cancer patients receiving dose-intense paclitaxel in combination with doxorubicin and cyclophosphamide experience a longer progression-free surv...
common
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rs887829 is a SNP in the UGT1A1 gene. The minor allele of this SNP has been reported to be associated with higher levels of serum bilirubin, which has an inverse correlation with coronary artery disease. . This study of 2,000+ patients reports a recessive protective effect against coronary artery disease for the minor allele, with an age-adjusted odds ratio of 0.24 (CI: 0.10-0.60, p=0.0014). [PharmGKB:Curated This variant is in the promoter region of UGT1A1 and associated with serum bilirubin levels and hyperbilirubinemia in a genome wide association scan from 4300 Sardinian individuals.] [GWAS:Bilirubin levels]
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rs1041983, also known as C282T, is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The allele associated with slow NAT2 metabolization for this SNP is rs1041983(T). Genosets gs154 and gs156 evaluate predicated NAT2 metabolizer phenotype based on rs1041983 and rs1801280. [PharmGKB:Curated in vitro study; PK: 22-fold reduction in Vmax vs wild type]
Normal common for Caucasians on the 23andme platform
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rs1799930 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. Also known as G590A. The risk allele for this SNP is rs1799930(A). [PharmGKB:Curated in vitro study; PK: 22-fold reduction in Vmax vs wild type] [OMIM:?]
common in clinvar
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[PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: The ABCC6 rs2238472 G variant was associated with toxicity in response to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.006 Type of association: CO; TOX] [OMIM:PSEUDOXANTHOMA ELASTICUM]
normal
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rs324420 is a SNP, also known as Pro129Thr, in the fatty acid amide hydrolase FAAH gene, which has shown associations with some substance use disorders. rs324420(C) encodes the more common Pro, while the (A) allele encodes the Thr. Among 80 individuals with drug abuse or alcoholism and over 1,000 controls, the odds ratio for risk of problem drug or alcohol use among rs324420(A;A) individuals was 4.5 (CI: 2.2 - 8.4); the odds ratio for risk of street drug use was 2.2 (CI: 1.3–3.7); and the odds ratio for risk of combined street drug use and problem drug/alcohol use was 4.9 (CI: 2.5–9.7) When this study was pooled with the results of another study of 249 subjects with documented multiple different drug addictions compared to drug free individuals of the same ethnic backgrounds, t...
common in clinvar
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rs1800566 (C609T, Pro187Ser) is a snp within NQO1 (NAD(P)H dehydrogenase (quinone 1)). A Ser (T) at this location denotes the NQO1*2 allele. influences the risk of breast cancer according to the 23andMe blog rs1800566 increases susceptibility to Lung cancer 0.48 times for heterozygotes (CT) [PharmGKB:Curated Risk or phenotype-associated allele: C/T. Phenotype: There was no association between the NQO1*2 polymorphism and the risk of anthracycline-related CHF. Study size: 145. Study population/ethnicity: Nested case-control study was conducted within a cohort of 1979 patients enrolled in the Childhood Cancer Survivor Study who received treatment with anthracyclines and had available DNA. Significance metric(s): OR = 1.04; p = 0.97. Type of association: CO; TOX; ADR.] [OMIM:NAD(P)H DEHYDROGE...
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rs1053049, rs6902123, and rs2267668 in PPARD affect Lifestyle Intervention induced changes in overall adiposity, hepatic fat storage, and relative muscle mass. Our findings provide a mechanistic explanation for the involvement of these genetic variations in the development of insulin resistance and type-2 diabetes. [OMIM:PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR-GAMMA, COACTIVATOR 1, ALPHA;]
normal
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influences statin response *rs72559745 (SLCO1B1*1) AA AA *rs56061388 (SLCO1B1*3) TT TT *rs4149056 (SLCO1B1*5) TT TT *rs55901008 (SLCO1B1*6) TT TT rs4149056, also known as 37041T>C or V174A, is a SNP in the SLCO1B1 gene, which encodes the 'organic anion transporting polypeptide 1B1' (OATP1B1) protein. This protein, found primarily in the liver, regulates the uptake of numerous drugs and natural compounds. The rs4149056(C) SNP defines the SLCO1B1*5 allele. The rs4149056(C) allele gives rise to an amino acid change (from valine to alanine at residue 174) which has reduced uptake/transport activity. Therefore, drugs metabolized by OATP1B1 tend to build up to higher circulating concentrations than they would otherwise.. The drugs known (or in some cases, thought) to be transported less well ...
common in clinvar
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Technology to accelerate pangenomic scanning for unknown point mutations in exonic sequences: cycling temperature capillary electrophoresis (CTCE). Genetic variation in the one-carbon transfer pathway and ovarian cancer risk. Strong association of a common dihydropyrimidine dehydrogenase gene polymorphism with fluoropyrimidine-related toxicity in cancer patients. Genetic variation in TYMS in the one-carbon transfer pathway is associated with ovarian carcinoma types in the Ovarian Cancer Association Consortium. [PharmGKB:Curated Patients heterozygous for the C allele of this SNP exhibited increased incidence of medium-severe nausea and vomiting (as defined by WHO criteria) relative to those carrying only the T allele. The patient population consisted of individuals with gastric or colon ca...
common in complete genomics
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[PharmGKB:Curated Risk or phenotype-associated allele: T Phenotype: The CYP4B1:rs4646487 T variant was associated with toxicity in response to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s):p = 0.008 Type of association: CO; TOX]
Magnitude: 0
Frequency: 75.2%
Repute:Good
References:16
Frequency: 75.2%
Repute:Good
References:16
common on affy axiom data
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CYP2C8 SNP, defining the CYP2C8*3 allele (along with rs11572080). Individuals carrying this SNP may show increased risk of developing acute gastrointestinal bleeding during the use of NSAIDs that are CYP2C8 or CYP2C9 substrates, such as aceclofenac, celecoxib, diclofenac, ibuprofen, indomethazine, lornoxicam, meloxicam, naproxen, piroxicam, tenoxicam and valdecoxib. [PharmGKB:Curated Risk or phenotype-associated allele: G. Phenotype: In woman, the risk of acute myocardial infarction (AMI) tended to be higher for subjects carrying the CYP2C8*3*3 genotype versus *1*1 (OR = 1.9). The CYP2C8*3 variants are 416G>A (rs10509681) and 1196A>G (rs11572080). Tested in all subjects, the risk of AMI was also higher in individuals carrying the CYP2C8*3 allele (*3*3; *1*3 versus*1*1) [1.2 (1.0-1.5...
common on affy axiom data
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[PharmGKB:Curated Risk or phenotype-associated allele: T Phenotype: The SPG7:rs2292954 T variant was associated with toxicity in response to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.0004 Type of association: CO; TOX]
normal
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rs4244285 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*2 variant. This variant is the most common reason for poor metabolism of compounds like mephenytoin (an anti-convulsant), some antidepressants, the anti-platelet drug Plavix, and some drugs used for ulcer conditions of various types. The risk allele is rs4244285(A). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (trade name Prevacid). In Caucasians, SNPs in CYP2C19 are relatively rare (in contrast to SNPs in CYP2D6), but SNPs in this gene are common in Asians. Ulcer treatment with omeprazole to reduce Helicobacter pyl...
Magnitude: 0
Frequency: 77.1%
Repute:Good
References:17
Frequency: 77.1%
Repute:Good
References:17
common on affy axiom data
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CYP2C8 SNP, defining the CYP2C8*3 allele (along with rs10509681). Individuals carrying this SNP may show increased risk of developing acute gastrointestinal bleeding during the use of NSAIDs that are CYP2C8 or CYP2C9 substrates, such as aceclofenac, celecoxib, diclofenac, ibuprofen, indomethazine, lornoxicam, meloxicam, naproxen, piroxicam, tenoxicam and valdecoxib. [PharmGKB:Curated Risk or phenotype-associated allele: A. Phenotype: This variant was associated with increased risk for neurotoxicity with paclitaxel treatment. Study size: 132. Study population/ethnicity: Patients with Neoplasms receiving paclitaxel; Spain. Significance metric(s): HR = 1.54 (0.96-2.47); p = 0.072. Type of association: PK; TOX.]
Magnitude: 0
Frequency: 77.9%
Repute:Good
References:1
Frequency: 77.9%
Repute:Good
References:1
common in complete genomics
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[PharmGKB:Curated The CYP3A43*1B allele is characterized by the silent 1150C>T substitution exon 11.]
common on affy axiom data
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[PharmGKB:Curated Drug efflux and cell surface expression (by MRK-16 and C219 probes) of P-gp was not different between wild-type and variant forms (single mutants: N21D, F103L, S400N, A893S, A998T, and double mutants: 21D-S400N, N21D-A893S, and S400N-A893S) in an in vitro vaccinia virus-based transient expression system. Fluroescent substrates included calcein AM, bodipy-FL-forskolin, bodipy-FL-verapamil, bodipy-FL-vinblastine, bodipy-FL-prazosin, bisantrene, and bodipy-FL-paclitaxel. There was a slight increase in wild-type P-gp efflux of bodipy-FL-paclitaxel over mutants.]
normal
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rs2231142, also known as Q141K and C421A, is a SNP in the ABCG2 gene, indicating a missense variant. 'Our data indicate that at least 10% of all gout cases in whites are attributable to this causal variant.' A is the risk allele. A large study totaling 7,699 participants in the Framingham cohort and 4,148 participants in the Rotterdam cohort was conducted, with genome-wide significant SNPs then replicated in 11,000+ Caucasian and ~4,000 African-American individuals who took part in the study of Atherosclerosis Risk in Communities (ARIC). This study calculated an odds ratio of 1.74 for rs2231142 (CI: 1.51-1.99, p = 3.3x10e-15). A genetic score comprised of this SNP plus 2 others may stratify risk for gout. Among non-small cell lung cancer patients treated with gefitinib, there's a 4-5x high...
common in complete genomics
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[PharmGKB:Curated Risk or phenotype-associated allele: A allele. Phenotype: Carriers of either one or two alleles of the A allele required 19% lower warfarin maintenance dose (2.6 ± 1.3 mg) compared to GG homozygotes (3.2 ± 1.6 mg) (p < 0.0001). The combined effect of variants in four genes, as well as age, explained 26.6% of the overall interindividual warfarin dose variability, with VKORC1 (rs9923231 A allele) accounting for 19.1%, CYP2C9 (rs1799853 T allele, or rs1057910 C allele) for 3.2%, EPHX1 (rs2292566 A allele) for 1.7%, CYP4F2 (rs2108622 C allele) gentoypes for 1.1%, and age for 1.5%. Study size: 283. Study population/ethnicity: Hospitalized Caucasian patients aged 75 years or older, recruited Sep 2002-Nov 2004 in Ivry, France, and Oct 2005-Mar 2008 from 14 French ce...
common in clinvar
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Variations in the peroxisome proliferator-activated receptor-gamma gene and melanoma risk. PPAR-gamma gene polymorphisms and psoriatic arthritis. The Genetics of PPARG and the Skeleton. The association of Pro12Ala polymorphism of peroxisome proliferator-activated receptor-gamma gene with serum osteoprotegerin levels in healthy Korean women. Association of stearoyl-CoA desaturase 1 activity with familial combined hyperlipidemia. Polymorphism of genes related to insulin sensitivity and the risk of biliary tract cancer and biliary stone: a population-based case-control study in Shanghai, China. PPAR Genomics and Pharmacogenomics: Implications for Cardiovascular Disease. Association of FTO with obesity-related traits in the Cebu Longitudinal Health and Nutrition Survey (CLHNS) Cohort. Differen...
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rs2066853 has been associated with increased risk for colorectal polyps depending on the amount of meat eaten or overall exposure to heterocyclic amines. lung cancer in a Chinese population heterozygous rs2158041 OR=1.53 for GA vs compared with the (G;G) and rs7811989 OR=1.48 for (G;A) compared with the GG genotype) *rs2066853 (p.Arg554Lys) and cumulative cigarette smoking and the Lys/Lys genotype conferred an increased risk of lung cancer in the heavy smokers OR=3.36 [PharmGKB:In-Depth Very common variant with controversial associations.]
common in complete genomics
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[PharmGKB:Non-Curated Increased metformin uptake in transfected cells] [GWAS:Blood metabolite levels]
common on affy axiom data
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[PharmGKB:Curated The DPYD:496A>G variant was associated with toxicity of fluoropyrimidine-based chemotherapy in patients with gastroesophageal and breast cancer, but did not reach significance in patients with colorectal malignancies.]
common in clinvar
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rs1736557, also known as Val257Met, is a SNP in the FMO3 gene. It has been linked to trimethylaminuria; see variant .0002, OMIM 136132. [OMIM:?]
normal
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rs2031920 is a SNP in the CYP2E1 gene. The rs2031920(T) allele defines the CYP2E1_-1055C>T variant. [OMIM:CYTOCHROME P450, SUBFAMILY IIE; CYP2E1]
common on affy axiom data
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[PharmGKB:Curated Risk or phenotype-associated allele: A. Phenotype: This SNP was part of a haplotype associated with acute cardiotoxicity in response to doxorubicin. Study size: 1697. Study population/ethnicity: Participants of the German non-Hodgkin lymphoma study. Significance metric(s): OR = 2.3; 95% CI, 1.0 to 5.4. Type of association: PD; ADR; TOX.]
common in complete genomics
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The association reported in was not replicated in . Glucocorticoid receptor gene haplotype structure and steroid therapy outcome in IBD patients. Molecular mechanism of glucocorticoid resistance in inflammatory bowel disease. Genetic polymorphisms of the glucocorticoid receptor may affect the phenotype of women with anovulatory polycystic ovary syndrome.
normal
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The rs3758581(A) SNP defines a CYP2C19 allele known as V331I. Analysis of 50 SNPs in CYP2D6, CYP2C19, CYP2C9, CYP3A4 and CYP1A2 by MALDI-TOF mass spectrometry in Chinese Han population.
common in complete genomics
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[PharmGKB:Curated The g.22,060G variant segregates with g.23,238C>T (with one exception). The allele containing both of these polymorphisms has been designated FMO2*2C.]
common in complete genomics
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[PharmGKB:Curated Risk or phenotype-associated allele: T. Phenotype: CYP2B6*2 genotype in the transplant recipient was associated with hemorrhagic cystitis. Study size:107 . Study population/ethnicity: Donors and patients with leukemia after HLA-identical hematopoietic stem cell transplantation, France. Significance metric(s): p = 0.03. Type of association: TOX]
Magnitude: 0
Frequency: 92.9%
Repute:Good
References:3
Frequency: 92.9%
Repute:Good
References:3
common in complete genomics
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[PharmGKB:Curated Risk or phenotype-associated allele: UGT1A8*3 (defining allele: 830A, 277Tyr). Phenotype: In vitro catalytic activity and protein expression. Genetic analysis of UGT1A8 (exclusively expressed in extrahepatic tissue) in 69 individuals identified four alleles, of which UGT1A8*3 was defined as having tyrosine at amino acid 277. In vitro studies in HEK293 cells show UGT1A8*3 (830A, 277Y) has a dramatic reduction in catalytic activity compared to wildtype, but no loss in protein expression. Study size: 69. Study population/ethnicity: Lung cancer patients and family members and other volunteers who served as controls. Type of association: GN; FA]
normal
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rs2070672 is a SNP in the CYP2E1 gene. The rs2070672(G) allele defines the CYP2E1*7_-352A>G variant.
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Also known as Ile462Val A4889G CYP1A1*2C Genome amplification of single sperm using multiple displacement amplification. Decision forest analysis of 61 single nucleotide polymorphisms in a case-control study of esophageal cancer; a novel method. Multilocus analysis of SNP and metabolic data within a given pathway. CYP1A1 and CYP1B1 polymorphisms and their association with estradiol and estrogen metabolites in women who are premenopausal and perimenopausal. Dietary phytoestrogen intake is associated with reduced colorectal cancer risk. Associations between smoking, polymorphisms in polycyclic aromatic hydrocarbon (PAH) metabolism and conjugation genes and PAH-DNA adducts in prostate tumors differ by race. Cytochrome P450 1A1 (CYP1A1) polymorphisms and breast cancer risk in Korean women. Cor...
common in complete genomics
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[PharmGKB:Curated Increased risk for smokers to develop gastric cancer, no association for breast cancer.]
common in complete genomics
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[PharmGKB:Curated This variant is in exon 1b of ABCB1 and may be associated with tacrolimus pharmacokinetics in renal transplant recipients. It was also associated with lower ABCB1 mRNA expression and possibly being an useful invasive marker predicting poorly-differentiated colorectal adenocarcinomas and thereby the poor prognosis of the Japanese patients in the study.]
common in complete genomics
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[PharmGKB:Curated This variant is the defining SNP for CYP19A1*4. It is associated with significant decreases in levels of activity compared with the wild-type (WT) enzyme after transient expression in COS-1 cells.]
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[PharmGKB:Curated Drug efflux and cell surface expression (by MRK-16 and C219 probes) of P-gp was not different between wild-type and variant forms (single mutants: N21D, F103L, S400N, A893S, A998T, and double mutants: 21D-S400N, N21D-A893S, and S400N-A893S) in an in vitro vaccinia virus-based transient expression system. Fluroescent substrates included calcein AM, bodipy-FL-forskolin, bodipy-FL-verapamil, bodipy-FL-vinblastine, bodipy-FL-prazosin, bisantrene, and bodipy-FL-paclitaxel. There was a slight increase in wild-type P-gp efflux of bodipy-FL-paclitaxel over mutants.]
common in clinvar
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rs1142345 is a SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The risk allele for this SNP is rs1142345(G), and when it is the only variant in the TPMT gene, it encodes the TPMT*3C allele. While still rare, it is more common in African-Americans (2.4% of all alleles) than in Caucasians. Note that if the same allele also carries the rs1800460(A) SNP, the allele is actually a TPMT*3A allele (OMIM). The medicine 6-Mercaptopurine is metabolized by TPMT. Individual differences in TPMT activity associated with this SNP are now used to determine appropriate dosage range and interval for treatment. 23an...
common in complete genomics
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[PharmGKB:Curated system: membrane vessicles from HEK cells transfected with WT or variant; FA: variant had approx 50% decrease in transport of tritium labelled 17[beta]-estradiol-17[beta]-D-glucuronide and tritium labelled methotrexate]
common in clinvar
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rs4987076 is a SNP tagging the NAT1*17 allele. See OMIM 108345.0002 for more information. [OMIM:NAT1*17 ALLELE]
Magnitude: 0
Frequency: 95.6%
Repute:Good
References:2
Frequency: 95.6%
Repute:Good
References:2
normal
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rs6413419, also known as 4768G>A or V179I, is a SNP in the CYP2E1 gene. The rs6413419(A) allele defines the CYP2E1*4 variant.
common in complete genomics
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[PharmGKB:Curated Risk or phenotype-associated allele: T. Phenotype: In a study of bacterial expressed and purified human CBR3 proteins, the 93Ile variant had significantly reduced maximal reaction velocity (V(max)) for both anthracyclines compared with the wild-type enzyme. Type of association: FA.]
common in complete genomics common for Caucasians on the 23andme platform
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rs1801279 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The risk allele for this SNP is rs1801279(A). [PharmGKB:Curated Homozygous A allele is slow acetylator phenotype (altered rates of metabolism of arylamines). May be associated with higher risk for bladder cancer and lower risk for colorectal cancer.]
common in complete genomics
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[PharmGKB:Curated Human lymphocyte cell lines homozygous for the A allele of this variant, common in Japanese populations, exhibit reduced surface membrane levels of ABCC4 protein and increased sensitivity to 6-mercaptopurine toxicity relative to cell lines homozygous for the G allele. The A-allele and G-allele cell lines have similar overall protein expression levels.]
common in complete genomics
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NAT2 slow acetylation, GSTM1 null genotype, and risk of bladder cancer: results from the Spanish Bladder Cancer Study and meta-analyses. Genetic variation in N-acetyltransferase 1 (NAT1) and 2 (NAT2) and risk of non-Hodgkin lymphoma.
common in clinvar
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rs1799931 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The risk allele for this SNP is rs1799931(A). [PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: The NAT2:rs1799931 G variant was associated with toxicity in response to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.003 Type of association: CO; TOX] [OMIM:?]
common in complete genomics
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rs1800584 is a rare SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The rs1800584(A) SNP defines the TPMT*4A allele (OMIM). wikipedia thiopurine drugs metabolized by TPMT include azathioprine, mercaptopurine, and thioguanine [PharmGKB:In-Depth This splicing variant results in very low TPMT activity and risk for hematologic toxicity as a result of treatment with thiopurines.]
Magnitude: 0
Frequency: 98.2%
Repute:Good
References:0
Frequency: 98.2%
Repute:Good
References:0
normal
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rs28365083, also known as 27289C>A, is a SNP in the CYP3A5 gene. The rs28365083(A) allele defines the CYP3A5*2 variant, which is nonfunctional. Polymorphisms in the cytochrome P450 genes CYP1A2, CYP1B1, CYP3A4, CYP3A5, CYP11A1, CYP17A1, CYP19A1 and colorectal cancer risk. Genotyping panel for assessing response to cancer chemotherapy. Polymorphisms of drug-metabolizing enzymes (GST, CYP2B6 and CYP3A) affect the pharmacokinetics of thiotepa and tepa. Pazopanib-induced hyperbilirubinemia is associated with Gilbert's syndrome UGT1A1 polymorphism.
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The complex global pattern of genetic variation and linkage disequilibrium at catechol-O-methyltransferase. Influence and interaction of genetic polymorphisms in catecholamine neurotransmitter systems and early life stress on antidepressant drug response.
common in complete genomics
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[PharmGKB:Curated The variant is located in the promoter region of the GSTP1 gene and was significantly associated with the level of GSTP1 mRNA in Mexican Americans. The G(-18)A variant is tightly linked with the well studied Ile 105 Val polymorphism, which is associated with various clinical phenotypes.]
normal
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rs9332130, also known as 815A>G, 10598A>G or E272G, is a SNP in the CYP2C9 gene. The rs9332130(G) allele defines the CYP2C9*10 variant.
normal
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rs2256871, also known as 752A>G, 10535A>G or H251R, is a SNP in the CYP2C9 gene. The rs2256871(C) allele defines the CYP2C9*9 variant.
common in complete genomics
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[PharmGKB:Curated Risk or phenotype-associated allele: A Phenotype: Kinetic studies using purified, histidine-tagged, recombinant enzymes demonstrated that the V88I mutation leads to a significantly reduced maximal rate of activity for doxorubicin and daunorubicin compared to wild type protein. Type of association: FA]
Magnitude: 0
Frequency: 99.1%
Repute:Good
References:1
Frequency: 99.1%
Repute:Good
References:1
common in complete genomics
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CYP2B6 (c.516G-->T) and CYP2A6 (*9B and/or *17) polymorphisms are independent predictors of efavirenz plasma concentrations in HIV-infected patients. [PharmGKB:In-Depth This variant decreases enzyme activity and affects metabolism of coumarin and nicotine; part of the CYP2A6*17 haplotype.]
common in complete genomics
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23andMe reports that the A allele of rs3918290 is associated with the rare recessive disorder dihydropyrimidine dehydrogenase deficiency (DPD), also known as hereditary thymine-uraciluria or familial pyrimidinemia. Note that the terms used in the literature for this gene can be confusing, since the gene is in reverse orientation to the chromosome strand on the reference genome. pharmgkb - defines *2A allele, which has a significantly higher chance of 5-fluorouracil toxicity Fluorouracil Toxicity [PharmGKB:In-Depth Heterozygosity for the A allele of this SNP is associated with mucositis and leukopenia drug toxicity in cancer patients treated with fluorouracil. Heterozygous males were more likely than heterozygous females to develop severe toxicity. In this study, no A/A homozygotes were ob...
normal
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rs4986909, also known as 1247C>T, 22026C>T or P416L, is a SNP in the CYP3A4 gene. The rs4986909(T) allele defines the CYP3A4*13 variant. [PharmGKB:In-Depth Defining variant for CYP3A4*13; in vitro, this allele did not result in detectable P450 holoprotein.]
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:9
Frequency: 100.0%
Repute:Good
References:9
normal
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rs10264272, also known as 14690G>A, is a SNP in the CYP3A5 gene. indicates that this corresponds with CYP3A5*6, however, this seems doubtful. CYP3A5 allele nomenclature found at http://www.cypalleles.ki.se/cyp3a5.htm indicates that CYP3A5*6 (also known as 14690G>A) is a splicing defect resulting in essentially no activity in the gene. This does not correspond with dbSNP, which indicates that is a nucleotide substition (624G-A) which only results in a 'silent' substitution of AAG (Lysine) to AAA (Lysine). [PharmGKB:In-Depth Nonfunctional allele present predominantly in the African American population.]
normal
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rs1041988 is a SNP in the CYP3A4 gene. The rs1041988(C) allele defines the CYP3A4*_23139T>C(I431T) variant.
normal
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rs1057909 is a SNP in the CYP2C9 gene. The rs1057909(G) allele defines the CYP2C9_42612A>G variant, about which little is known.
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:1
Frequency: 100.0%
Repute:Good
References:1
common in complete genomics
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[PharmGKB:Curated Greatly reduced the efficiency of metabolism of carvedilol.]
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:2
Frequency: 100.0%
Repute:Good
References:2
normal
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rs12720461 is a SNP in the CYP1A2 gene. The rs12720461(T) allele defines the CYP1A2*1K_-729C>T variant. [PharmGKB:Curated Likely disrupts transcription factor binding, leading to reduced function.]
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:2
Frequency: 100.0%
Repute:Good
References:2
common in complete genomics
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[PharmGKB:Curated study of 54 livers; variant not associated with altered midazolam clearance]
normal
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rs3091339 is a SNP in the CYP3A4 gene. The rs3091339(G) allele defines the CYP3A4*_11460A>G(K96E) variant.
normal
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rs3208363 is a SNP in the CYP3A4 gene. The rs3208363(G) allele defines the CYP3A4*_16907T>G(S252A) variant.
normal
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Something seems wrong between dbSNP and the results from 23andMe and FTDNA. See Talk:Rs4148323 for more information. rs4148323, a SNP also known as 211G>A or G71R, occurs in the UGT1A1 gene, and defines the UGT1A1*6 allele. This allele is associated with Gilbert's syndrome among Asians, Crigler-Najjar syndrome type II (CN-II), and transient familial neonatal hyperbilirubinemia. rs4148323(A) in exon 1 of the UGT1A1 gene is associated with hyperbilirubinemia. rs4148323 and several other nearby SNPs help predict serum total bilirubin levels, based on a study of 750 Japanese. [PharmGKB:Curated *6 is the most common UGT1A1 coding variant found in Asians. It may result in reduced capacity to metabolize irinotecan and hence irinotecan toxicity.] [OMIM:UDP-GLYCOSYLTRANSFERASE 1 FAMILY, POLYPEP...
normal
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rs4986907, also known as 485G>A, 14269G>A or R162Q, is a SNP in the CYP3A4 gene. The rs4986907(A) allele defines the CYP3A4*15A variant. [PharmGKB:In-Depth Defining variant for CYP3A4*15A.]
normal
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rs4986913, also known as 1399C>T, 23237C>T or P467S, is a SNP in the CYP3A4 gene. The rs4986913(T) allele defines the CYP3A4*19 variant. [PharmGKB:In-Depth Part of CYP3A4*19.]
common in complete genomics
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[PharmGKB:Curated Homozygous A allele is slow acetylator phenotype.]
normal
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rs4987161, also known as 566T>C, 15615T>C or F189S, is a SNP in the CYP3A4 gene. The rs4987161(C) allele defines the CYP3A4*17 variant. [PharmGKB:In-Depth Defining variant for CYP3A4*17, defective in metabolizing the hypertensive drug nifedipine in vitro; exhibited lower turnover numbers than wild-type for testosterone and chlorpyrifos in vitro.]
normal
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The rs6413438(T) allele defines the CYP2C19 allele known as CYP2C19*10. This allele may lead to reduced metabolism of S-mephenytoin at least in vitro. [PharmGKB:Curated This variant is the defining SNP for CYP2C19*10. This variant is associated with reduction in the metabolism of S-mephenytoin in vitro.]
common in complete genomics
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[PharmGKB:Curated This variant is the defining SNP for the FMO2*1 and FMO2*2 alleles. The major allele, FMO2*2, is characterized by a T at genomic position 23,238 and encodes a truncated inactive protein. The minor allele, FMO2*1, has a C at this position and encodes a full-length active protein. Thus, this SNP could potentially be associated with differential drug response.]
common in complete genomics
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[PharmGKB:Non-Curated Increased sensitivity to inhibition by TBA in oocytes]
common in complete genomics
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[PharmGKB:Non-Curated Increased sensitivity to inhibition by TBA in oocytes]
normal
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rs915909 is a SNP in the CYP2E1 gene. The rs915909(T) allele defines the CYP2E1_6498C>T(I321I) variant.
normal
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rs9332239, also known as 1465C>T, 50338C>T or P489S, is a SNP in the CYP2C9 gene. The rs9332239(T) allele defines the CYP2C9*12 variant. According to a 23andMe discussion This is one of the SNPs which were re-analyzed April 2009. Customers with older data may wish to redownload. SNPs effected rs4420638, rs34276300, rs3091244, rs34601266, rs2033003, rs7900194, rs9332239, rs28371685, rs1229984, and rs28399504.
G6PD Type B Resides within the glucose-6-phosphate dehydrogenase (G6PD) gene. The rs1050829 A allele is associated with G6PD 'type B', as well as, the production of 'normal' levels of G6PD enzyme.
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rs1050829 is a SNP within the G6PD gene and is located the X chromosome. G6PD codes for the enzyme glucose-6-phosphate dehydrogenase, which helps protect the cell from oxidative damage. Depending on genotype, an individual may possess one of two primary versions of the G6PD gene; type A and type B. Type A is predominantly found in people who have African ancestry. Mutations of G6PD can cause varying degrees of G6PD deficiency, which is a disease affecting red blood cells. For example, an A to G substitution mutation at the rs1050829 locus (also known as A376G) is associated with reduced production of G6PD enzyme. Other mutations causing G6PD deficiency include; rs1050828. The G6PD deficient genotype A- (~8-20% reduction of G6PD) is typically defined by the possession of both the rs1050829 ...
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in complete genomics
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[PharmGKB:Non-Curated Reduced uptake of estrone sulfate and methotrexate in oocytes] [GWAS:None]
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
common in complete genomics
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[PharmGKB:Curated Reduced metformin and MPP+ uptake in transfected cells]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
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rs12721634, also known as 44 T>C or L15P, is a SNP in the CYP3A4 gene. The rs12721634(C) allele defines the CYP3A4*14 variant. [PharmGKB:In-Depth Defining variant for CYP3A4*14.]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
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[PharmGKB:Non-Curated altered substrate specificity with respect to inosine and uridine]
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
normal
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The rs17882687(C) SNP defines the CYP2C19 allele known as CYP2C19*15, and also known as CYP2C19_55A>C or I19L.
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
normal
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The rs17884712(A) allele defines the CYP2C19 variant known as CYP2C19*9, which is associated with a slight decrease in the metabolism of S-mephenytoin (at least in vitro). [PharmGKB:Curated This variant is the defining SNP for CYP2C19*9 and associated with a modest decrease in the V(max) for 4'-hydroxylation of S-mephenytoin in vitro.]
normal
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rs1800460 is a SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The risk allele for this SNP is rs1800460(A), and when it is the only variation in the TPMT gene, it encodes the TPMT*3B allele. While still rare, it is more common in Caucasians (4.5% of all alleles) than in African-Americans (0.8%). Note that if the same allele also carries the rs1142345(G) SNP, the allele is actually a TPMT*3A allele (OMIM). The medicine 6-Mercaptopurine is metabolized by TPMT. Individual differences in TPMT activity associated with this SNP are now used to determine appropriate dosage range and interval for treatm...
common in complete genomics
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[PharmGKB:Curated This variant was present at a frequency of 0.126 in African American DNA samples from the Coriell Repository (HD100AA) and when expressed in COS-1 cells had the same level of immunoreactive protein as wild type.]
normal
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The rs2740574(G) allele encodes a variant form of CYP3A4 known as CYP3A4*1B. rs2740574(G) alleles are associated with an ~10 fold higher risk of aggressive prostate cancer in African American males. [PMID 16414488, OMIM A pooled study (1,400+ samples) along with a replication study conducted by members of the Ovarian Cancer Association Consortium found a 2.5-2.8x increased risk for ovarian cancer] for rs2740574(G;G) individuals (CI: 1.2-6.5, p=0.017). The authors note that CYP3A4 encodes a key enzyme in estrogen metabolism and which may be linked to ovarian carcinogenesis. [PharmGKB:Curated Risk or phenotype-associated allele: CYP3A4*1B, rs2740574 G allele. Phenotype: CYP3A4*1B (rs2740574 G) allele carriers show a significantly increased risk for SCLC (OR = 2.25, p = 0.02), which showed a...
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
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[PharmGKB:Non-Curated (i) Decreased intracellular calcein levels (increased function), (ii) increased intracellular BODIPy-FL- paclitaxel levels (decreased function), in transfected cells]
Magnitude: 0
Repute:Good
References:5
Repute:Good
References:5
normal
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rs28371685, also known as 1003C>T, 42542C>T or R335W is a SNP in the CYP2C9 gene. The rs28371685(T) allele defines the CYP2C9*11 variant, which has decreased activity. According to a 23andMe discussion This is one of the SNPs which were re-analyzed April 2009. Customers with older data may wish to redownload. SNPs effected rs4420638, rs34276300, rs3091244, rs34601266, rs2033003, rs7900194, rs9332239, rs28371685, rs1229984, and rs28399504. [PharmGKB:Curated Phenotype: In African Americans patients, weekly warfarin dose requirements were lower in those with the CYP2C9*8 allele (34 (30-47) mg; P = 0.023) and the CYP2C9 *2, *3, *5, *6, or *11 allele (33(28-40 mg); P < 0.001) as compared with those with the CYP2C9*1/*1 genotype (43 (35-56) mg). Adding the *5,*6,*8 and *11 alleles to a...
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
normal
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rs28371706, also known as 1023C>T or T107I, is a SNP in the CYP2D6 gene. The rs28371706(T) allele is found in several CYP2D6 variants: * CYP2D6*17 decreased activity variant * CYP2D6*40 non-functioning variant * CYP2D6*58 variant * CYP2D6*64 variant [PharmGKB:In-Depth Variant was identified as being part of the reduced function haplotype CYP2D6*17.]
Magnitude: 0
Repute:Good
References:5
Repute:Good
References:5
normal
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rs28371725, also known as 2988G>A, is a SNP in the CYP2D6 gene. The rs28371725(A) allele defines the CYP2D6*41 variant, which has decreased activity. 23andMe also has SNP i4001476 at the same position. [PharmGKB:In-Depth This variant is part of the CYP2D6*41 IM haplotype. Plasma concentrations of metoprolol were shown to be were 4.9-fold higher in the PMs, with greater reductions in heart rate, diastolic blood pressure, and mean arterial pressure in PMs than in non-PMs.]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
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rs28371759, also known as 878T>C, 20070T>C or L293P, is a SNP in the CYP3A4 gene. The rs28371759(C) allele defines the CYP3A4*18 variant. [PharmGKB:Curated In a study of 2,178 women of ages 40-79 years, this variant in the CYP3A4 gene was significantly associated with low bone mass. In vitro functional analyses indicate that CYP3A4*18 is a gain-of-function mutation in sex steroid metabolism, resulting in rapid oxidation of estrogens and testosterone.]
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
normal
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rs28383468, also known as 3705C>T or H30Y, is a SNP in the CYP3A5 gene. The rs28383468(T) allele defines the CYP3A5*H30Y variant, which is nonfunctional.
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
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rs28383479, also known as 19386G>A, is a SNP in the CYP3A5 gene. The rs28383479(A) allele defines the CYP3A5*9 variant, which is nonfunctional.
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
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rs28399424, also known as 5090C>T or R431W, is a SNP in the CYP1A2 gene. The rs28399424(T) allele defines the CYP1A2*6 decreased activity variant. [PharmGKB:Curated Reduced expression.]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
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[PharmGKB:In-Depth This variant is part of the *10 haplotype and affects nicotine metabolism.]
Magnitude: 0
Repute:Good
References:11
Repute:Good
References:11
common in complete genomics
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[PharmGKB:In-Depth Risk or phenotype-associated allele: TC. Phenotype: This variant is statistically correlated with the mean of maximum transaminase values (ALT) in patients from Mozambique, with ALT mean value of 91.68 U/l for TT, and 221.45 U/l for TC genotypes (p < 0.001). Study size: 156. Study population/ethnicity: HIV infected patients from Mozambique. Significance metric(s): p< 0.001. Type of association: GN; CO]
Magnitude: 0
Repute:Good
References:7
Repute:Good
References:7
normal
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rs28399504 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*4 variant. This variant has been linked to poor metabolism of compounds like mephenytoin. It is also known as M1V or Met1Val. The risk allele is rs28399504(G). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (Prevacid). According to a 23andMe discussion This is one of the SNPs which were re-analyzed April 2009. Customers with older data may wish to redownload. SNPs effected rs4420638, rs34276300, rs3091244, rs34601266, rs2033003, rs7900194, rs9332239, rs28371685, rs1229984, and rs28399504. Clopidogrel Efficacy [Pharm...
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
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rs3208361 is a SNP in the CYP3A4 gene. The rs3208361(G) allele defines the CYP3A4*_15635A>G(I193V) variant.
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
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Suspect: Variation suspected to be false positive due to artifacts of the presence of a paralogous sequence in the genome (Musumeci et al. 2010) (Sudmant et al. 2010) or evidence suggested sequencing error or computation artifacts. [PharmGKB:Curated The CYP2B6:1132C>T variant results in a truncated protein and high plasma levels of efavirenz in patients.]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
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[PharmGKB:Curated Risk or phenotype-associated allele: C. Phenotype: CYP2B6 mRNA expression and bupropion hydroxylase activity were approximately 2-fold higher in livers genotyped -82TC as in those genotyped -82TT. Study size: 85 (expression); 77 (activity). Study population/ethnicity: Non-tumorous liver samples from White individuals, Germany. Significance metric(s): p = 0.007 (expression); p = 0.042 (activity). Type of association: FA; PD]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in complete genomics
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[PharmGKB:Curated cell based studies; enhanced basal activity on cyp3a4 transcription wrt WT]
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
common in complete genomics
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[PharmGKB:Curated The CYP2B6*27 allele shows an 85% decrease in enzyme activity leading to high plasma levels of efavirenz in patients.]
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
normal
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rs41279854, also known as 29748T>C or F446S, is a SNP in the CYP3A5 gene. The rs41279854(G) allele defines the CYP3A5*10 variant, which is nonfunctional.
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
normal
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rs41279857, also known as 7298C>A or S100Y, is a SNP in the CYP3A5 gene. The rs41279857(T) allele defines the CYP3A5*S100Y variant, which is nonfunctional.
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
normal
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Defines the CYP2C19 variant known as CYP2C19*8. Carriers of the rs41291556(C) allele may have decreased activity and poor metabolizer (PM) phenotype. This variant is associated with a dramatic (approximately 90% and 70%) reduction in the metabolism of S-mephenytoin and tolbutamide in vitro. Clopidogrel Efficacy [PharmGKB:Curated This variant is the defining SNP for CYP2C19*8 and leads to decreased activity and poor metabolizer (PM) phenotype.This variant is associated with a dramatic (approximately 90% and 70%) reduction in the metabolism of S-mephenytoin and tolbutamide in vitro.]
common in complete genomics
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[PharmGKB:In-Depth Subjects with the G variant showed higher plasma pravastatin AUC and Cmax relative to A variant]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in complete genomics
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[PharmGKB:Curated Risk or phenotype-associated allele: T Phenotype: Kinetic studies using purified, histidine-tagged, recombinant enzymes demonstrated that the P131S mutation leads to decreased catalytic efficiency (Kcat/Km) for doxorubicin and daunorubicin compared to wild type protein. Type of association: FA]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
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[PharmGKB:Non-Curated Reduced estrone sulfate and cimetidine uptake in transfected cells]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
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[PharmGKB:Non-Curated Reduced thymidine uptake in oocytes]
normal
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rs4986893 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*3 variant. This variant has been linked to poor metabolism of compounds like mephenytoin as well as proguanil, and it therefore has implications for malaria prophylaxis. The risk allele is rs4986893(A). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (Prevacid). Clopidogrel Efficacy [PharmGKB:Curated In contrast to other PPIs, esomeprazole-induced healing of GERD appears to be unrelated to the CYP2C19*3 variant.] [OMIM:MEPHENYTOIN, POOR METABOLISM OF]
normal
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rs4986908 is a SNP in the CYP3A4 gene. The rs4986908(A) allele defines the CYP3A4*_14313G>A(E174H) variant. [PharmGKB:In-Depth Defining variant for CYP3A4*10.]
normal
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rs4986910, also known as 1334T>C, 23171T>C or M445T, is a SNP in the CYP3A4 gene. The rs4986910(C) allele defines the CYP3A4*3 variant. [PharmGKB:In-Depth Risk or phenotype-associated allele: CYP3A4*3 (rs4986910) 445Thr, 1334 C allele Phenotype: Two patients taking tacrolimus carried the CYP3A4*3 (445Thr) allele. The tacrolimus dose-adjusted C(0) in these 2 patients was higher than that in patients with the wild-type (455 Met/Met) genotype (n = 62), as follows: 134.9 (106.6-163.2) versus 83.83 (33.83-397.8) ng/mL per mg/kg, respectively. This difference was also observed at 12 months after transplantation, as follows: 147.3 (117.0-177.5) versus 88.79 (26.0-432.0) ng/mL per mg/kg. Study size: 64. Study population/ethnicity: Renal transplant recipients from the outpatient clinic of th...
normal
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rs5030862, also known as 124G>A or G42R, is a SNP in the CYP2D6 gene. The rs5030862(A) allele defines the CYP2D6*12 variant, which is inactive.
normal
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rs5030867, also known as 2935A>C or H324P, is a SNP in the CYP2D6 gene. The rs5030867(C) allele defines the CYP2D6*7 variant, which is inactive.
common in clinvar
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rs5030868, also known as c.653C>T, p.Ser218Phe and S218F, is a SNP located on the X-Chromosome and associated with moderate to severe Glucose-6-Phosphate Dehydrogenase (G6PD) deficiency. Often referred to as the “Mediterranean variant”, the 563C->T mutation encodes a non-synonymous Serine to Phenylalanine substitution at Amino Acid position 188 (S188F) resulting in reduced catalytic efficiency and stability G6PD . In red blood cells, G6PD acts as the primary electron source for reactions that neutralize reactive oxygen species; thus the red blood cells of G6PD deficient individuals are especially susceptible to damage from oxidative stress . The Mediterranean variant of G6PD has been associated with acute hemolytic anemia induced by the ingestion of fava beans, glibenclam...
common in complete genomics
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[PharmGKB:In-Depth This variant affects heat stability and affects nicotine metabolism; part of the CYP2A6*7 and CYP2A6*10 haplotypes.]
common in complete genomics
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Direct molecular haplotyping of multiple polymorphisms within exon 4 of the human catechol-O-methyltransferase gene by liquid chromatography-electrospray ionization time-of-flight mass spectrometry.
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Important Variant Information for CYP2J2. involved in metabolism of some drugs. rs890293, also known as -50C>T, is a SNP in the CYP2J2 gene. A study of 5,740 participants of the cardiovascular cohort of the 'Malmö Diet and Cancer' study was monitored for cardiovascular events over 10 years, with the conclusion being there was no significant association between this SNP and either hypertension or ischemic events. [PharmGKB:In-Depth Although this promoter SNP is the most-studied CYP2J2 variant, its in vivo effects remain unclear due to conflicting experimental findings.]
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[PharmGKB:Non-Curated Increased resistance to daunorubicin, doxorubicin, valinomycin, or actinomycin D in transformed yeast]
normal
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rs1573496 is a SNP in the ADH7 alcohol dehydrogenase 7 gene. A study of over 3,800 cases of 'upper aerodigestive' cancers (mouth/throat, voice box, and esophageal cancers) concluded that the rs1573496(G) allele has a protective effect. Carriers of this allele had a 0.68x (decreased; p=10<sup>-9</sup>) risk of having one of these cancer types. A Genome-Wide Association Study of Upper Aerodigestive Tract Cancers Conducted within the INHANCE Consortium. The data in this paper, makes it seem that (G;G) was much more common. This is inconsistent with the HapMap frequencies, suggesting the sequence may have been flipped. Diplotype trend regression analysis of the ADH gene cluster and the ALDH2 gene: multiple significant associations with alcohol dependence. Multiple ADH genes modulat...
common in complete genomics
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[PharmGKB:Curated Alleles positive for this variant are designated CYP2C8*4. In in vitro experiments, the paclitaxel 6 alpha-hydroxylase acivity associated with CYP2C8*4 appeared lower than the wildtpe but the difference was not significant.]
common on affy axiom data
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[PharmGKB:Curated Risk or phenotype-associated allele: A. Phenotype: This SNP was part of a haplotype associated with acute cardiotoxicity in response to doxorubicin. Study size: 1697. Study population/ethnicity: Participants of the German non-Hodgkin lymphoma study. Significance metric(s): OR = 2.3; 95% CI, 1.0 to 5.4. Type of association: PD; ADR; TOX.]
common in complete genomics
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[PharmGKB:Curated This variant is the defining SNP for CYP3A7*2 which has increased catalytic acitivity compared to wild type.]
normal
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Also known as CYP2E1_-1295G>C, this SNP is reported to mark the c2 allele of CYP2E1. The rs3813867(C) allele defines the CYP2E1_-1295G>C variant allele. [OMIM:CYTOCHROME P450, SUBFAMILY IIE; CYP2E1]
normal
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rs1057911 is a SNP in the CYP2C9 gene. The rs1057911(T) allele defines the CYP2C9_50298A>T variant, about which little is known. Warfarin
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[PharmGKB:Curated A study in 1,090 Caucasian prostate cancer cases found significant associations involved CYP3A43 P340A genotypes and history of benign prostatic hyperplasia (BPH). These results of the study suggest that androgen metabolism may act in concert with inflammatory phenotypes such as BPH in determining prostate cancer severity.]
common in clinvar
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minor form is a slow metaboliser according to pharmgkb [PharmGKB:In-Depth This variant results in enzyme inactivity and is considered to be part of the %22slow metabolizer%22 group; part of the CYP2A6*2 haplotype.] [OMIM:?] [GWAS:Smoking behavior]
common in complete genomics
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[PharmGKB:Curated The variant is part of the CYP2C8*2 allele. In an in vitro study, the CYP2C8*2 allele exhibited a two-fold lower clearance for paclitaxel than the wildtype.]
normal
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rs12721627, also known as 554C>G, 15603C>G or T185S, is a SNP in the CYP3A4 gene. The rs12721627(G) allele defines the CYP3A4*16 variant. [PharmGKB:Curated in vitro study; PK: variant shows substrate altered kinetics compared to wild type]
normal
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The rs17878459(C) SNP defines the CYP2C19 allele known as CYP2C19*2B, or as E92D.
normal for 23andMe appears common for 23andMe users
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rs1800462, also known as A80P, is a rare SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The risk allele for this SNP (in orientation to the dbSNP entry) is rs1800462(C), and it encodes the TPMT*2 allele. It may occur at a frequency of 1 in 200 alleles among Caucasians. wikipedia thiopurine drugs metabolized by TPMT include azathioprine, mercaptopurine, and thioguanine [PharmGKB:In-Depth The TPMT:238G>C SNP was cloned from a patient with severe mercaptopurine toxicity. It results in a non-synonymous protein change TPMT:Ala80Pro that has a 100-fold reduction in catalytic activity compared to w...
normal common for Caucasians on the 23andme platform
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rs28371686, also known as 1080C>G, 42619C>G or D360E, is a SNP in the CYP2C9 gene. The rs28371686(G) allele defines the CYP2C9*5 variant, which appears to have decreased activity. [PharmGKB:Curated Phenotype: In African Americans patients, weekly warfarin dose requirements were lower in those with the CYP2C9*8 allele (34 (30-47) mg; P = 0.023) and the CYP2C9 *2, *3, *5, *6, or *11 allele (33(28-40 mg); P < 0.001) as compared with those with the CYP2C9*1/*1 genotype (43 (35-56) mg). Adding the *5,*6,*8 and *11 alleles to a model containing the *2 and *3 alleles plus the VKORC1 -1639 G>A allele (along with clinical variables) explained 36% vs. 30% of the variability in dose requirements. Study size: 226 . Study population/ethnicity: African-American . Type of association: PD;GN;...
common in clinvar
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[OMIM:THYROXINE-BINDING GLOBULIN DEFICIENCY, PARTIAL, MONTREAL TYPE]
common in clinvar
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[OMIM:THYROXINE-BINDING GLOBULIN DEFICIENCY, PARTIAL, GARY TYPE]
common in complete genomics
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[PharmGKB:Curated This variant is the defining SNP for CYP8A1*1C haplotype.]
common in complete genomics
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rs6413413, also known as Thr60Ser, is a SNP in the alcohol dehydrogenase 1B ADH1B gene. The rs6413413(A) allele is the more common, encoding the amino acid threonine (Thr); the quite rare rs6413413(T) allele encodes the variant serine (Ser). On it's own, this SNP is said to explain 2.5% of the variability in the rate at which alcohol is metabolized, based on a study of 250 Spaniards. More significantly (in a statistical sense), this study concluded that combinations of this SNP and others were shown to affect alcohol metabolism; most of these combinations are represented by the gs211 genoset. Note that the effects of alcohol are higher in individuals who break down (basically, detoxify) ethanol more slowly.
316 snps
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Magnitude: 3
Frequency: 15.9%
Repute:Bad
References:13
Frequency: 15.9%
Repute:Bad
References:13
1.28x increased risk of Atrial Fibrillation and cardioembolic stroke. This is one copy of a mutant version (and one of the normal version) which slightly affects the formation of the heart and makes people slightly more likely to get Atrial Fibrillation (quivering of the top chambers of the heart caused by chaotic electrical signals) and slightly more likely to have a cardioembolic stroke (blocked blood flow to the brain). But also check the other SNP nearby (rs2200733) which affects Atrial Fibrillation even more. 23andMe gave this a 4 star confidence rating as it has been heavily studied. It has been confirmed in Europeans.
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Two SNPs from chromosome 4q25, rs2200733 and rs10033464, were found to be associated with atrial fibrillation in a study of both European and Asian populations. The odds ratio associated with one or more copies of either risk allele was ~1.4x. In 1,661 Icelandic ischemic stroke samples and two large European replication sets combined, rs10033464 was associated with cardioembolic stroke (CES) (odds ratio 1.27, p = 6.1 x 10e-4). rs2200733 and rs10033464 are strongly associated with AF in four cohorts of European descent. Variation in the 4q25 chromosomal locus predicts atrial fibrillation after coronary artery bypass graft surgery. Chromosome 4q25 variants and atrial fibrillation recurrence after catheter ablation. Common variants in KCNN3 are associated with lone atrial fibrillation. Associ...
1.2x risk Rheumatoid Arthritis
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rs6920220 has been reported in a large study to be associated with rheumatoid arthritis. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.20 (CI 1.06-1.36), and for homozygotes, 1.72 (CI 1.33-2.22). rheumatoid arthritis *rs6920220 [P= 2.6 x 10(-6), OR 1.22 (1.13-1.33)]. *rs5029937 *rs13207033 protective [P= 0.0001, OR 0.86 (0.8-0.93)] perfectly correlated with rs10499194 The combination of the carriage of both risk alleles of rs6920220 and rs5029937 together with the absence of the protective allele of rs13207033 was strongly associated with RA when compared to carriage of none [OR of 1.86 (95% CI) (1.51-2.29)]. This equates to an effect size of 1.50 (95% CI 1.21-1.85) Lack of association or interactions between the IL-4, IL-4Ralpha an...
Normal (A2/A2): Better avoidance of errors. Normal OCD risk, normal Tardive Diskinesia risk, lower ADHD risk. Less Alcohol dependence. Higher risk of Postoperative Nausea. Lower obesity. Bupropion is effective. This DRD2 TaqIA A2/A2 version causes a normal amount of Dopamine Receptors. Learns from mistakes more easily. Men may have a higher risk of Obsessive Compulsive Disorder but lower risk of ADHD. Women have higher Persistence. Higher risk of Tardive Diskinesia when taking dopamine receptor antagonists. Lower risk of alcoholism and smoking addiction. Faster recovery from traumatic brain injury. 1.6x risk of early postoperative nausea within 6 hours of surgery. Bupropion (Wellbutrin, Budeprion, Prexaton, Elontril, Aplenzin, Zyban, Voxra) works to quit smoking. Lower obesity due to incr...
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rs1800497, a SNP also known as the TaqIA (or Taq1A) polymorphism of the dopamine D2 receptor DRD2 gene (even though it is actually located over 10,000bp downstream of the gene), gives rise to the DRD2*A1 allele. This allele (rs1800497(T)) is associated with a reduced number of dopamine binding sites in the brain . Reduced response to errors and increased addictive behavior It has been postulated to play a role in alcoholism, smoking, and certain neuropsychiatric disorders. The reduced number of dopamine binding sites may play a role in nicotine addiction by causing an 'understimulated' state that can be relieved by smoking (and/or use of other drugs). A wide variety of reports have been published over more than ten years either linking rs1800497 to aspects of nicotine use and smoking cessa...
Magnitude: 2.5
Frequency: 9.7%
Repute:Bad
References:12
Frequency: 9.7%
Repute:Bad
References:12
Higher risk of childhood acute lymphoblastic leukemia Consistently, when we further classified children into age groups of those aged less than 5 years, those aged 5 to 10 years, and those aged greater than 10 years, there was a trend for decreasing allelic odds ratio (ie, relative risk of ALL conferred by each copy of the C allele at rs10821936) as age increased: 2.01 (95% CI = 1.85 to 2.19), 1.8 (95% CI = 1.6 to 2.02), and 1.48 (95% CI = 1.3 to 1.68), respectively.
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[PharmGKB:Curated Phenotype: This SNP is associated with risk of childhood acute lymphoblastic leukemia in blacks and also with racial differences in frequency of the disease . The frequency of the risk allele, C, was significantly higher(0.33) in black children with ALL enrolled in St. Jude clinical trials than in controls of African ancestry (0.163 ASW,0.20 YRI). Risk Allelle: C allele. Study size/population/ethnicity: patients-93 black children with newly diagnosed ALL; controls- 112 unrelated subjects of African ancestry from the HapMap project(52 from American Southwest and 60 from Yoruba) . Significance metric(s): OR = 2.08; 95% CI = 1.32-3.27; p = 0.0015 . Type of association: CO; GN. The association of the C allele (one or two copies) with risk for the ALL subtype B-hyperdiploid AL...
1.3x risk of rheumatoid arthritis; 1.55x risk of SLE; 1.42x risk of Sjögren's syndrome; increased risk of type-1 diabetes; and increased risk of primary biliary cirrhosis.
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rs7574865, a SNP in the third intron of the STAT4 gene, has been reported in a large study of Swedes to be associated with both rheumatoid arthritis (RA) and lupus (SLE). Among other studies, it has been confirmed in a meta-analysis of 8 studies totaling 7,381 patients and over 10,000 controls from both European and Asian populations. The risk allele (oriented to the dbSNP entry) is (T); the odds ratio associated the presence of a risk allele was 1.3 for rheumatoid arthritis and 1.55 for lupus (SLE). The paper states that, 'Homozygosity of the risk allele, as compared with absence of the allele, was associated with a more than doubled risk for lupus and a 60% increased risk for rheumatoid arthritis.' A study of 124 Caucasian patients with primary Sjögren's syndrome, an autoimmune dise...
Magnitude: 2.5
Frequency: 38.9%
Repute:Bad
References:118
Frequency: 38.9%
Repute:Bad
References:118
increased risk for type-2 diabetes
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rs13266634 is a SNP in the zinc transporter protein member 8 SLC30A8 gene that has primarily been associated with type-2 diabetes in several studies. This SNP is also known as the Arg325Trp or R325W variant; the (C) allele encodes the arginine (R), and the (T) allele encodes the tryptophan (W). significantly associated p = 0.0073; in 1,630 Japanese subjects with type-2 diabetes and in 1,064 controls The major alleles of the SLC30A8 SNP rs13266634 and the HHEX SNP rs7923837 associate with reduced insulin secretion, but not with insulin resistance. 46% of European non-diabetic offspring of type-2 diabetes patients are rs13266634(C;C) homozygotes; they are diabetes-prone and characterised by a 19% decrease in first-phase insulin release following an intravenous glucose load. * Note: this SNP,...
~1.3x increased obesity risk
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rs1421085 is a SNP located in the first intron of the FTO (fat mass and obesity associated) gene on chromosome 16. This SNP showed the most association with obesity in the original work by Dina et al . The rs1421085 T-to- C single-nucleotide alteration underlies the association between FTO and obesity by disrupting ARID5B-mediated repression of IRX3 and IRX5. This disruption leads to a developmental shift from browning to whitening programs and loss of mitochondrial thermogenesis Within the FTO gene, many SNPs appear to be co-inherited. The SNP showing the strongest association with body weight (i.e. body mass index, BMI) is not rs1421085, although this SNP is one of co-inherited SNPs in the FTO gene region. For more information, refer to the FTO gene or the most studied of FTO SNPs, rs993...
3x higher risk for age-related macular degeneration
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rs5888 is a SNP in the scavenger receptor class B, member 1 SCARB1 gene. In a case-control study of two Caucasian populations totaling 2,498 patients, rs5888(C;T) heterozygotes had an increased odds ratio of 2.9 (CI: 1.6-5.3, p<0.002) for age-related macular degeneration (ARMD) based on a pooled analysis. Subgroup analysis indicated that the odds ratio for exudative forms of ARMD was even higher (3.6; CI: 1.7-7.6, p>0.0015) for rs5888(C;T) heterozygotes.
2.5x risk for AMD; higher mortality among nonagenarians To minimize your risk of age related macular degeneration, consider a diet rich in vitamins C and E, lutein, zeaxanthin and the minerals zinc and copper, such as kale, spinach and broccoli. source
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rs1061170 is a SNP in the complement factor H CFH gene; it is also known as Tyr402His. The rs1061170(T) allele encodes the more common Tyr (Y), while the generally rarer rs1061170(C) encodes the His (H). This SNP has been associated primarily with age related macular degeneration, and to a lesser extent, with longevity. This research paper shows that CFH Y402H is the relevant mutation. A haplotype of rs1061170 rs3753394 rs800292 rs1329428 (TGTC) was found to confer a significantly increased likelihood of exudative AMD. rs1061170 (aka Y402H 1277 T>C) was not associated with exudative AMD. CFH variations appear to contribute to ARMD in Caucasians, but not in Japanese CFH variant rs1061170 Y402H is strongly associated with both dry and wet AMD rs1061170(C) alleles are significantly associa...
CYP3A5*3 homozygote; CYP3A5 non-expressor Impacts metabolism of tacrolimus, an immunosuppressive drug used in organ transplantation. This is the most common phenotype in caucasian and many other populations. Only in africans is expressing the gene common.
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rs776746, also known as 6986A>G, is a SNP encoding the (nonfunctional) CYP3A5*3 allele of the CYP3A5 gene. CYP3A5*3 has been studied especially in connection with the metabolism of tacrolimus, an immunosuppressive drug used in organ transplantation. The optimal therapeutic dose is in a relatively narrow window, so blood concentration monitoring is recommended. CYP3A5*3 carriers tend to build up higher levels of tacrolimus than CYP3A5*1 carriers, unless their tacrolimus intake is reduced. Risk of testicular germ cell cancer in relation to variation in maternal and offspring cytochrome p450 genes involved in catechol estrogen metabolism. Polymorphisms in the cytochrome P450 genes CYP1A2, CYP1B1, CYP3A4, CYP3A5, CYP11A1, CYP17A1, CYP19A1 and colorectal cancer risk. Prevalence of common dis...
higher cancer risk ? (ambiguous flip)
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(C;C) predisposes to papillary thyroid carcinoma. Among 42 patients with familial breast cancer and 82 patients with ovarian cancer, those with at least one rs2910164(C) SNP tended to have been diagnosed at an earlier age than those with only (G) alleles. For the breast cancer patients, the difference in median age was between 45 vs 56 (p = 0.029) and for ovarian cancer patients, 45 vs 50, (p = 0.014). (G;G) males were two-fold more susceptible to hepatocellular carcinoma (OR = 2.016, 95% CI = 1.056-3.848, P = 0.034) perhaps an ambiguous flip? [OMIM:MICRO RNA 146A; MIRN146A]
Magnitude: 2.5
Repute:Bad
References:2
Repute:Bad
References:2
CYP3A5*7 homozygote; nonexpressor for CYP3A5
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rs41303343, also known as 27131_27132insT, is a SNP in the CYP3A5 gene. The rs41303343(T) allele defines the CYP3A5*7 variant, which is nonfunctional.
1.3x risk for T2D; obesity risk one copy of the genotype which increases production of the appetite stimulating hormone ghrelin. This increases your risk for obesity and Type-2 diabetes by approximately 20%.
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rs9939609 is a SNP in the fat mass and obesity associated FTO gene, aka the 'Fat Gene' The original paper describing it is here . 2015 research suggests rs1421085] may be the causal snp. The researchers identified 10 different FTO] SNPs in the first intron of the gene that associated with both BMI and type-2 diabetes. Because they all correlated with each other, they chose to examine one of the SNPs (rs9939609) in detail. rs9939609 has also been reported in a large study to be associated with type-2 diabetes. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.34 (CI 1.17-1.52), and for homozygotes, 1.55 (CI 1.3-1.84). In a different study, this SNP was found in a linkage block in the FTO gene with rs1121980; see rs1121980 for the associa...
higher risk of of coronary heart disease coronary heart disease
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rs662, also known as Q192R, is a SNP in the PON1 gene. It codes for amino acid 192 of the paraoxonase (PON) protein. Variants of this SNP affect PON catalytic efficiency and are correlated with Heart disease and trait-anxiety scores. The normal form, rs662(A), encodes a glutamine (Q), while the variant, rs662(G)), encodes an arginine (R). . While some populations show an association between this SNP and Heart disease, not all do. Perhaps the most striking finding was reported in Japanese patients with non-insulin dependent diabetes mellitus (NIDDM). NIDDM patients with either one or two rs662(G) alleles had a 9 fold higher risk of coronary heart disease compared with rs662(A;A) NIDDM patients. table of odds for cardiovascular disease outcomes 274 ovarian epithelial carcinoma cases and 452 ...
3.9x increased risk of wet ARMD age related macular degeneration
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rs1136287, also known as Met72Thr, is a SNP in the PEDF gene. Analysis of 86 Taiwanese Chinese patients with wet age related macular degeneration (ARMD) found the (T) allele to be more frequent in patients than in controls (50% vs 31%; p =.0005). The rs1136287(T;T) genotype was also more prevalent in patients than in controls (odds ratio 3.9, p = .0015).
~1.5-3x increased risk for ischemic stroke
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rs2231137, also known as Val12Met, is a SNP in the ATP-binding cassette, sub-family G (WHITE), member 2 ABCG2 gene. The (G) allele encodes the Val. In a study of incident ischemic stroke during 14 years of follow-up in a population-based study of older adults known as the Cardiovascular Health Study (CHS), rs2231137 was associated with stroke in both white (hazard ratio, 1.46, CI: 1.05 - 2.03) and black (hazard ratio, 3.59, CI, 1.11 - 11.6) participants. The risk of ischemic stroke was higher in Val allele homozygotes than in Met allele carriers. The adjusted hazard ratio for Val allele homozygotes, compared with Met allele carriers, was 1.50 (90% CI, 1.06 to 2.12) in whites and 3.62 (90% CI, 1.11 to 11.9) in black participants (Table 4). [PharmGKB:Curated control size=7; M12 cases=6; PK=...
3.5x asthma risk in certain populations
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This SNP, in the GSTP1 gene influences asthma risk; the (A) allele encodes the Ile, while the (G) allele encodes the Val. This SNP is also known as GSTP1Val105, or GSTP1 Ile105Val. Despite evidence of antioxidant effects of vitamin E in vitro and in animal studies, large, randomized clinical trials have not substantiated a benefit of vitamin E in reducing inflammation in humans. In healthy control subjects, the effect of α-tocopherol supplementation on the production of inflammatory cytokines appears to be dependent on an individual's genotype. These genotype-specific differences may help explain some of the discordant results in studies that used vitamin E. Persons having the alleles AA or AG had an increase in interleukin-6 (IL-6) upon supplementing alpha-tocopherol (the most common...
0.43x decreased risk for esophageal cancer
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rs6505162 is a SNP located in the pre-miRNA region of mir423. The major allele is rs6505162(C). A study of 346 Caucasians with esophageal cancer found that compared with the homozygous wild-type genotype of rs6505162, individuals with the heterozygous and homozygous variant genotype had a significantly reduced esophageal cancer risk with odds ratios of 0.58 (CI: 0.41-0.82) and 0.43 (CI: 0.27-0.68), respectively. After stratifying by gender, smoking, and age, the authors discovered that the protective effect was significant only for individuals under 64 years of age, regardless of sex or whether they smoked. Other unfavorable genotypes (ie SNPs) were also identified that were not as significant as rs6505162, and the overall risk of esophageal cancer increased with increasing numbers of unfa...
2x increased risk for macular degeneration
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linked to blindness in age related macular degeneration rs3753394, rs800292, rs1061147, rs1061170, rs380390, and rs1329428 Significant associations were detected for AMD with rs3753394 rs800292 rs1329428 A haplotype of rs1061170 rs3753394 rs800292 rs1329428 (TGTC) was found to confer a significantly increased likelihood of exudative AMD CFH variations appear to contribute to ARMD in Caucasians, but not in Japanese [GWAS:None]
Carrier of one CYP1A2*1F allele; Slow Caffeine Metabolizer. One copy of the slow caffeine metaboliser SNP, and one copy of the fast version. This makes you more strongly affected by drinking coffee, as caffeine is broken down slower in the liver. Supposedly this increases the risk of heart attacks, although other studies show caffeine is generally good for the heart. It also makes caffeine more effective at preventing Breast Cancer, Alzheimer's Disease, and Parkinson's disease. Too much caffeine will shrink your breasts.
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rs762551, also known as -164A>C or -163C>A, is a SNP encoding the CYP1A2*1F allele of the CYP1A2 gene. For historic reasons, the rs762551(C) allele is considered the wild-type, even though it is the rarer allele in most populations. The rs762551(A) allele is the 'fast metabolizer' allele known as CYP1A2*1F; the (C) allele is by comparison a slower metabolizer of certain substrates (including caffeine). In terms of genotypes, only rs762551(A;A) individuals are considered fast metabolizers. Individuals who are rs762551(A;C) heterozygotes or rs762551(C;C) homozygotes are both considered slow metabolizers. The CYP1A2 gene encodes a member of the cytochrome p450 family of proteins, which metabolize nutrients and drugs. One well known substrate of CYP1A2 is caffeine; individuals who are ca...
Possible risks. Complex. MTHFR rs1801131 is involved in converting 5-methylfolate (5MTHF) to tetrahydrofolate (THF). Unlike MTHFR C677T, this mutation does not lead to elevated homocysteine levels.
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rs1801131 is a SNP in the MTHFR gene, representing an A>C mutation at mRNA position 1298, resulting in a glu429-to-ala (E429A) substitution (hence this SNP is also known as A1298C or E429A). A diplotype (according to the authors, but perhaps actually a genoset) of rs1801131 and rs1801133 has been linked to increased risk for several types of brain cancer. The highest risk of meningioma was associated with heterozygosity for both MTHFR SNPs (odds ratio 2.11, CI: 1.42-3.12, p=0.002). The corresponding odds ratio for glioma was 1.23 (CI: 0.91-1.66, p=0.02. In general, risks were increased with genotypes associated with reduced MTHFR activity. rs1801131 shows no consistent association with schizophrenia overall in 12 studies totaling 3,000+ patients [PharmGKB:Curated Risk or phenotype-asso...
0.71x decreased risk for dry age related macular degeneration
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rs3775291 is a SNP in the TLR3 gene associated with an amino acid change in the corresponding protein. In the orientation as shown in dbSNP, the more common rs3775291(G) allele encodes a leucine while the rarer rs3775291(A) allele encodes a phenylalanine. rs3775291 has been associated with one form of age related macular degeneration (ARMD), specifically, the form known as 'dry' ARMD, also known as geographic atrophy. A study of 3 case-control groups of Americans of European descent, comprising about 900 ARMD patients in total, indicated that having one rs3775291(A) allele reduces the odds of having dry ARMD about 30%, and being a rs3775291(A;A) homozygote cuts your odds by more than half. Specifically, the odds ratio of having dry ARMD with one minor allele is 0.712 (CI: 0.50-1.0), and fo...
1.2x risk of coronary artery disease
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rs599839 and rs4970834 explain about 1% of the variation in circulating LDL-cholesterol levels. 'When we look at this particular genetic variance, of all the cholesterol variation among the population, 1% of it can be attributed to this particular locus,' said Sandhu. 'This is equivalent to more established genes for LDL regulation, particularly APOE.' rs646776 also linked. Pharmacogenetic meta-analysis of genome-wide association studies of LDL cholesterol response to statins found each minor allele to increase statin effectiveness by 1.3% (rs646776, β=−0.013, s.e.=0.002, P=1.05 × 10−9 and rs12740374, β=−0.013, s.e.=0.002, P=1.05 × 10−9). 23andMe blog coronary artery disease and heart attack SNP Risk Version Effect *rs646776 T 1.19 *rs1746...
some risk linked to a number of metabolic conditions including obesity, coronary artery disease, insulin resistance and therefore diabetes, left ventricular hypertrophy, and hypertension. It has also been linked to how well a patient responds to Viagra (sildenafil).
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rs5443, a SNP in the G-protein beta3 subunit (GNB3) gene that is more commonly known as the C825T variant, has been linked to a number of metabolic conditions including obesity, coronary artery disease, insulin resistance and therefore diabetes, left ventricular hypertrophy, and hypertension. It has also been linked to how well a patient responds to Viagra (sildenafil). Several studies have been unable to replicate one or more of the associations in at least some populations between this SNP and these conditions. The more notable studies include: *rs5443(T) allele carriers are 2-3 fold more likely to be obese in Caucasian, Chinese, and African American populations. *rs5443(T) carriers are clearly at higher risk for hypertension, but this review indicates that whether they are also at incre...
cardiovascular differences This is found in high frequency male athletes from power sports such as jumpers, throwers, and sprinters. There may be negative health consequences with increased risk of cardiovascular disorders. and response Mexicans with this SNP, and also a T at rs1800783, have lower LDL cholesterol. People with this SNP, and also a T at rs1800783, may be less responsive to hypnosis. Notably, this SNP does not change the amino acid (it is in the promoter region and doesn't encode the protein's amino acid sequence). The population frequencies in HapMap are incorrect.
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The NOS3 gene encodes nitric oxide synthase 3, and is also known as eNOS; rs2070744 is a SNP in the promoter region that is associated with higher levels of the corresponding mRNA (and possibly protein). Associations for the risk allele (C) of this SNP include: * Rheumatoid Arthritis , and, * cardiovascular mortality in high-risk patients * Progression (but not occurence) of prostate cancer Men who carry the C allele responded more favorably to the antihypertensive effects of aerobic exercise Current HapMap data for this SNP appears wrong (ss42994451). The population diversity information is instead being estimated based on ss48295994 P1, and should be replaced what a new HapMap ss# is available. [PharmGKB:Curated Risk or phenotype-associated allele: C. Phenotype: Subjects carrying the eN...
long form of 5-HTTLPR. less sensitive to pain 23andMe reports that this genotype is not reliable on their platform. 23andMe users should ignore this result. happier, less sensitive to pain You consider perpetrating unintentional harm as more acceptable The genotype of this SNP is not meaningful on 23andme v3. *https://www.23andme.com/you/community/thread/6192/
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According to David Hinds of 23andMe on community forums, 'nearly everyone (99.97%) is getting called as CC, and there is no clear heterozygote cluster' ... 'the genotype calls for rs25531 on our platform are not meaningful.' Looking at OpenSNP frequency data, this seems to be universal for direct to consumer genotyping services at this stage. The minor allele (G) of rs25531 is almost always in phase with the long (L) allele of the 5-HTTLPR, which is the most commonly studied variation in this region. The (L) long allele may be associated with lower levels of serotonin. The article and video from 'The Atlantic' suggests that children with the short allele (A), may need and benefit greatly from more maternal support *http://www.theatlantic.com/doc/200912/dobbs-orchid-gene In contrast to earl...
significantly higher anxiety levels after moderate caffeine consumption
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Variation at this SNP, rs5751876, also referred to as 1976C>T or 1976T>C, appears to influence how an individual responds to moderate levels (150mg) of caffeine. T/T carriers displaying significantly increased subjective levels of anxiety after consumption. However a PharmGKB variant annotation suggests it is (C;C) genotypes who are more sensitive to caffeine. rs5751876 is not associated with how much coffee one drinks, though, nor with risk for Parkinson's disease, based on a study of 1,200 subjects. 'rs2298383 shows functional potential based on in silico analyses and might therefore represent the true underlying causal variant'
No reduction in heart disease risk from drinking alcohol This is the genotype known as B1B2, and as reported in the Mehlig et al. 2014 article, from a risk for coronary heart disease perspective this genotype is the same as the B1B1 genotype in showing no decrease in risk from consuming alcohol.
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rs708272, also known as the TaqIB polymorphism of the CETP gene, may influence the levels of the 'good' cholesterols, the high density lipoprotein (HDL) cholesterols. Generally, the B2 allele is considered to lead to higher HDL levels. However, high HDL cholesterol, at least when combined with another HDL raising SNP (rs1800588), doesn't appear to actually protect individuals from coronary artery disease, at least based on one study of ~800 Caucasian male patients. A similarly confusing picture emerges from a study of two populations of 10,000+ individuals each. The distribution of the CETP genotype was observed to be different in population-based studies compared with studies in populations selected by high cardiovascular risk, and contradictory results were seen when trying to figure out...
warfarin sensitivity (~2.5 mg/day)
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rs8050894, is located on chromosome 16 in the gene VKORC1. VKORC1 is the primary target of the drug warfarin (Coumadin), a commonly used oral anticoagulant. rs8050894 is one of several polymorphisms found in VKORC1 that is associated with specific warfarin doses (). Other polymorphisms in VKORC1 (rs7196161, rs9923231, rs9934438, rs2359612) are equally predictive of warfarin dose requirement in both European and Asian-descent individuals. Other polymorphisms found in the gene cytochrome P450 2C9 (CYP2C9) influence the metabolism of warfarin and have a smaller effect on warfarin dose. These polymorphisms are rs1799853 (CYP2C9*2) and rs1057910 (CYP2C9*3). In several hundred Europeans, no association was found between rs8050894 and risk for ischemic stroke. Genetic-based dosing in orthopedic p...
increased risk of coronary artery disease
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rs1800888, also known as Ile164, is a SNP in the beta 2 adrenergic receptor ADRB2 gene. The rs1800888(T) encodes the much rarer Ile allele. In a study of 330 patients undergoing percutaneous coronary intervention (PCI), patients carrying a rs1800888(T) allele showed a higher incidence of new acute myocardial infarction (17.5% vs. 4.5%, p = 0.001), new PCI (37.5% vs. 13.1%, p < 0.0001), and cardiac death (10% vs. 3.1%, p = 0.036). Regression analysis identified rs1800888(T) as an independent predictor of cardiac death (odds ratio 3.731, CI: 1.004 - 13.867, p = 0.049) and an overall major adverse cardiac event (odds ratio 4.1, CI: 1.945 - 8.640, p = 0.0001). A replication study was done on a population of 150 patients with peripheral artery disease. The presence of the rs1800888(T) allele...
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[OMIM:?] [GWAS:Rheumatoid arthritis]
if testicular cancer patient, 5x poorer response to bleomycin chemotherapy Testicular cancer patients may be treated with bleomycin, a cytotoxic drug that is essential component of chemotherapy regimens for this cancer, officially known as disseminated testicular germ-cell cancer (TC). rs1050565 is a SNP in the BLMH gene. This gene encodes a protein that can inactivate bleomycin. Based on a study of 300 TC patients treated with bleomycin, a testicular cancer patient with a rs1050565(G;G) genotype has an odds ratio of 4.97 (CI: 2.17 - 11.39) for TC-related death compared to (A;G) or (A;A) genotypes. The rs1050565(G;G) genotype also shows a higher prevalence of early relapses. Note that this gene affects bleomycin metabolism; the GG does not mean that a person is more likely to get testicula...
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Testicular cancer patients may be treated with bleomycin, a cytotoxic drug that is essential component of chemotherapy regimens for this cancer, officially known as disseminated testicular germ-cell cancer (TC). rs1050565 is a SNP in the BLMH gene. This gene encodes a protein that can inactivate bleomycin. Based on a study of 300 TC patients treated with bleomycin, a testicular cancer patient with a rs1050565(G;G) genotype has an odds ratio of 4.97 (CI: 2.17 - 11.39) for TC-related death compared to (A;G) or (A;A) genotypes. The rs1050565(G;G) genotype also shows a higher prevalence of early relapses. [PharmGKB:Curated Testicular germ cell cancer patients carrying the homozygous G/G allele of this variant showed reduced survival and higher prevalence of early relapses after treatment with...
Magnitude: 2
Frequency: 12.3%
Repute:Bad
References:22
Frequency: 12.3%
Repute:Bad
References:22
increased Coronary Heart disease risk
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rs10455872, was associated with about 1.5-fold increased risk of Coronary Heart Disease. celera Genetic variation in LPAL2, LPA, and PLG predicts plasma lipoprotein(a) level and carotid artery disease risk. Lipoprotein(a) genetic variants associated with coronary and peripheral vascular disease but not with stroke risk in the Heart Protection Study. Single-nucleotide polymorphisms in LPA explain most of the ancestry-specific variation in Lp(a) levels in African Americans. Variation in LPA is associated with Lp(a) levels in three populations from the Third National Health and Nutrition Examination Survey. Cost-effectiveness model of use of genetic testing as an aid in assessing the likely benefit of aspirin therapy for primary prevention of cardiovascular disease. [OMIM:?] [GWAS:None]
increased anxiety in response to caffeine associated with increased anxiety in response to caffeine
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Variation at this SNP, rs2298383, appears to influence how an individual responds to moderate levels (150mg) of caffeine. [PharmGKB:Curated Risk or phenotype-associated allele: rs2298383 T allele. Phenotype: Carriers of 1 or 2 copies of the T allele for rs2298383 showed increased risk of any (OR = 2.23, CI 1.03-5.07, p = 0.03) or gastrointestinal-specific (OR = 2.65, CI = 0.8-11.35, p = 0.09) adverse events. Study size: 309 RA patients, including 147 good MTX responders, 101 MTX inefficacy failures, and 61 adverse event (AE) MTX failures (e.g. gastrointestinal (n = 24), abnormal liver function tests (n = 20), haematological (n = 7), skin rashes (n = 6), and other (n = 17). Study population/ethnicity: Rheumatoid arthritis (RA) patients aged over 18 yrs, of White Caucasian ethnic origin, cl...
Higher risk of bleeding during coronary angiography
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rs3842787, also known as 50C>T, is a SNP in the signal peptide region of the cyclooxygenase-1 PTGS1 gene. A study of 696 European patients undergoing elective diagnostic coronary angiographies (CAGs) because of suspected or proven stable coronary artery disease found that 23 experienced bleeding, perhaps the most common complication of this type of invasive coronary procedure. After controlling for various variables (especially gender), two co-inherited SNPs, rs10306114 and rs3842787, were found to be associated with higher risk for bleeding in otherwise low risk patients who (i) did undergo percutaneous coronary intervention and (ii) did not take clopidogrel. Having the less common haplotype (rs10306114(G) and/or rs3842787(T)) increases the bleeding risk upon CAG ~12 fold (p = 0.012). ...
lower ITPA production; be aware if treated with ribavirin or mercaptopurine see discussion at rs1127354
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rs1127354 (Pro32Thr/P32T, 94C>A) is a SNP within the ITPA (Inosine triphosphate pyrophosphatase) gene. (note: rs1127354 supersedes rs41320251) abolishes ITPA activity in homozygous individuals and reduces the activity to 25% in heterozygous subjects, mercaptopurine metabolism (sig. higher methyl mercaptopurine nucleotides levels + higher probability of severe febrile neutropenia in A carriers treated with mercaptopurine) Mutations in the gene encoding the Wnt-signaling component R-spondin 4 (RSPO4) cause autosomal recessive anonychia. Pharmacogenomic studies of the anticancer and immunosuppressive thiopurines mercaptopurine and azathioprine. Investigation of candidate polymorphisms and disease activity in rheumatoid arthritis patients on methotrexate. Variants in the ITPA gene protect a...
influences dosage for Parkinson's patients Parkinson's disease patients needed higher dosages of levodopa and have worse outcomes
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[PharmGKB:Curated Risk or phenotype-associated allele: C/C. Phenotype: This variant modulates the effect of the SLC47A1 rs2289669 polymorphism on the glucose lowering effect of metformin. In users with the SLC22A1 rs622342 CC genotype there was a significant association with change in HbA1c levels and the genetic variation at the SLC47A1 rs2289669 (G to A) polymorphism (-0.68; 95% CI: -1.06 to -0.30; P=0.005). The multiplicative interaction between these two genotypes was statistically significant (-0.52; 95% CI: -0.94 to -0.11; P=0.015). Study size: 98. Study population/ethnicity: Caucasian. metric(s): P=0.005. Type of association: GN.]
MI risk, aspirin resistance 23andMe blog lower odds of early stent thrombosis
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The 'A2' allele of the platelet specific alloantigen system is encoded by rs5918(C), and it has been implicated as increasing the risk of myocardial infarctions, heart disease, and resistance to blood-thinning benefits of aspirin. On its own, the A2 allele is implicated especially in early onset heart disease ; in combination with the 4G allele of the PAI1 gene, rs1799889, the increased risk of myocardial infarction in a Finnish study population was 4 fold higher (odds ratio = 4.5, p=0.001), particularly in males (odds ratio = 6.4, p=0.0005) . Olympic skater Sergei Grinkov, who had this risk factor, died of a heart attack at age 28. A2 allele carriers also appear to be relatively resistant to the anti-thrombotic (i.e. anti-clotting) actions normally associated with aspirin] use. A protecti...
Magnitude: 2
Frequency: 29.2%
Repute:Bad
References:108
Frequency: 29.2%
Repute:Bad
References:108
1.2x increased risk for type-2 diabetes
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rs10811661 replicated as significant for type-2 diabetes risk in 1,900 Japanese patients, with odds ratio of 1.27 (CI: 1.15-1.40, p = 1.9 x 10e-6) rs10811661 is mentioned in part 2 of a series significantly associated with type-2 diabetes p = 0.0024; in 1,630 Japanese subjects with type-2 diabetes and in 1,064 controls 1,638 type 2 diabetes patients and 1,858 controls *rs10811661 in the vicinity of CDKN2B (OR 1.20, 95% CI: 1.06-1.37, p = 0.004) T2D and normal glucose tolerant (NGT) individuals. (3,295 T2D and 3,595 NGT), strong associations with T2D were found for *CDKAL1 (OR(rs7756992) = 1.30[1.19-1.42], P = 2.3x10(-9)) *CDKN2A/2B (OR(rs10811661) = 0.74[0.66-0.82], P = 3.5x10(-8)) *IGFBP2 (OR(rs1470579) = 1.17[1.07-1.27], P = 0.0003) SNPs. T2D risk increased strongly when risk alleles, in...
Slightly increased lifespan?
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This SNP, a variant in the TP53 gene, is 1 of 25 SNPs reported to represent independently minor, but cumulatively significant, increased risk for breast cancer. For details of all 25 SNPs in this group, along with the two methods used to calculate overall risk estimates for breast cancer, refer to the SNPedia breast cancer entry. For this particular SNP, the G allele encodes an arginine at position 72 of the protein (where there's normally a proline), and the SNP is commonly called the Arg72 variant, although P72R and Arg72Pro are also common in the literature. Minor allele homozygotes, i.e. rs1042522(C;C) genotypes, live on average 3 years longer than major allele (G;G) homozygotes, based on a study of 9,200+ Danish individuals. The increased longevity is speculated to be related to the i...
1.8x increased risk for high blood pressure
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rs4961 is a variation in the adducin 1 ADD1 gene, encoding a change from a glycine to a tryptophan, so it is also known as G460W or Gly460Trp. Originally, a study of 477 Italian patients indicated that carriers of one or two rs4961(T) alleles were at 1.8x increased risk for hypertension (CI: 1.32-2.43). This study also indicated that carriers of the risk (T) allele responded better to diuretics and sodium-restricted diets, in that they tended to lower their blood pressure by ~10 mmHg points compared to rs4961(G;G) homozygotes similarly treated. Subsequent studies have tended to confirm this association, and to extend it to risk for heart disease. They also have tended to confirm that risk allele carriers respond better to therapy. In a study of ~2200 Belgian patients, rs4961(T) carriers we...
Smokes normal (lower) number of cigarettes if a smoker. Less nicotine dependence. Also smokes each cigarette less deeply. Therefore there is a reduced risk of lung cancer and a reduced (0.8x) risk of Peripheral Artery Disease. This doesn't affect whether people start smoking though.
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rs1051730, also known as D398N, is a SNP in the nicotinic acetylcholine receptor alpha 3 subunit CHRNA3 gene. In two recent (2008) studies, together comprising over 6,000 lung cancer patients of European ancestry, the rs1051730(T) allele was very significantly associated with increased risk. Having one copy (i.e. being a rs1051730(C;T) genotype) increased risk for lung cancer about 1.3x, and having two copies (rs1051730(T;T) individuals) represented 1.8x increased risk. Up to 14% of lung cancer incidence may be attributable to this allele. An independent study published at the same time concluded that (T) allele carriers for SNP rs1051730 are not at higher risk of becoming smokers compared to (C) carriers. However, if they do smoke, (T) carriers are quite likely to smoke more cigarettes th...
better odds of living to 100
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This SNP may be related to longevity. One study found that Ashkenazi who lived to age 95 or older are more likely to have two copies of the C allele.
1.2x increased risk for type-2 diabetes
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rs4402960 replicated as significant for type-2 diabetes risk in 1,900 Japanese patients, with odds ratio of 1.23 (CI: 1.11-1.36, p = 8.1 x 10e-5) associated with type-2 diabetes significantly associated with type-2 diabetes p = 0.00009; in 1,630 Japanese subjects and in 1,064 controls 1,638 type-2 diabetes patients and 1,858 controls *rs4402960 borderline (OR 1.10, 95% CI: 0.99-1.22). Neither rs4402960 or rs1470579 were found to be associated with type-2 diabetes in a study of 3,000 French Caucasians. This SNP was confirmed to be associated with type-2 diabetes in a study of 500+ Japanese patients plus pooled meta-analysis with 6 previous association studies (also of Japanese). Note: rs4402960 is fairly tightly linked (r<sup>2</sup>=0.87) with another IGF2BP2 gene SNP also asso...
Normal (higher) risk of ADHD symptoms. This is one normal and one rare form of the CLOCK gene. In addition to possibly affecting evening preference, it has been linked to normal Attention Deficit Hyperactivity Disorder symptom scores.
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rs1801260, a SNP in the CLOCK gene known as 3111 T/C, has been reported to influence sleep and activity patterns in patients affected by bipolar depression. From this article's abstract: 'Compared to T/T homozygotes, carriers of the C allele had a similar degree of severity of depression, but showed higher activity levels in the evening, a delayed sleep onset (mean 79 min later), and a reduced amount of sleep during the night (mean 75 min less).' Allele frequencies of T3111C SNP of hClock were significantly different between schizophrenics and controls (chi(2) = 19.738, P < 0.05). Schizophrenics had a significantly higher frequency of the C allele compared with controls (OR = 2.613, 95% CI = 1.693-4.034). (Han Chinese population.) There was a strong, significant association (P < 0.00...
Magnitude: 2
Frequency: 40.7%
References:30
Frequency: 40.7%
References:30
Shorter QT interval
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rs10494366, a SNP in the NOS1AP gene encoding the nitric oxide synthase I adaptor protein, accounts for some of the variation seen in abnormal heart rhythms, in particular, the QT interval. Based on studies totaling ~4,000 individuals of Caucasian ancestry, homozygotes for one allele have shorter QT intervals, while homozygotes for the other allele have a longer QT interval. A follow-up study determined that one rs10494366(G) allele was associated with a 3.8-ms (CI: 3.0 - 4.6ms, p=7.8x10(-20)) increase in QT interval duration, and two (G) alleles had twice that increase. No increase in risk for sudden death due to a cardiac problem was associated with this SNP, though. rs10494366 minor homozygotes had a 9.3 msec longer QT interval compared to major homozygotes (p=5.7x10(-5)); rs10918594 mi...
Magnitude: 2
Frequency: 43.1%
References:13
Frequency: 43.1%
References:13
CYP2C19*17 ultra fast metabolizer; drug metabolism effects; also 0.77x decreased breast cancer risk
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rs12248560(T) defines the CYP2C19*17 allele, an ultra fast metabolizer phenotype of the CYP2C19 gene. CYP2C19*17 is likely to lead to less effective drug treatment by, for example, proton pump inhibitors (such as omeprazole) and antidepressants. On the other hand, cancer patients who are CYP2C19*17 carriers are more likely to benefit from tamoxifen treatment, presumably because they break it down more rapidly into the antiestrogenic metabolites endoxifen and 4-hydroxytamoxifen. A study of 1,000+ breast cancer patients showed a 0.77x decreased risk of breast cancer for carriers of a CYP2C19*17 allele (CI: 0.65-0.93, p = 0.005). Analysis of a subgroup of such carriers who were using hormone therapy for ten years or longer showed an even stronger effect (odds ratio 0.57, CI: 0.39-0.83, p = 0....
Faster aging. Increased risk for Dementia. Less good cholesterol. This reduces HDL ('good') cholesterol. HDL cholesterol removes cholesterol from artery walls and improves health. This SNP seems to be associated with higher blood pressure, less longevity, and more diseases of aging, in particular memory decline and dementia, and lower odds of living to 100, especially in Ashkenazi Jews. Attempting to raise HDL cholesterol may (or may not) be useful to mitigate the effects of this SNP.
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This SNP rs5882 in the CETP gene referred to as ILE405VAL and RSAI405V has been related to ageing and exceptional long life. A study in Ashkenazi Jews showed that individuals homozygotic for the G allele have significantly longer lifespans. New research also indicates that G homozygotes have an average of 70% less risk of dementia and Alzheimer's disease. The study also found that heterozygotes have a lower risk of dementia and Alzheimer's disease but more study is needed to determine the risk reduction for heterozygotes. See Association of a Functional Polymorphism in the Cholesteryl Ester Transfer Protein (CETP) Gene With Memory Decline and Incidence of Dementia and CETP Variant Linked to Slower Cognitive Decline and Reduced Dementia Risk . [PharmGKB:Curated Risk or phenotype-associated...
increased risk for celiac disease
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rs3184504 is a nonsynonymous SNP in the SH2B3 gene, and it is also known as R262W. In a recent (2008) study of non-HLA SNP associations of 1600+ celiac disease patients, this SNP was considered one of the most significant. The odds ratio for the minor allele was 1.19 (CI:1.10-1.30, p=1.33x10e-7). rs653178, another SNP in strong linkage disequilibrium (r<sup>2</sup>>0.99) with rs3184504, was also associated with celiac disease. associated with type-1 diabetes 23andMe blog coronary artery disease and heart attack SNP Risk Version Effect *rs646776 T 1.19 *rs17465637 C 1.14 *rs1746048 C 1.17 *rs6725887 C 1.17 *rs11206510 T 1.15 *rs3184504 T 1.13 *rs2306374 C 1.15 *rs3782886 C 1.44 23andMe blog blood pressure Pharmacogenetic implications for eight common blood pressure-associated...
higher risk for endometrial cancer
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rs4633 is a variant at codon 62 of the COMT gene, however, it does not change the amino acid sequence of the COMT protein. In a study of 150 (Caucasian) cases of endometrial cancer, a significant increase in rs4633(T;T) genotype was observed in patients compared to controls (OR = 2.39, CI: 1.31-4.37, p = 0.004). Furthemore, the frequency of the C-G haplotype of rs4633-rs4680 was significantly higher in controls (p < 0.0001) than in patients. This correlated with lower expression levels of the COMT protein in carriers of these alleles. pubmed 1180576 Schizophrenia Susceptibility Genetic basis for individual variations in pain perception and the development of a chronic pain condition [PharmGKB:Curated On the basis of subjects' pain responsiveness, haplotypes involving rs6269 (A/G), rs46...
Magnitude: 2
Frequency: 46.0%
Repute:Bad
References:90
Frequency: 46.0%
Repute:Bad
References:90
adults likely to be 0.22 BMI units higher
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A study of 60,000 adults indicates that rs17782313(C) alleles are associated with higher body mass index (BMI), with even greater effect in children. The average increase in BMI is 0.22 BMI units (p = 2.8 x 10<sup>-15</sup>). Note that rs10871777 is considered an equivalent SNP in Caucasian and Asian populations. The rs17782313(C) allele is equivalent to the rs10871777(G) allele. The rs17782313](C) allele is significantly associated with higher intakes of total energy and dietary fat. In addition, the SNP was related to greater long-term weight change and increased risk of diabetes in women. rs17782313(C) more snacking, however rs1421085(C) did not influence eating behavior obesity and type-2 diabetes *rs1121980 *rs7498665 *rs4752856 *rs17782313 *rs2815752 *rs10938397 [PharmGK...
~0.80x reduced cancer risk
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rs763110, also known as -844C>T, is a SNP in the FAS ligand FASLG gene. A meta-analysis of 19 published studies, including 11,105 cancer cases and 11,372 controls, concluded that the rs763110(C;T) and (T;T) genotypes were associated with a significantly reduced (about 0.80x) cancer risk of all cancer types.
Women have lower risk of Endometriosis but normal risk for Endometrial Cancer, and more cognitive impairment with age. Men have zero risk, but can pass this on to their daughters. This is the normal version of Estrogen Receptor 1 (alpha). It has more cognitive decline than the rare version, with old women only remembering half as much details on the East Boston Memory Test immediate recall test.
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rs9340799 is a SNP in the estrogen alpha receptor ESR1 gene, and it is also known as the -351A>G variant. Among women, rs8179176, rs9340799, rs1256065, and rs1256030 were associated with likelihood of developing cognitive impairment with ageing. In men, rs728524, rs1255998, and rs1256030 were associated with cognitive impairment. A study of 6,200+ Dutch individuals did not replicate previously reported associations between this SNP (rs9340799) and risk of ischemic stroke. A study of 702 cases with invasive endometrial cancer concluded that the less common alleles of SNP rs9340799 lowered risk for the disease. The odds ratio was 0.75 (CI: 0.60-0.93) for (A;G) and 0.53 (CI: 0.37-0.77) for (G;G) compared to rs9340799(A;A) individuals. Endometriosis Uterine Fibroids [PharmGKB:Curated SNP i...
2x higher risk for skin cancer; possibly other cancers
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rs25487 is a SNP also known as Gln399Arg, located in the DNA repair gene XRCC1. The (A) allele encodes the Gln amino acid. In one study of ~1000 Caucasians, the rs25487(A;A) genotype had significantly reduced risk of both basal cell [BCC; odds ratio 0.7, CI: 0.4-1.0] and squamous cell cancer (SCC; odds ratio 0.6, CI: 0.3-0.9). In a study of ~300 Koreans, rs25487(A;G) and (G;G) genotypes had an approximately 2-fold increased risk of basal cell cancer compared to rs25487(A;A) individuals (adjusted odds ratio 2.324, CI: 1.11-4.86, respectively). A small study (113 cases) of Hispanics with non-small cell lung cancer found an odds ratio of 1.52 per rs25487(A) allele (CI: 1.01-2.28). A study of 200 patients with Hodgkin disease compared to controls concluded that some risk was associated with th...
1.6x increased prostate cancer risk
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This SNP is upstream of the IL10 gene, and is also known as the -1082G>A IL10 SNP. Dust mite exposure modifies the effect of functional IL10 polymorphisms on allergy and asthma exacerbations. Dust mite exposure significantly modified the relation between 3 SNPs in IL10 (rs1800896, rs3024492, and rs3024496). Homozygosity for the minor allele of each of the 3 SNPs was associated with increased risk of occurrence ( approximately 3-fold to 39-fold increase). A study of 258 prostate cancer cases concluded that the rs1800896(A) allele, known to result in lower levels of this anti-inflammatory cytokine, was positively associated with risk (AG vs. GG, odds ratio of 1.69, CI: 1.10-2.60; AA vs. GG, OR of 1.81, CI: 1.11-2.96).
Normal risk of sexual dysfunction when taking SSRI Antidepressants.
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rs6311 (-1438A>G / A-1438G or -1438G>A / G-1438A) is a SNP located upstream (and within the promoter region of) HTR2A. Multiple Regulatory Variants Modulate Expression of 5-Hydroxytryptamine 2A Receptors in Human Cortex. The minor A allele of rs6311 reduces expression of a previously unannotated extension of the 5' untranslated region of HTR2A mRNA. rs6311 together with rs6314 have a modest effect on depression severity, when examined in the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) study. Three (rs643627-rs594242-rs6311: A-C-T), two (rs594242-rs6311: C-T) and a single functional (rs6311: T) marker were protective against suicidal behavior. The complementary markers (rs594242-rs6311: G-C and rs6311: C) were associated with increased risk for non-violent and impu...
Normal (lower) risk of Type 2 Diabetes and Gestational Diabetes. Normal insulin secretion in the pancreas. This has been confirmed in most races.
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This SNP in TCF7L2 influences the risk of Type-2 diabetes (T2D). This SNP is also known as IVS3C>T. rs7903146(C;T) rs7903146(T;T) strongly predicted future type-2 diabetes. Considered in context with rs7903146 rs12255372 rs10885406. Note: this is one of two SNPs within the TCF7L2 gene that have been reported to be associated with type-2 diabetes, the other being rs4506565. They have approximately equal power to estimate risk for type-2 diabetes, and the results from one correlate 92% of the time with the other. Full text of the paper is available from from Plos Medicine. Or from NCBI as . TCF7L2 polymorphisms and progression to diabetes in the Diabetes Prevention Program. reconfirmed in a diverse population Associated in a study of ~1000 Hispanic-Americans with reduced insulin secretion...
somewhat less likely to respond to certain antidepressants
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rs2235015 is a SNP in the ABCB1 gene (also known as the MDR1 gene), which encodes a protein that transports certain molecules across the blood-brain barrier. SNPs in ABCB1 may thus influence the intracerebral concentrations of certain drugs and thus their efficacy or potential for adverse side effects. rs2032583 is near 9 SNPs found within a tight linkage block (r<sup>2</sup> >= 0.8 ) such that the minor allele at any one of them predicts (with ~80%+ accuracy) that the other SNPs will also be the minor allele. The list of the 9 SNPs is shown below. rs2235015 has an r<sup>2</sup> value of >0.5 with this group. When treated for depression with substrates of the protein encoded by ABCB1, carriers of one or two minor alleles at these ABCB1 SNPs have been reported ...
Slower metaboliser for some drugs
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rs1045642, also known as C3435T, is a SNP located in the ABCB1 gene. It is often studied in conjunction with rs2032582. C3435T has been mentioned by: * A 'Silent' Polymorphism in the MDR1 Gene Changes Substrate Specificity (for example, to verapamil) * (R)-lansoprazole (Prevacid) concentrations are significantly increased in CYP2C19 extensive metabolizers with ABCB1 C3435T C allele. * In a Korean population, plasma concentrations of fexofenadine (Allegra) were 17% lower in 2677AA/3435CC subjects and 47% higher in the 2677TT/3435TT subjects compared to 2677GG/3435CC subjects. * In contrast, in this study no association was observed between the C3435T polymorphism and fexofenadine plasma or urine concentrations in a German Caucasian population. * A meta-analysis including 9 case-control stud...
Better response to amphetamine Individuals with the C/C genotype at rs460000 (N = 83) reported approximately twofold higher ratings of stimulation and euphoria relative to the A/A+A/C (N = 69) genotype group, at both the 10 and 20 mg doses.
2.1x increased risk of Crohn's disease
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rs1050152, a SNP in the SLC22A4 gene known as L503F, has been associated with an autoimmune disease, in this case, Crohn's disease, odds ratio = 2.1 (CI = 1.31–3.39, p = 0.002), based on a study of 203 cases and 200 controls. The risk allele is rs1050152(T). A nearby SNP (rs2631367) in the promoter region of the SLC22A5 gene defines a haplotype along with rs3792876, with odds ratio reported as similar for either SNP or the haplotype. Referring to the TC risk haplotype, the population risk attributable to heterozygotes was 19%, and for homozygous haplotype carriers, 27%. [PharmGKB:Non-Curated Higher gabapentin exposure and lower renal clearance/tubular secretion in individuals carrying this variant] [OMIM:?]
1.5x increased risk for multiple sclerosis
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The (C) allele of rs6897932, located in the alternatively spliced exon 6 of IL7RA gene and encoding the amino acid threonine rather than isoleucine at amino acid position 244, is associated with a slight increase (18%) in risk of developing multiple sclerosis. [PMID 17660817; Nature Genetics 39, 1083 - 1091 (2007) SG Gregory et al.] Note that the (C) allele is the most common at this position in all known populations and influences the ratios of the alternative isoforms (membrane bound and soluble) of the gene. blog post giving perspective on the significance of this snp a significant risk factor for multiple sclerosis in four independent (overall P = 2.9 x 10(-7)) influences the amount of soluble and membrane-bound isoforms of the protein by putatively disrupting an exonic splicing silenc...
lower warfarin dosing
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rs2108622 is a SNP in the cytochrome P450, family 4, subfamily F, polypeptide 2 CYP4F2 gene. In the males rs2108622(G) was significantly higher in cerebral infarction patients (P = 0.025) A study of Italian patients concluded that rs2108622(T;T) patients require 5.49 mg/day of warfarin versus 2.93 mg/day for (C;C) patients. Analysis of variance indicates that about 7% of mean weekly warfarin dose variance is explained by CYP4F2 genotype. A study of 370 Brazilian ('admixed') patients concludes that prospective CYP4F2 genotyping is of little value to these patients, presumably due to ethnic-based differences. [PharmGKB:Curated Risk or phenotype-associated allele: no allelic association. Phenotype: Improved pharmacogenetic algorithm-based warfarin dosing. Study size: 370. Study population/et...
5% higher risk of Age related macular degeneration
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rs800292 is a SNP in the complement factor H CFH gene; it has been linked to blindness in age related macular degeneration. This SNP is also known as 184G>A, I62V, or Val62Ile. A haplotype of rs1061170 rs3753394 rs800292 rs1329428 (TGTC) was found to confer a significantly increased likelihood of exudative AMD CFH variations appear to contribute to ARMD in Caucasians, but not in Japanese A study of Chinese AMD patients reports that carriers of both rs11200638 and rs800292 risk alleles pushes the odds ratio for AMD up to 23x. Overall, an 'extremely high' population attributable risk (PAR) of 78% reported for these SNPs. rs800292 was associated with polypoidal choroidal vasculopathy (PCV) in a study of 130 Japanese patients. age related macular degeneration Susceptibility genes for age-re...
Magnitude: 2
Frequency: 67.3%
Repute:Bad
References:3
Frequency: 67.3%
Repute:Bad
References:3
7x less likely to respond to certain antidepressants
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rs10248420 is a SNP in the ABCB1 gene (also known as the MDR1 gene), which encodes a protein that transports certain molecules across the blood-brain barrier. SNPs in ABCB1 may thus influence the intracerebral concentrations of certain drugs and thus their efficacy or potential for adverse side effects. rs10248420 is one of 9 SNPs found within a tight linkage block (r<sup>2</sup> >= 0.8 ) such that the minor allele at any one of them predicts (with ~80%+ accuracy) that the other SNPs will also be the minor allele. The list of the 9 SNPs is shown below. When treated for depression with substrates of the protein encoded by ABCB1, carriers of one or two minor alleles at these ABCB1 SNPs have been reported to respond better than non-carriers. The antidepressant drugs that are kn...
2x risk of severe alcohol withdrawal. Possible increased odds of ADHD. Alcoholics with this are twice as likely to have seizures during alcohol withdrawal.
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rs27072, a SNP in the dopamine transporter SLC6A3 gene, has been associated with more severe symptoms upon alcohol withdrawal, such as seizures, in a study of 250 Caucasian alcohol-dependent patients. Two haplotypes appear to be tagged by this SNP and a neighbor, rs27048. The rs27072 polymorphism has been shown to be significantly associated with ADHD in clinical samples of Canadian children aged 6 to 16 [Feng et al., 2005] and the significant association was also reported by Ouellet-Morin et al. in a Canadian twin study, 2008 (Am. J. of Medical Genetics Part B, 147B:1442-1449 (2008). The interaction between the dopamine transporter gene and age at onset in relation to tobacco and alcohol use among 19-year-olds. Association of promoter variants of human dopamine transporter gene with schiz...
Magnitude: 2
Frequency: 71.7%
Repute:Bad
References:1
Frequency: 71.7%
Repute:Bad
References:1
7x less likely to respond to certain antidepressants
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rs11983225 is a SNP in the ABCB1 gene (also known as the MDR1 gene), which encodes a protein that transports certain molecules across the blood-brain barrier. SNPs in ABCB1 may thus influence the intracerebral concentrations of certain drugs and thus their efficacy or potential for adverse side effects. rs11983225 is one of 9 SNPs found within a tight linkage block (r<sup>2</sup> >= 0.8 ) such that the minor allele at any one of them predicts (with ~80%+ accuracy) that the other SNPs will also be the minor allele. The list of the 9 SNPs is shown below. When treated for depression with substrates of the protein encoded by ABCB1, carriers of one or two minor alleles at these ABCB1 SNPs have been reported to respond better than non-carriers. The antidepressant drugs that are kn...
7x less likely to respond to certain antidepressants. This version of a blood brain barrier protein blocks many common antidepressants from entering the brain, including: amitriptyline (Elavil), citalopram (Celexa), paroxetine (Paxil), and venlafaxine (Effexor). That makes those antidepressants 7 times less effective.
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rs2032583 is a SNP in the ABCB1 gene (also known as the MDR1 gene), which encodes a protein that transports certain molecules across the blood-brain barrier. SNPs in ABCB1 may thus influence the intracerebral concentrations of certain drugs and thus their efficacy or potential for adverse side effects. rs2032583 is one of 9 SNPs found within a tight linkage block (r<sup>2</sup> >= 0.8 ) such that the minor allele at any one of them predicts (with ~80%+ accuracy) that the other SNPs will also be the minor allele. The list of the 9 SNPs is shown below. When treated for depression with substrates of the protein encoded by ABCB1, carriers of one or two minor alleles at these ABCB1 SNPs have been reported to respond better than non-carriers. The antidepressant drugs that are know...
7x less likely to respond to certain antidepressants
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rs2235040 is a SNP in the ABCB1 gene (also known as the MDR1 gene), which encodes a protein that transports certain molecules across the blood-brain barrier. SNPs in ABCB1 may thus influence the intracerebral concentrations of certain drugs and thus their efficacy or potential for adverse side effects. rs2235040 is one of 9 SNPs found within a tight linkage block (r<sup>2</sup> >= 0.8 ) such that the minor allele at any one of them predicts (with ~80%+ accuracy) that the other SNPs will also be the minor allele. The list of the 9 SNPs is shown below. When treated for depression with substrates of the protein encoded by ABCB1, carriers of one or two minor alleles at these ABCB1 SNPs have been reported to respond better than non-carriers. The antidepressant drugs that are know...
7x less likely to respond to certain antidepressants
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rs2235067 is a SNP in the ABCB1 gene (also known as the MDR1 gene), which encodes a protein that transports certain molecules across the blood-brain barrier. SNPs in ABCB1 may thus influence the intracerebral concentrations of certain drugs and thus their efficacy or potential for adverse side effects. rs2235067 is one of 9 SNPs found within a tight linkage block (r<sup>2</sup> >= 0.8 ) such that the minor allele at any one of them predicts (with ~80%+ accuracy) that the other SNPs will also be the minor allele. The list of the 9 SNPs is shown below. When treated for depression with substrates of the protein encoded by ABCB1, carriers of one or two minor alleles at these ABCB1 SNPs have been reported to respond better than non-carriers. The antidepressant drugs that are know...
7x less likely to respond to certain antidepressants
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rs4148739 is a SNP in the ABCB1 gene (also known as the MDR1 gene), which encodes a protein that transports certain molecules across the blood-brain barrier. SNPs in ABCB1 may thus influence the intracerebral concentrations of certain drugs and thus their efficacy or potential for adverse side effects. rs4148739 is one of 9 SNPs found within a tight linkage block (r<sup>2</sup> >= 0.8 ) such that the minor allele at any one of them predicts (with ~80%+ accuracy) that the other SNPs will also be the minor allele. The list of the 9 SNPs is shown below. When treated for depression with substrates of the protein encoded by ABCB1, carriers of one or two minor alleles at these ABCB1 SNPs have been reported to respond better than non-carriers. The antidepressant drugs that are know...
Magnitude: 2
Frequency: 72.3%
Repute:Good
References:7
Frequency: 72.3%
Repute:Good
References:7
24% chance (lower than average) of docetaxel-induced leukopenia/neutropenia
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rs12762549 and rs11045585 can be used to predict whether docetaxel will induce leukopenia/neutropenia, according to a study of ~100 Japanese patients. When patients were classified into three groups by the scoring system based on the genotypes of these two SNPs, patients with a score of 1 or 2 were shown to have a significantly higher risk of docetaxel-induced leukopenia/neutropenia as compared to those with a score of 0 (P = 0.0000057; odds ratio [OR], 7.00; 95% CI [confidence interval], 2.95-16.59). This prediction system correctly classified 69.2% of severe leukopenia/neutropenia and 75.7% of non-leukopenia/neutropenia into the respective categories. [Effect percentages provided in table are raw population fractions taken from the referenced study based on rs11045585 only. Total populat...
Magnitude: 2
Frequency: 89.1%
Repute:Good
References:1
Frequency: 89.1%
Repute:Good
References:1
common/normal; aspirin use reduces colorectal cancer risk a bit see discussion at rs16973225
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rs16973225 is a SNP on chromosome 15q25.2 near the IL16 gene. In a long-term study of ~17,000 individuals and aspirin or NSAID use, the few (9%) with either an (A;C) or (C;C) genotype showed no risk reduction for colorectal cancer compared with (A;A) individuals among those taking anti-inflammatory drugs, who did benefit (prevalence, 28% vs 38%; (A;A) odds ratio 0.66 when taking aspirin/NSAID, CI: 0.62-0.71, p = 1.9 × 10e−30). If this data is robust and all other factors are equal, this indicates that most people will lower their colorectal cancer risk by taking aspirin or NSAIDs, since most people have rs16973225(A;A) genotypes. However, the few people who are rs16973225(A;C) or are rs16973225(C;C) will not change their risk one way or the other by taking aspirin. This same study reached ...
Alcohol Flush: Normal, doesn't flush. Normal hangovers. Normal risk of Alcoholism. Normal risk of Esophageal Cancer. Disulfiram is effective for alcoholism. Two working copies of Aldehyde Dehydrogenase (ALDH2) mean you won't turn bright red when you drink alcohol, unlike most Asians. After your body turns alcohol into the dangerous acetaldehyde, this gene quickly turns the acetaldehyde into vinegar. It also stops the acetaldehyde in cigarettes from causing Esophageal Cancer. It reduces hangovers compared to Asians, but less hangovers and flushing obviously increases the risk of alcoholism. Alcoholism can be treated effectively with the drug Disulfiram (Antabuse) which would stop this gene from working and cause the Asian flush in non-Asians. PMC2659709 [http://www.ncbi.nlm.nih.gov/pmc/art...
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rs671 is a classic SNP, well known in a sense through the phenomena known as the 'alcohol flush', also known as the 'Asian Flush' or 'Asian blush', in which certain individuals, often of Asian descent, have their face, neck and sometimes shoulders turn red after drinking alcohol. The rs671(A) allele of the ALDH2 gene is the culprit, in that it encodes a form of the aldehyde dehydrogenase 2 protein that is defective at metabolizing alcohol. This allele is known as the ALDH*2 form, and individuals possessing either one or two copies of it show alcohol-related sensitivity responses including facial flushing, and severe hangovers (and hence they are usually not regular drinkers). Perhaps not surprisingly they appear to suffer less from alcoholism and alcohol-related liver disease. Disulfiram (...
Magnitude: 2
Repute:Bad
References:5
Repute:Bad
References:5
Higher risk of bleeding during coronary angiography
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rs10306114, also known as -842A>G, is a SNP upstream of the cyclooxygenase-1 PTGS1 gene. A study of 696 European patients undergoing elective diagnostic coronary angiographies (CAGs) because of suspected or proven stable coronary artery disease found that 23 experienced bleeding, perhaps the most common complication of this type of invasive coronary procedure. After controlling for various variables (especially gender), two co-inherited SNPs, rs10306114 and rs3842787, were found to be associated with higher risk for bleeding in otherwise low risk patients who (i) did undergo percutaneous coronary intervention and (ii) did not take clopidogrel. Having the less common haplotype (rs10306114(G) and/or rs3842787(T)) increases the bleeding risk upon CAG ~12 fold (p = 0.012).
Magnitude: 2
Repute:Good
References:179
Repute:Good
References:179
~80% of such hepatitis C patients respond to treatment
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rs12979860 is a SNP near the IL28B gene, encoding interferon-lambda-3 (IFN-lambda-3). Several studies now indicate that this SNP predicts hepatitis C treatment-induced viral clearance. It is associated with an approximately twofold change in response to pegylated interferon-alpha (PEG-IFN-alpha) plus ribavirin (RBV) treatment, both among patients of European ancestry (p = 1.06 x 10e-25) and African-Americans (p = 2.06 x 10e-3). These studies indicate that the virus was eradicated in ~80% of (C;C) patients, compared to only about 25% of those with (T;T), while (C;T) response was intermediate. FDA PGx mentions about rs12979860 with respect to Boceprevir, Simeprevir, Sofosbuvir, and Telaprevir 23andMe blog rs8099917(C) less likely to respond to Hepatitis C treatment. A functional SNP rs368234...
Carrier of one CYP2D6 decreased or non-functioning variant. Your body may have a reduced ability to process some medicines. You are a carrier for rs1065852(T;T)
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The wild type (normal) allele at this SNP is (C). The (T) variant indicates the presence of a non-wild type CYP2D6 variant, but it appears in many different variants so it can not be used to determine the presence of any particular variant. The most common variants it appears in are CYP2D6*10 and CYP2D6*4, but these are not the only ones. While this is the defining mutation for CYP2D6*10, it is not possible by itself for this mutation to determine a particular variant. In addition, the CYP2D6*4 variant includes this mutation, but the defining mutation 1846G>A SNP is not available in the common direct to consumer testing services. While it is not possible for this mutation to identify one particular variant, all the variants in which it appears have reduced or no CYP2D6 activity. If two ...
1.9x increased risk for type-2 diabetes
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rs4506565 has been reported in a large study to be associated with type-2 diabetes. The risk allele (oriented to the dbSNP entry) is (T); the odds ratio associated with heterozygotes is 1.36 (CI 1.2-1.54), and for homozygotes, 1.88 (CI 1.56-2.27). Note: this is one of two SNPs within the TCF7L2 gene that have been reported to be associated with type-2 diabetes, the other being rs7903146. They have approximately equal power to estimate risk for type-2 diabetes, and the results from one correlate 92% of the time with the other. [PharmGKB:Curated Phenotype: In a meta-analysis of 21 GWAS cohorts, this SNP was found to be associated with fasting glucose level. Study size: 46,181. Significance metric(s): p = 1.2 x 10(-8). Study population/ethnicity: Non-diabetic Individuals of European descent....
1.4x increased risk for lupus
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rs1734791 is one of several SNPs in the methyl CpG binding protein 2 (MECP2) that have been associated with risk for systemic lupus erythromatosis (SLE). The MECP2 gene is located on the X chromosome, which may be instructive since lupus is a predominantly female disease. An initial survey of 600 Korean patients, followed by 1,000 Caucasian patients, ultimately led to a meta-analysis indicating an odds ratio for the rs1734791(A) risk allele of 1.39 (CI: 1.24–1.57, p = 7.2×10-08). Variants within MECP2, a key transcription regulator, are associated with increased susceptibility to lupus and differential gene expression in patients with systemic lupus erythematosus. A common MECP2 haplotype associates with reduced cortical surface area in humans in two independ...
Homozygous for CYP2D6 variants (non-CYP2D6*1)
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rs1135840, also known as 4180G>C or S486T, is a SNP in the CYP2D6 gene. The wild type (normal) allele at this SNP is (G). The (C) variant indicates the presence of a non-wild type CYP2D6 variant, but it appears in many different variants so it can not be used to determine the presence of any particular variant. Please be careful when interpreting results for this SNP as it is in dbSNP and SNPedia in minus orientation where the risk allele is C, but test results are usually in plus orientation where the risk allele is G. This SNP has an ambiguous flip which can make this very confusing. Polymorphisms affecting gene transcription and mRNA processing in pharmacogenetic candidate genes: detection through allelic expression imbalance in human target tissues. [PharmGKB:Curated Risk or phenot...
0.86x decreased risk of Atrial Fibrillation This is the normal version which makes the heart form properly and makes people less likely to get Atrial Fibrillation (quivering of the top chambers of the heart caused by chaotic electrical signals) and less likely to have an Ischemic Stroke (blocked blood flow to the brain). But also check the other SNP nearby (rs10033464) which slightly affects Atrial Fibrillation too. 23andMe gave this a 4 star confidence rating as it has been heavily studied. It has been confirmed in Europeans and Asians.
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Two SNPs from chromosome 4q25, rs2200733 and rs10033464, were found to be associated with atrial fibrillation in a study of both European and Asian populations. The odds ratio associated with one or more copies of either risk allele was ~1.4x. The results derived from a study of 78 Italians with atrial fibrillation (AF) and atrial flutter (AFL) agree with previously reported findings from the Icelandic study (), which also found that the rs2200733(T) was associated with AF/AFL disease. In 1,661 Icelandic ischemic stroke samples and two large European replication sets combined, rs2200733 was associated with cardioembolic stroke (CES) (odds ratio 1.54, p = 8.05 x 10e-9). rs2200733 even showed association to ischemic stroke that was not classified as cardioembolic stroke. rs2200733 and rs1003...
3x higher risk of multiple sclerosis Rs3135388(C;T) is highly correlated with the HLA-DRB1*1501 allele. There is a 3x higher risk of multiple sclerosis associated with the (C;T) genotype.
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rs3135388(T) is highly (> 99%) correlated with the HLA-DRB1*1501 allele; the risk allele (T) is associated with a 3 to 6 fold higher risk for developing multiple sclerosis. The risk per allele (or per haplotype) appears additive. It has also been associated with other autoimmune diseases, such as systemic lupus erythematosis (SLE) (see) and, when linked with DQB1*0602, narcolepsy. The HLA-DRB1*1501 allele is fairly common; for example, it occurs in 15-30% of individuals of Northern European ancestry. Note: most publications refer to the risk allele as rs3135388(A), but in dbSNP and SNPedia orientation, it is rs3135388(T). An interesting series of correlations have been woven together to suggest that a possible way to lower the risk of rs3135388(T) carriers developing multiple sclerosis ...
Among asthmatics, 1.5x more likely to show less response to inhaled glucocorticoids
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rs37973 is a SNP in the promoter region of the glucocorticoid induced transcript 1 GLCCI1 gene on chromosome 7. Based on 4 populations totaling 900+ asthma patients, the rs37973(G) allele was associated (p = 0.0007, pooled data) with lower amounts of improvement of lung function in response to inhaled glucocorticoids such as budesonide. The mean (±SE) increase in forced expiratory volume in 1 second (FEV1) in treated rs37973(G;G) patients was about one third of that seen in rs37973(A;A) patients (3.2±1.6% vs. 9.4±1.1%). Based on dividing the response into highest vs lowest quartiles of response, the allelic odds ratio of falling into the lowest responding quartile based on an additive genetic model was calculated to be 1.52 (CI: 1.13 - 2.03). Genotype accounted for about 7% ...
1.31x increased risk of heart disease
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Affects heart disease risk for both men and women, based on a study of two Finnish population cohorts (HR = 1.31 (1.08-1.60) for CVD, uncorrected p = 0.006 multiplicative model). A meta-analysis of publications through July 2009, totaling 4,386 cases (vs 40,089 controls) concluded that apart from a very weak association with myocardial infarction for the rs1801020 (T;T) + (C;T) compared with (C;C) genotype, (odds ratio 1.13, CI: 1.00 - 1.27), the evidence for an association between F12 -4C>T and venous thromboembolism and myocardial infarction was weak. [OMIM:COAGULATION FACTOR XII; F12]
complex; generally greater risk for cancer progression
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rs1801274 is a SNP in the Fc fragment of IgG, low affinity IIa, receptor (CD32) FCGR2A gene. rs1801274(C) encodes the arginine (R) allele, with the (T) allele encoding the variant histidine (H). The (H) isoform is considered high-binding to IgG2 and IgG3, while the (R) isoform is considered low-binding. This SNP is known in the literature by many names, including A519C and H131R. What's the importance of this? FcgR isoforms expressed on immune system cells have been linked to the pathogenic consequences triggered by autoantibodies or immune complexes in autoimmune diseases such as rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE), as well as to the efficacy of some immunotherapeutic treatments such as rituximab. Many studies have been published about this FCGR2A SNP, roughly...
Minorly increased risk of mental illness and osteoarthritis
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rs16944 is a SNP in the interleukin 1, beta gene, a member of the cytokine family involved in the inflammatory response. The rs16944 G;G genotype is associated with risk for multiple mental illnesses. An increased risk for schizophrenia was found in a genetic association study of 2111 Caucasian individuals with an odds ratio of 1.24 (95% CI 1.09, 1.41) . Studies examining the brains of schizophrenic and bipolar individuals found reduced gray matter and hypoactivity associated with the G;G genotype. Additionally, this genotype is associated with impaired ability to achieve remission in a study of 256 Caucasian individuals with depression (odds ratio = 1.74; 95% confidence interval 1.2-4.3). The rs16944 A allele increases susceptibility to Osteoarthritis, with 1.80 times for heterozygotes (A...
Slightly (~1.5x) higher risk for Caucasian mothers to give birth to NTD children There is a slightly higher risk (~1.5x at most) for Caucasian mothers with this genotype to give birth to children with neural tube defects; see discussion at rs2236225.
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rs2236225, also known as c.1958G>A, G1958A, p.Arg653Gln and R653Q, is a SNP in the MTHFD1 gene on chromosome 14. This SNP is best known for it's potential role in raising risk for neural tube defects, with some studies finding a slight effect in certain populations (for example, Irish and Italians) and other studies finding no effect (for example, in the Dutch). A 2014 meta-analysis of nine studies totaling 4,302 cases of children born with neural tube defects concluded that Caucasian mothers carrying one or two rs2236225(T) alleles were at slight increased risk, of about 1.5 - 1.7x, of having affected children compared to mothers with no (T) alleles. However, they cautioned that their results should be 'viewed with caution' given the statistical uncertainties inherent in these studies....
Magnitude: 1.5
Frequency: 55.8%
Repute:Bad
References:1
Frequency: 55.8%
Repute:Bad
References:1
1.3x higher risk for Crohn's disease
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rs17221417 has been reported in a large study to be associated with Crohn's disease. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.29 (CI 1.13-1.46), and for homozygotes, 1.92 (CI 1.58-2.34). Pharmacogenetics: data, concepts and tools to improve drug discovery and drug treatment. Individual disease risk and multimetric analysis of Crohn disease. Gene variants influencing measures of inflammation or predisposing to autoimmune and inflammatory diseases are not associated with the risk of type 2 diabetes. [OMIM:NUCLEOTIDE-BINDING OLIGOMERIZATION DOMAIN PROTEIN 2; NOD2]
maybe: higher scores on anxiety-related personality traits; greater placebo response One study of (only) 25 people shows this genotype was a significant predictor of clinical placebo response, being associated with greater improvement in anxiety symptoms. A criticism of this study has also been published, and it has not been replicated since the original publication years ago. This SNP has been linked to several psychiatric and/or behavioral phenomena, including: *higher scores on anxiety-related personality traits *obsessive compulsive disorder *panic disorder with a possible gender-dependent effect
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rs4570625, also known as G-703T, is a SNP in the tryptophan hydroxylase 2 TPH2 gene. This SNP has been linked to several psychiatric and/or behavioural phenomena, including: * rs4570625 and rs4565946 linked to the pathogenesis of early-onset obsessive compulsive disorder * rs4570625 and rs11178997 in TPH2's regulatory region display preferential transmission * rs4570625(G;G) homozygosity was a significant predictor of clinical placebo response, being associated with greater improvement in anxiety symptoms. g2b2mh is rs4570625(G;G) is a significant predictor of clinical placebo response? maybe not panic disorder with a possible gender-dependent effect Transmission disequilibrium of polymorphic variants in the tryptophan hydroxylase-2 gene in attention-deficit/hyperactivity disorder. Associa...
Normal (higher) risk of Bipolar Disorder. This is the most common version of this SNP, so most people have this. But it is suspected of having a higher risk of Bipolar Disorder compared to the other rare versions of this SNP.
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Bipolar disorder failed to replicate in [PharmGKB:Non-Curated GWAS Results: A genome-wide association study implicates diacylglycerol kinase eta (DGKH) and several other genes in the etiology of bipolar disorder (Initial Sample Size: 461 cases, 563 controls; Replication Sample Size: 772 cases, 876 controls; Risk Allele: rs1012053-A).] [GWAS:Bipolar disorder]
1.3x increased risk for type-2 diabetes
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rs5219, also known as E23K, is a SNP in the KCNJ11 gene. The association between type-1 diabetes and rs5219 is mentioned as being replicated in ; there is also a 90% correlation between rs5219 and rs5215. This SNP is one of 4 relatively common SNPs reported to represent risk for type-2 diabetes in the DESIR prospective study of 3,877 Caucasian participants. Under an additive model, the odds ratio for the minor (risk) allele (T) is 1.15 (CI: 0.95-1.4, p=0.2, ie not significant). But for the 4 SNPs, each risk allele increased type-2 diabetes risk by 1.34x (p=2x10e-6), with an odds ratio of 2.48 (CI: 1.59-3.86) for carriers of 4 or more compared to those with one or none (risk alleles). Genotyping of ~4000 Chinese as well a meta-analysis concluded that rs5219 was associated with type-2 diabet...
1.2x increased risk for schizophrenia
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rs1344706 is a SNP in the ZNF804A gene, and it is probably the first SNP to have been reported as achieving genome-wide significance for psychosis. Reviews the literature, and concludes that rs1344706 is 'robustly, if modestly' associated with increased risk for schizophrenia. A genome-wide association study of schizophrenia (479 cases, 2,937 controls) followed by additional testing and a meta-analysis concluded that the strongest evidence for association was around ZNF804A (rs1344706; p = 1.61 x 10e-7) and that the finding was strengthened when the affected phenotype included bipolar disorder (p = 9.96 x 10e-9). Executive function, neural circuitry, and genetic mechanisms in schizophrenia. Apoptotic engulfment pathway and schizophrenia. Persistence criteria for susceptibility genes for sc...
Magnitude: 1.2
Frequency: 55.8%
Repute:Good
References:3
Frequency: 55.8%
Repute:Good
References:3
decreased risk of schizophrenia in limited study
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Associated with schizophrenia in a study of Croatians. Due to the limited number and diversity of the studied population, more study is needed to confirm any link. The C allele was associated with an decreased risk of schizophrenia. [PharmGKB:Curated This variant along with 3 other SNPs near DRD4 (4 SNP haplotype: rs3758653; rs916457; rs762502; rs11246226) is associated with tardive dyskinesia in male schizophrenia patients.]
1.2x increased risk for T2D in some populations
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This SNP is in a linkage block in the FTO gene with rs1121980; see rs1121980 for the association of this block with early onset obesity since it showed the strongest association. This SNP did not show any association with obesity, type-2 diabetes or any other related traits in a study of 3,210 Chinese subjects. Furthermore, the minor allele frequency was much lower in Chinese populations compared to populations of European descent. However, a more recent study of 4,189 Chinese Han subjects combined with a meta-analysis of published studies concluded that rs8050136(A) was associated with both increased risk for type-2 diabetes and obesity. rs8050136 associated with increased food intake, but not of impaired energy expenditure. [PharmGKB:Non-Curated GWAS results: Genome-wide association yie...
complex! see rs4880
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The rs4880(T) allele, part of the codon for amino acid valine at codon 16 of the antioxidant protein from the mitochrondrial superoxide dismutase 2 SOD2 gene, is the most common in most populations studied. The rs4880(C) allele gives rise to an alanine at this position is it also known as Val16Ala manganese superoxide dismutase, or A16V. There appears to be some conflict in the literature over the effect of this SNP. Having a valine at codon 16 is said to reduce enzyme activity , and thus lead to increased oxidative stress, yet in at least one study of the actual enzyme levels measured in people, SOD2 activity was 33% higher in (C;T) or (T;T) individuals compared to (C;C) individuals . Regardless of how this resolves, several phenotypic associations have been reported for this SNP, includi...
more likely to gain weight if taking olanzapine
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The ancestral allele is C. The rs7412(T) allele, also known as Arg176Cys, generally indicates the presence of an Apoε2 allele; see the ApoE page for a full discussion of the ApoE alleles and their association with Alzheimer's disease. Another SNP related to ApoE is rs429358. In a study of 67 mostly Caucasian patients prescribed the atypical antipsychotic olanzapine, carriers of a rs7412(C) allele were more likely to gain significant weight compared to rs7412(T;T) carriers, as assessed by physiogenomic analysis of corresponding weight profiles. Two other SNPs, rs5092 and rs4765623, were also significantly associated with weight profiles in these patients. Current limitations of SNP data from the public domain for studies of complex disorders: a test for ten candidate genes for obesity ...
preterm birth rs4696480 (T-16934A and Arg753Gln) and rs5743708) (Thr399Ile) earlier birth for infants carrying two (-16934TA/AA and 753ArgGln/GlnGln)
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preterm birth rs4696480 (T-16934A and Arg753Gln) and rs5743708) (Thr399Ile) earlier birth for infants carrying two (-16934TA/AA and 753ArgGln/GlnGln)
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Association between SLC6A12 gene and negative symptoms of schizophrenia in Korean population.
carrier of one CYP1A2*1K_-739T>G allele
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rs2069526 is a SNP in the CYP1A2 gene. The rs2069526(T) allele defines the CYP1A2*1K_-739T>G variant. [PharmGKB:Curated Present in reduced function haplotype, unlikely to be causative.]
Frequency: 1.8%
References:1
References:1
possible increased Alzheimer's risk
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The rs1803274(A) allele encodes a version of the butyrylcholinesterase enzyme known as the K variant; it may also be known as CHE*539T or BCHE*539T. The allele produces a 30% reduction in serum butyrylcholinesterase activity, and it is often co-inherited with the SNP encoding the so-called 'atypical' butyrylcholinesterase, rs1799807. Although not replicated by other studies, some studies have found, at least in certain populations, a possible association between this SNP and risk for Alzheimer's disease (independent of ApoE4 status): * reports ~2x increased Alzheimer's risk for carriers of one or more rs1803274(A) alleles, based on a study of 135 Canadian patients * reports ~3.5x increased Alzheimer's risk for carriers of one or more rs1803274(A) alleles, based on a study of 175 patients f...
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[PharmGKB:Curated Protective allele: C; Phenotype: upon treatment with amlodipine, patients with C/C or C/T compared to a T/T genotype were twice as likely to reach a target mean arterial pressure (MAP) <107mmHG; study size: 145; study population: African-American men and women with early hypertensive nephrosclerosis ; significance value: hazards ratio 2.0; p-value 0.01]
0.42x reduced lymphoma risk
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Associated with (reduced) risk for follicular lymphoma. Based on studying ~1,300 patients in 2 populations, for (C;C) homozygotes, the odds ratio was 0.42 (CI: 0.23-0.77), and for the (C;T) heterozygotes, 0.64 (CI: .46-.88), p(trend) = 4x10e-4. estrogen receptor-positive breast cancer risk (C) have an Odds Ratio (OR) = 1.05 [95% Confidence Intervals (CI) 1.02-1.09] relative to t-allele homozygotes, P= 0.004. [PharmGKB:Curated In a French study population, the C allele of this SNP, which is located in intron 4 of ESR1, was associated with increased incidence of type 2 diabetes (diabetes mellitus, type 2). The C allele of this SNP was associated with increased fasting plasma glucose levels in Swedish males, although there was no significant association in the Swedish cohort between this SNP...
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[GWAS:Obesity-related traits]
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[PharmGKB:Curated Risk or phenotype-associated allele: TT genotype. Phenotype: In AML patients receiving cytarabine, the TT genotype for rs532545 was associated with decreased 5-year overall survival (13%) relative to the CC genotype (25%) (p = 0.05), and significantly higher lactate dehydrogenase levels relative to the CC and CT genotypes (p = 0.01). Patients with the TT genotype had greater than 50% increased risk for death compared with patients with the CC genotype (HR = 1.56, p = 0.02). Study size: 360. Study population/ethnicity: AML patients. /Caucasian Germans. Significance metric(s): Type of association: GN; CO; PD; TOX; ADR]
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Associated with Attention deficit hyperactivity disorder. [PharmGKB:Non-Curated Genome-wide association study of response to methylphenidate in 187 children with attention-deficit/hyperactivity disorder. (Initial Sample Size: 187 children; Replication Sample Size: NR); (Region: 22q13.31; Reported Gene: Intergenic; Risk Allele: rs9627183-C) This variant is associated with Attention-deficit/hyperactivity disorder.] [GWAS:Attention-deficit/hyperactivity disorder]
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[PharmGKB:Curated This promoter variant is associated with breast cancer risk reduction in two of three case control studies. Functional studies showed that it altered nuclear protein binding patterns and was associated with the up-regulation of transcription, possibly resulting in increased COMT activity.]
3x risk of predisposition to childhood asthma in a Japanese population
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rs569108, a SNP in the MS4A2 gene, has been linked in a Japanese population to a predisposition to childhood asthma, with an odds ratio of 3 . The risk allele in dbSNP orientation is (C). [Note: no (C;C) homozygotes were observed in this population.] Gene-environment interaction effects on the development of immune responses in the 1st year of life. Analysis of polymorphisms in 16 genes in type 1 diabetes that have been associated with other immune-mediated diseases. A meta-analysis of candidate gene polymorphisms and ischemic stroke in 6 study populations: association of lymphotoxin-alpha in nonhypertensive patients. Association of 77 polymorphisms in 52 candidate genes with blood pressure progression and incident hypertension: the Women's Genome Health Study. A candidate gene association...
Frequency: 9.8%
References:1
References:1
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part of a three marker haplotype rs737865-rs4680-rs165599 COMT haplotypes at rs737865 and rs165599 may predict a favorable outcome for bupropion treatment for smoking cessation. We have typed the IVS 1 rs737865 and 3' rs615599 sites and also included a novel IVS 1 indel polymorphism. We report that the schizophrenia-associated haplotype is significantly heterogeneous in populations worldwide. may affect non-Hodgkin lymphoma, anxiety-related personality traits Also mentioned in these PMIDs * * * * * * [PharmGKB:Curated This variant may predict a favorable outcome for bupropion treatment for smoking cessation] [OMIM:CATECHOL-O-METHYLTRANSFERASE; COMT]
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[PharmGKB:Curated Risk or phenotype-associated allele: None. Phenotype: Variants identified in a screen of 13 genes involved in the gemcitabine drug metabolic pathway. For the non-synonymous CDA:79A>C (K27Q) SNP, the C allele (27Gln) was at frequency 0.36 and 0.04 in Europeans and Africans, respectively. There was a significant difference between ethnic groups in genotype frequency distribution (p < 0.001) Study size: 180. Study population/ethnicity: Healthy, unrelated blood donors of European (n = 95) and African (n = 85) descent. Significance metric(s): p < 0.001. Type of association: GN.]
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rs4149601 has been associated with hypertension. This SNP by itself was associated with diastolic blood pressure (DBP) (p=0.03) and DBP progression over time (p=0.04); in genotypic combination with intronic NEDD4L SNP rs2288774 it was associated with systolic blood pressure (SBP) (p=0.01), DBP (p=0.04), and progression of both SBP (p=0.03) and DBP (p=0.05) over time. Polymorphism in NEDD4L is associated with increased salt sensitivity, reduced levels of P-renin and increased levels of Nt-proANP. Expression, transcription, and possible antagonistic interaction of the human Nedd4L gene variant: implications for essential hypertension. Two polymorphisms in NEDD4L gene and essential hypertension in Chinese Hans - a population-based case-control study. Physiological interaction between alpha-ad...
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[PharmGKB:Curated Risk or phenotype-associated allele: undetermined. Phenotype: The variant allele was not associated with warfarin maintenance dose variability (p = 0.4450). Study size: 283. Study population/ethnicity: Hospitalized Caucasian patients aged 75 years or older, recruited Sep 2002-Nov 2004 in Ivry, France, and Oct 2005-Mar 2008 from 14 French centers. Significance metric(s): not significant. Type of association: GN; PK.]
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rs1045280(T) associated with tardive dyskinesia in Chinese patients with schizophrenia (OR(T) = 1.58, 95% CI = 1.14-2.19, P = 0.007)
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rs2193225 has been reported to be associated with increased risk for nicotine dependence. [PharmGKB:Curated A study on 2037 individuals from 602 nuclear families of African-American or European-American origin found a significant associations of this SNP in the NRXN1 gene with smoking quantity, the heaviness of smoking index and the Fagerstr?m test for nicotine dependence in the European-American sample.]
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[PharmGKB:Non-Curated altered kinetics of gemcitabine in transfected cells]
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MCP-1 gene haplotype association in biopsy proven giant cell arteritis. Polymorphisms in the genes encoding chemokine receptor 5, interleukin-10, and monocyte chemoattractant protein 1 contribute to cytomegalovirus reactivation and disease after allogeneic stem cell transplantation. Monocyte chemotactic protein-1 single nucleotide polymorphisms do not confer susceptibility for the development of adult onset polymyositis/dermatomyositis in UK Caucasians. Association of the -2510A/G chemokine (C-C motif) ligand 2 polymorphism with knee osteoarthritis in a Korean population. Comprehensive analysis of the candidate genes CCL2, CCR2, and TLR4 in age-related macular degeneration. Polymorphisms affecting gene transcription and mRNA processing in pharmacogenetic candidate genes: detection through ...
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prostate cancer rs3212649 (OR=1.67 (1.07-2.6), P=0.0009) and rs1126643 (OR=1.52 (1.01-2.28), P=0.0088).
Frequency: 12.4%
References:1
References:1
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[GWAS:None]
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[GWAS:None]
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[PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: The PPAR delta SNP rs6922548 A>G was associated with positive clincial response (partial or complete response) to treatment. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.0011 Type of association: PD; CO]
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23andMe blog blood pressure High Blood Pressure (Hypertension) [GWAS:Diastolic Blood Pressure]
CYP1A2_1545T>C homozygote
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rs2470890 is a SNP in the CYP1A2 gene. The rs2470890(C) allele defines the CYP1A2_1545T>C variant. Low-penetrance alleles predisposing to sporadic colorectal cancers: a French case-controlled genetic association study. [PharmGKB:Curated Weakly associated with tardive dyskinesia and schizophrenia.]
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[PharmGKB:Curated Associations were found between genotypes of SNPs in the ALOX5 (rs2115819) and MRP1 (rs119774) genes and changes in FEV(1) (p < 0.05) in asthma patients treated with montelukast.]
0.68x decreased risk for bladder cancer
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rs5275, also known as exon1-+837T>C, is a SNP in the PTGS2 gene. A study of 635 Caucasian bladder cancer patients found a reduced risk associated with the minor (C) allele of rs5275, (odds ratio 0.68, CI: 0.54-0.87, p=0.002, remaining significant after multiple comparison adjustment). (T;T) genotype of PTGS2 8473T>C (rs5275) was significantly correlated with a better survival when compared to the combined T/C and C/C genotype (Hazard ratio [HR] = 0.47; P value = 0.046 and HR = 0.16; P = 0.013, respectively) in colorectal cancer Allellic variants in regulatory regions of cyclooxygenase-2: association with advanced colorectal adenoma. Association of frequent consumption of fatty fish with prostate cancer risk is modified by COX-2 polymorphism. Cyclooxygenase-2 polymorphisms in Parkinso...
Frequency: 13.3%
References:4
References:4
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Altered brain-derived neurotrophic factor blood levels and gene variability are associated with anorexia and bulimia. Brain-derived neurotrophic factor ( BDNF) gene: no major impact on antidepressant treatment response. Association analysis of brain-derived neurotrophic factor gene polymorphisms in asthmatic families. Pharmacogenetics of antidepressant response. Brain-derived neurotrophic factor (BDNF) gene: a gender-specific role in cognitive function during normal cognitive aging of the MEMO-Study? Brain-derived neurotrophic factor gene polymorphisms, neurotransmitter levels, and depressive symptoms in an elderly population.
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[PharmGKB:Curated Risk or phenotype-associated allele: rs3761422 T allele. Phenotype: Carriers of 1 or 2 copies of the T allele for rs3761422 showed increased risk of any (OR = 2.11, CI = 1.04-4.39, p = 0.02) or gastrointestinal-specific (OR = 1.91, CI = 0.69-5.77, p = 0.17) adverse events. Study size: 309 RA patients, including 147 good MTX responders, 101 MTX inefficacy failures, and 61 adverse event (AE) MTX failures (e.g. gastrointestinal (n = 24), abnormal liver function tests (n = 20), haematological (n = 7), skin rashes (n = 6), and other (n = 17). Study population/ethnicity: Rheumatoid arthritis (RA) patients aged over 18 yrs, of White Caucasian ethnic origin, classified as having RA according to ARA criteria that were retrospectively recruited from University Hospital of North Sta...
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hepatocellular carcinoma in Chinese populations *increased risk rs4646421 (OR 1.30, 95% CI 1.05-1.61) *increased risk rs2198843 (OR 1.33, 95% CI 1.05-1.69) *reduced risk rs4886605 (OR 0.70. 95% CI 0.52-0.94)
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[GWAS:Ulcerative colitis]
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rs231775, also known as +49A/G, is a SNP in the CTLA4 gene. which is linked to Hashimoto thyroiditis In a meta-analysis of CTLA4 gene SNPs, rs231775 was most associated with vitiligo; however, the association seems to hold only in the subgroup of patients with other autoimmune diseases. rs231775 (CTLA4_+49_G/A P=0.0219) and rs733618 (CTLA4_-1722_T/C P=0.0096) susceptibility to Graves' disease associated with the development of placental abruption and preeclampsia, with women having the G allele being at risk rs231775 was not associated with type-1 diabetes in a study of 207 Portuguese patients. [PharmGKB:Curated This SNP affects risk for Autoimmune Thyroid Disorder (AITD). The G allele is generally thought to be the risk-conferring allele, but this study found that which allele confers ri...
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[GWAS:Response to haloperidol in psychosis]
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[PharmGKB:Curated The G allele of this variant is more frequent in patients with major depressive disorders (MDD) than in controls in a study consisting of 188 Chinese MDD patients and 346 controls.]
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[PharmGKB:Curated The T allele of this variant is more frequent in patients with major depressive disorders (MDD) than in controls in a study consisting of 188 Chinese MDD patients and 346 controls.]
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news rs4355801, was associated with a 20% increased risk of osteoporosis (significant at P=0.038). At least one copy of the risk allele (A) of rs4355801 was found in 79% of study participants. Participants carrying at least one copy of each risk allele -- 22% of the study population -- had a 50% increased risk of osteoporosis, which was significant at P=0.0026, and a 29% increased risk of osteoporotic fractures (significant at P=0.014). rs3736228 associated with decreased bone mineral density (p=6.3x10(-12) for lumbar spine and p=1.9x10(-4) for femoral neck) and an increased risk of both osteoporotic fractures (odds ratio [OR] 1.3, 95% CI 1.09-1.52, p=0.002) and osteoporosis (OR 1.3, 1.08-1.63, p=0.008). rs4355801 associated with decreased bone mineral density (p=7.6x10(-10) for lumbar spi...
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[OMIM:CHOLINERGIC RECEPTOR, NEURONAL NICOTINIC, ALPHA POLYPEPTIDE 5; CHRNA5]
0.62x reduced risk for sarcoidosis
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rs1049550, also known as R230C, is a SNP in the annexin A11 ANXA11 gene. 499 German individuals with sarcoidosis and 490 controls; Validation in an independent sample 1,649 cases, 1,832 controls. rs2789679: P = 3.0 x 10(-13), rs7091565: P = 1.0 x 10(-5)rs1049550, T > C, R230C was found to be strongly associated with sarcoidosis. rs2789679 P = 3.0 x 10(-13), rs7091565: P = 1.0 x 10(-5), allele-based test). Extensive fine mapping located the association signal to a region between exon 5 and exon 14 of ANXA11. A common nonsynonymous SNP (rs1049550, T > C, R230C) was found to be strongly associated with sarcoidosis Note that several ANXA11 SNPs are all tightly linked: rs1953600, rs2573346, rs2784773 and rs1049550. [PharmGKB:Curated A genome-wide association study in 499 German individua...
Frequency: 16.8%
References:11
References:11
if less milk in teenage females, less bone?
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A very small study of 117 healthy European peri- and postmenarcheal girls (14.9 +/- 1.6 years) were followed for 4 years along with their calcium intake. Girls with rs4516035(C;T) and (C;C) genotypes had 13% lower spine mineral content if their milk intakes were below 260 mL/day, compared to either genotype-matched girls with higher milk intakes or to girls with the (T;T) genotype. If this is real, it suggests that rs4516035(C;T) and (C;C) female teens need more milk than rs4516035(T;T) girls to have optimal bone density. rs4516035 and the more aggressive tumour location in head-neck and trunk (OR=1.54, p=0.020)
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Association between variants in the genes for adiponectin and its receptors with insulin resistance syndrome (IRS)-related phenotypes in Mexican Americans. Association of adiponectin gene variations with risk of incident myocardial infarction and ischemic stroke: a nested case-control study. Adiponectin gene ADIPOQ SNP associations with serum adiponectin in two female populations and effects of SNPs on promoter activity. FOXO3A genotype is strongly associated with human longevity. Common variants in the adiponectin gene (ADIPOQ) associated with plasma adiponectin levels, type 2 diabetes, and diabetes-related quantitative traits: the Framingham Offspring Study. Adipokine genes and prostate cancer risk. The association of SNPs in ADIPOQ, ADIPOR1, and ADIPOR2 with insulin sensitivity in a coh...
normal
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rs2293347, also known as D994D, is a SNP in the epidermal growth factor receptor EGFR gene. In a study of therapeutic outcome and survival in 84 advanced non-small-cell lung cancer (NSCLC) patients treated with Gefitinib, the response rate for rs2293347(G;G) patients was almost double that of other genotypes for this SNP (71.2% versus 37.5%, p=0.0043). The rs2293347(G;G) genotype was also associated with longer progression-free survival compared with the rs2293347(A;G) or (A;A) genotypes (11 months versus 3 months, p=0.0018).
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[GWAS:Systemic lupus erythematosus]
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rs6721498 has been reported to be associated with increased risk for nicotine dependence. [PharmGKB:Curated A study on 2037 individuals from 602 nuclear families of African-American or European-American origin found a significant associations of this SNP in the NRXN1 gene with smoking quantity, the heaviness of smoking index and the Fagerstr?m test for nicotine dependence in the African-American sample.]
Frequency: 18.6%
References:5
References:5
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Replication analysis confirms the association of ARID5B with childhood B-cell acute lymphoblastic leukemia. [PharmGKB:Curated This SNP located in intron 3 of the ARID5B gene differed between pediatric acute lymphoblastic leukemia (ALL) and non-ALL groups (rs10994982, P = 5.7 x 10(-9), OR = 1.62) and also distinguished B-hyperdiploid ALL from other subtypes (rs10994982, P = 0.003, OR 1.72). This SNP was in linkage disequilibrium with rs10821936 (r2 = 0.42, P < 1 10-10). The study found found that the same alleles of this ARID5B SNP rs10994982 that were associated with B-hyperdiploid ALL were also associated with greater methotrexate polyglutamate accumulation (P = 0.021).] [OMIM:?]
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[PharmGKB:Curated Risk or phenotype-associated allele: AA. Phenotype: Homozygous AA at this SNP was associated with chronic cardiotoxicity in response to doxorubicin. Study size: 1697. Study population/ethnicity: Participants of the German non-Hodgkin lymphoma study. Significance metric(s): OR = 2.5; 95% CI, 1.3 to 5.0. Type of association: PD; ADR; TOX.]
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[PharmGKB:Curated A significant association between major cytogenetic response (MCyR) and the rs2290573 polymorphism mapped to 15q22.33 was observed in imatinib-treated patients (P = 0.00037, Bonferroni corrected P = 0.025). Individuals with a CC genotype had a MCyR rate of 52% compared with individuals with a CT or TT genotype that had a MCyR rate of 89% (odds ratio, 6.72; 95% confidence interval, 1.51-29.91). CO: The time to progression at 18 months was significantly different between CC and CT/TT genotype using log-rank test or Wilcoxon test (P < 0.03): Six of 29 imatinib-treated patients (21%) with a CC genotype experienced progression events vs five of 84 patients (6%) with a CT or TT genotype. Study size=113]
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[GWAS:None]
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[PharmGKB:Curated Several studies showed an associaction of this SNP in DTNBP1 with schizophrenia and other psychotic disorders, including substance-induced psychosis]
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a significant association between rs3924999 and Alzheimer's disease with psychosis [OMIM:NEUREGULIN 1; NRG1]
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[PharmGKB:Curated Risk or phenotype-associated allele: C Phenotype: The CHST3:rs4148943 C variant was associated with positive clincial response (partial or complete response) to treatment. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.0001 Type of association: PD; CO]
Frequency: 19.5%
References:4
References:4
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[PharmGKB:In-Depth A study of 124 White patients, which received a high-dose regimen consisting of cyclophosphamide, thiotepa and carboplatin as intravenous infusions, concludes patients homozygous for the GSTP1 C341T allele may have enhanced exposure to thiotepa and tepa.]
Frequency: 19.5%
References:1
References:1
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haplotype less common in schizophrenia rs2273206(T), rs2273207(G), rs2228480(G). [PharmGKB:Curated Risk or phenotype-associated allele: not available in abstract. Phenotype: Positive association between rs2228480 SNP and thyroglobulin levels in thyroid cancer. Study size: 106 cases and 302 controls. Study population/ethnicity: Thyroid cancer patients and healthy individuals. Significance metric(s): not available in abstract. Type of association: CO; GN.]
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Vascular endothelial growth factor gene haplotypes in Kawasaki disease. Genetic variation in VEGF does not contribute significantly to the risk of congenital cardiovascular malformation. EGFR pathway polymorphisms and bladder cancer susceptibility and prognosis. A systematic meta-analysis of genetic association studies for diabetic retinopathy. The role of vascular endothelial growth factor SNPs as predictive and prognostic markers for major solid tumors. Polymorphisms in the VEGFA and VEGFR-2 genes and neovascular age-related macular degeneration. Human genetics of diabetic retinopathy: current perspectives. Genetics of VEGF serum variation in human isolated populations of cilento: importance of VEGF polymorphisms. [PharmGKB:Curated This variant in the promoter region of the VEGFA gene w...
increased risk for RA
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Several studies have all found that rs2240340, a SNP in the PADI4 gene, is associated with risk for developing rheumatoid arthritis (RA). The risk allele in dbSNP orientation is (T). The largest study involved over 2,000 RA patients, and although implicating PTPN22 SNPs with greater risk, PADI4 SNP rs2240340 was also implicated. The odds ratio varied between the two (European) populations a bit, but when combined, was 1.10 (CI: 1.00 - 1.21) for the risk allele. Additional studies include: rs2240340 was modestly associated with rheumatoid arthritisin a study of 950 unrelated Japanese subjects with RA, with an odds ratio of 1.22 (CI: 1.04 - 1.43,p=0.012). rs2240340 was associated with rheumatoid arthritis with an odds ratio of 1.97 (CI: 1.44 – 2.69), based on 830 cases and...
Frequency: 20.4%
References:7
References:7
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rs12422149 linked to asthma [PharmGKB:Curated In an 80-patient study, the A allele of this variant was associated with significantly reduced plasma concentrations of montelukast and with poor response to treatment with montelukast.]
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Genome-wide association study of genetic determinants of LDL-c response to atorvastatin therapy: importance of Lp(a). [GWAS:None]
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Genetic predictors of the maximum doses patients receive during anti-epileptic drugs carbamazepine and phenytoin Possible commercial test [PharmGKB:Curated This SNP is associated with required dose levels of antieptilectic drugs. It affects alternative splicing and hence the proportions of neonate and adult alternative transcripts of SCN1A in adult brain tissue. The effect of the polymorphism appears to be modified by Nova2 expression levels.] [OMIM:SODIUM CHANNEL, NEURONAL TYPE I, ALPHA SUBUNIT; SCN1A]
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[PharmGKB:Curated This SNP is not associated with dichotomy in the severity of early onset nicotine addiction, as assessed by the FTND (Fagerstrom Test of Nicotine Dependence). Haplotype B, which contains this SNP, is also not associated with this phenotype.]
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Pharmacogenetics of antidepressant response. [GWAS:Treatment response to citalopram]
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Investigation of Crohn's disease risk loci in ulcerative colitis further defines their molecular relationship. Assessing the reproducibility of asthma candidate gene associations, using genome-wide data. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Allele-specific chromatin remodeling in the ZPBP2/GSDMB/ORMDL3 locus associated with the risk of asthma and autoimmune disease. Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations. An investigation of genome-wide studies reported susceptibility loci for ulcerative colitis shows limited replication in north Indians. [OMIM:INFLAMMATORY BOWEL DISEASE 22; IBD22] [GWAS:Crohn's disease]
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Common variants in the adiponectin gene (ADIPOQ) associated with plasma adiponectin levels, type 2 diabetes, and diabetes-related quantitative traits: the Framingham Offspring Study. The association of SNPs in ADIPOQ, ADIPOR1, and ADIPOR2 with insulin sensitivity in a cohort of adolescents and their parents. Association of the adiponectin gene variations with risk of ischemic stroke in a Korean population.
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[PharmGKB:Curated SNP is associated with development of hepatic or gastrointestinal toxicity to methotrexate in patients with psoriasis.]
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[GWAS:Acute lymphoblastic leukemia (B-cell precursor)]
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[PharmGKB:Curated Risk or phenotype-associated allele: rs5760410 G allele. Phenotype: Carriers of 1 or 2 copies of the G allele for rs5760410 showed increased risk of any (OR = 3.07, CI 1.22-8.76, p = 0.01) or gastrointestinal-specific (OR = 4.58, CI = 1.01-42.05, p = 0.03) adverse events. Study size: 309 RA patients, including 147 good MTX responders, 101 MTX inefficacy failures, and 61 adverse event (AE) MTX failures (e.g. gastrointestinal (n = 24), abnormal liver function tests (n = 20), haematological (n = 7), skin rashes (n = 6), and other (n = 17). Study population/ethnicity: Rheumatoid arthritis (RA) patients aged over 18 yrs, of White Caucasian ethnic origin, classified as having RA according to ARA criteria that were retrospectively recruited from University Hospital of North Staf...
~10% more likely to respond to citalopram
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rs1954787, located in an intron of the GRIK4 gene, was found to be associated with a somewhat increased rate of successful response to treatment of depression with the drug citalopram. From the abstract of this article: 'The effect size of (this) GRIK4 marker alone was modest, but homozygote carriers of the treatment-response-associated marker alleles of both the GRIK4 and HTR2A (see rs7997012) genes were 23% less likely to experience nonresponse to (citalopram) treatment relative to participants who did not carry any of these marker alleles.' * See also Anxiety Blog posting [PharmGKB:Curated A study in 1,816 eligible patients from the STAR*D cohort found that genetic variation in a kainic acid-type glutamate receptor is reproducibly associated with response to the antidepressant citalopr...
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[PharmGKB:Curated This variant was shown to be assoicated with antidepressant treatment response in a study consisting of 188 Chinese MDD patients and 346 controls.The G allele was less frequent in responders than nonresponders] [GWAS:Plasminogen activator inhibitor type 1 levels (PAI-1)]
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Genetic variation in the dopamine pathway and smoking cessation.
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[PharmGKB:Curated Risk or phenotype-associated allele: A Phenotype: The CHST3:rs1871450 A variant was associated with positive clincial response (partial or complete response) to treatment and toxicity to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.048 (response); p = 0.006 (TOX) Type of association: PD; CO; TOX]
Frequency: 24.6%
References:1
References:1
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[PharmGKB:Curated Risk or phenotype-associated allele: A Phenotype: The CHST3:rs12418 A variant was associated with positive clincial response (partial or complete response) to treatment. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.0005 Type of association: PD; CO]
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[PharmGKB:Curated Risk or phenotype-associated allele: C Phenotype: The CHST3:rs4148945 C variant was associated with positive clincial response (partial or complete response) to treatment and toxicity to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.011 (response); p = 0.010 (TOX) Type of association: PD; CO; TOX]
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[PharmGKB:Curated Risk or phenotype-associated allele: C Phenotype: The CHST3:rs4148947 C variant was associated with positive clincial response (partial or complete response) to treatment. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.0023 Type of association: PD; CO]
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[PharmGKB:Curated Risk or phenotype-associated allele: A Phenotype: The CHST3:rs4148950 A variant was associated with positive clincial response (partial or complete response) to treatment and toxicity to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s):p = 0.024 (response); p = 0.006 (TOX) Type of association: PD; CO; TOX]
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g2b2mh blog In a population of healthy individuals, those that carry common variants (such as rs760761, rs1018381, rs2619522) located in the dysbindin (DTNBP1) gene, a risk factor for schizophrenia, show minor cognitive impairments such as decreased attentional capacity, worse performance on memory tasks, and alterations in schizotypal beliefs and experiences. [OMIM:DYSTROBREVIN-BINDING PROTEIN 1; DTNBP1]
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Gene variants associated with deep vein thrombosis. Updated analysis of gene variants associated with deep vein thrombosis. per risk allele odds ratio *rs13146272 in CYP4V2 (risk allele frequency, 0.64) OR 1.24 (95% CI, 1.11-1.37) for rs13146272 *rs2227589 in SERPINC1 (risk allele frequency, 0.10) OR 1.29 (95% CI, 1.10-1.49) for rs2227589 *rs1613662 in GP6 (risk allele frequency, 0.84) OR 1.15 (95% CI, 1.01-1.30) for rs1613662 A study of 453 VTE cases and 1,327 controls was able to replicate the 'mild effects' of this SNP on risk for VTE, however they felt that stronger associations were found between increased VTE risk and either the Factor V Leiden mutation (rs6025)or having blood types O or A2. An evaluation of candidate genes of inflammation and thrombosis in relation to the risk of ve...
carrier of one CYP2E1*1B allele
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rs2070676, also known as 9896C>G, is a SNP in the CYP2E1 gene. The rs2070676(G) allele defines the CYP2E1*1B variant.
carrier of one CYP2E1_10463T>C(F421F) allele
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rs2515641 is a SNP in the CYP2E1 gene. The rs2515641(T) allele defines the CYP2E1_10463T>C(F421F) variant.
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association with rheumatoid arthritis and type-1 diabetes point to a general risk locus for autoimmune diseases. Also, of SNPs outside the HLA region, this SNP and one other (rs13119723) in the region of the IL21 gene showed the strongest association with celiac disease in a study of ~800 Caucasian patients and a meta-analysis of two further populations. A genome-wide association study of psoriasis and psoriatic arthritis identifies new disease loci. Association study of IL2/IL21 and FcgRIIa: significant association with the IL2/IL21 region in Scandinavian coeliac disease families. Translational mini-review series on the immunogenetics of gut disease: immunogenetics of coeliac disease. Common variants at CD40 and other loci confer risk of rheumatoid arthritis. Gene variants influencing mea...
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Association of adiponectin gene variations with risk of incident myocardial infarction and ischemic stroke: a nested case-control study. Single nucleotide polymorphisms at the adiponectin locus and risk of coronary heart disease in men and women. Variants of the adiponectin and adiponectin receptor 1 genes and breast cancer risk. Common variants in the adiponectin gene (ADIPOQ) associated with plasma adiponectin levels, type 2 diabetes, and diabetes-related quantitative traits: the Framingham Offspring Study. Variants of the adiponectin (ADIPOQ) and adiponectin receptor 1 (ADIPOR1) genes and colorectal cancer risk. The association of SNPs in ADIPOQ, ADIPOR1, and ADIPOR2 with insulin sensitivity in a cohort of adolescents and their parents. Association of the adiponectin gene variations wit...
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[PharmGKB:Curated The Ala (C) allele of this SNP is associated with grade 3 to 4 neutropenia and diarrhea and is an independent predictor of diarrhea in patients with colorectal neoplasms.]
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Genetic polymorphisms of tumour necrosis factor receptor superfamily 1A and 1B affect responses to infliximab in Japanese patients with Crohn's disease. Comprehensive follow-up of the first genome-wide association study of multiple sclerosis identifies KIF21B and TMEM39A as susceptibility loci.
Frequency: 26.5%
References:2
References:2
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Overlap of disease susceptibility loci for rheumatoid arthritis and juvenile idiopathic arthritis. Genetic variants in the prediction of rheumatoid arthritis. Investigation of rheumatoid arthritis susceptibility genes identifies association of AFF3 and CD226 variants with response to anti-tumour necrosis factor treatment. [PharmGKB:Curated This SNP located on chromosomes 10p15 is associated with susceptibility to rheumatoid arthritis in a validation study of 4,106 individuals with rheumatoid arthritis and an expanded reference group of 11,238 subjects.] [GWAS:Rheumatoid arthritis]
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Cholesterol ester transfer protein, interleukin-8, peroxisome proliferator activator receptor alpha, and Toll-like receptor 4 genetic variations and risk of incident nonfatal myocardial infarction and ischemic stroke. Cholesteryl ester transfer protein (CETP) genetic variation and early onset of non-fatal myocardial infarction. Genetic-epidemiological evidence on genes associated with HDL cholesterol levels: a systematic in-depth review.
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rs20417, also known as -765G>C (and -899G >C in some older publications), is a SNP in the Prostaglandin endoperoxidase synthase 2 PTGS2 gene on chromosome 1. A 2012 review of three of the most studied PTGS2 gene variants concluded the following about rs20417: * The C variant is associated with lower promoter activity compared with the G variant; * The C variant is found in a haplotype with -1195G>A (rs689466) in Pima Indians, Chinese Asians, and Australian Caucasians, and with -1290A>G (rs689465) in a Caucasian Australian population; * The epidemiological relevance of rs20417 is unclear and/or conflicting despite numerous studies (and this includes studies of myocardial infarction, diabetes, asthma, various cancers, and the use of NSAIDs to reduce coronary heart disease risk). ...
Frequency: 27.4%
References:6
References:6
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per the 23andMe blog, the minor allele of this SNP (A) was associated with decreased cholesterol and triglycerides {| border='1' |- !SNP !Rarer allele !LDL !HDL !TG |- | rs6544713 || T || + || || |- | rs2650000 || A || + || || |- | rs471364 || C || || - || |- | rs1800961 || T || || - || |- | rs7679 || C || || - || + |- | rs2967605 || T || || - || |- | rs2409722 || T || || || - |- | rs10903129 || A || - || - || - |- | rs6756629 || A || - || + || - |- | rs12670798 || C || + || + || + |- | rs7395662 || A || - || + || + |- | rs174570 || T || - || - || + |- | rs2271293 || A || - || + || - |- | rs2624265 || C || || || + |- | rs2167079 || T || || + || |- | rs9891572 || T || || + || |- | rs4844614 || T || + || || |- | rs5031002 || G || + || || |- |} [PharmGKB:Non-Curated GWAS results: Loci influe...
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Some evidence exists that the T;T and C;T genotypes are associated with less euphoria and energy in response to a given dose of a stimulant drug, e.g. dextroamphetamine, than occurs for the C;C genotype. See [especially figure 3 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3377371/figure/F3/]
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23andMe blog hearing loss linked to a chemotherapy drug named Cisplatin. [PharmGKB:Curated Risk or phenotype-associated allele: A. Phenotype: This variant was associated with cisplatin-induced hearing loss from a large candidate gene screen in 2 pediatric cohorts.. Study size: 54 (discovery); 112 (replication). Study population/ethnicity: Children with neoplasms receiving cisplatin; Canada. Significance metric(s): OR = 5.52 (CI 1.91, 15.95); p = 0.000182 Type of association: CO; TOX; ADR] [OMIM:?]
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[PharmGKB:Curated In a Chinese population, this SNP was significantly associated with blood pressure response to nifedipine treatment.]
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[OMIM:SOLUTE CARRIER FAMILY 18 (VESICULAR MONOAMINE), MEMBER 2; SLC18A2]
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[PharmGKB:Curated In a GWAS of 3497 Dutch subjects from the Netherlands Study of Depression and Anxiety or from the Netherlands Twin Registry, this SNP was found to be associated with Current Smoking (p = 0.00007972;OR for minor allele C:1.276).]
among alcoholics, likely to be heavier drinkers
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rs1042173 is a SNP in the solute carrier family 6 (neurotransmitter transporter, serotonin), member 4 SLC6A4 gene. A study of 275 patients seeking treatment for alcoholism concluded that Caucasians of with the rs1042173(T;T) genotype consumed an average of 11.17 drinks per drinking day, compared with an average of 8.58 for carriers of a rs1042173(G) allele (p = 0.0034). While this held true for both men and women, this association was not seen in Hispanics.
Frequency: 28.3%
References:8
References:8
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Each G allele is associated with 0.89 x odds of high blood pressure, according to 23andMe. 23andMe blog blood pressure High Blood Pressure (Hypertension) [GWAS:Systolic blood pressure]
Normal risk for autoimmune diseases
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The rs3087243 SNP is also known in the literature as the CT60 G>A or the +6230G>A polymorphism, and it is located in the CTLA4 gene. In Asian (Japanese) populations, the presence of an rs3087243(G) allele represents a 1.3 fold increased risk of autoimmune thyroid disease, and for those with autoimmune thyroid disease, a 1.5 fold increased risk of type-1 diabetes. However, in individuals without autoimmune thyroid disease, no association was seen between this SNP and type-1 diabetes. The authors speculate that earlier studies may have reported associations between this SNP and type-1 diabetes that were actually primarily based on the association with autoimmune thyroid disease. This same SNP, rs3087243, has also been implicated as a (minor) risk factor for developing rheumatoid arthri...
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rs1799939, also known as Gly691Ser, is a variant in the RET gene. This SNP has been reported to be associated with primary vesicoureteric reflux (pVUR) patients in Quebec, but it was not found in a study of 221 unrelated index cases of pVUR from the Irish population or in 190 full siblings of 160 of the index cases. [OMIM:REARRANGED DURING TRANSFECTION PROTOONCOGENE; RET]
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[PharmGKB:Curated This variant is significantly associated with the efficacy of anti-TNF treatment in rheumatoid arthritis (Adjusted P-value: 0.0000002; OR: 11.2 (2.3, 108.1)). The study is a genome-wide association study using the Illumina HapMap300 SNP chip on 89 RA patients prospectively followed after beginning of anti-TNF therapy.] [GWAS:Treatment response to TNF antagonists]
0.67x decreased risk for lung cancer
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rs2308327, also known as K178R, is a SNP in the MGMT gene. The more common allele, rs2308327(A), encodes a lysine (K) at codon 178, while the (G) allele encodes an arginine (R). In a pooled analysis of 200+ lung cancer patients, the rs2308327(G) allele was reported to provide a protective effect against lung cancer, and furthermore, more (G) alleles meant more protection, particularly for smokers. The odds ratios reported (p=0.003) were 0.67 (CI: 0.45-1.01) for heterozygotes, and 0.10 (CI: 0.01-0.94) for rs2308327(G;G) homozygotes. In a study of 300+ colon cancer cases, rs2308327(G), in linkage disequilibrium with the previously reported MGMT Ile(143)Val rs2308321 SNP, had an inverse association with colorectal cancer risk (odds ratio 0.52, CI: 0.35-0.78, unadjusted p(trend) = 0.0003 for t...
carrier of one CYP2E1*7_-333T>A allele
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rs2070673 is a SNP in the CYP2E1 gene. The rs2070673(A) allele defines the CYP2E1*7_-333T>A variant.
Frequency: 29.2%
References:4
References:4
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[PharmGKB:Curated The -58C allele of the human beta2 bradykinin receptor gene has been associated with hypertension in a Chinese Han population and an African American population.]
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[OMIM:CYTOCHROME P450, SUBFAMILY I, POLYPEPTIDE 1; CYP1B1]
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Epistatic interaction of CREB1 and KCNJ6 on rumination and negative emotionality. Effect sizes in experimental pain produced by gender, genetic variants and sensitization procedures. [PharmGKB:Curated Risk or phenotype-associated genotype: AA. Phenotype: The average methadone dose during the first year of substitution therapy were significantly larger in AA carriers (n=4) than in the other rs2070995 genotypes (p=0.003). Study Size: 85. Study population: Caucasian.]
Frequency: 29.5%
References:1
References:1
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[GWAS:None]
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Genetic polymorphisms in the nucleotide excision repair pathway and lung cancer risk: a meta-analysis. Polymorphisms in DNA repair genes, smoking, and bladder cancer risk: findings from the international consortium of bladder cancer.
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rs2308321, also known as Ile143Val or I143V, is a SNP in the MGMT gene. The more common (A) allele encodes the Ile, while the (G) allele encodes the Val. This change at codon 143 is often reported to be linked to a change at codon 178, rs2308327.
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prostate cancer treatment response rs2279115 and rs7121 Complex haplotype structure of the human GNAS gene identifies a recombination hotspot centred on a single nucleotide polymorphism widely used in association studies. Polymorphism in maternal LRP8 gene is associated with fetal growth. Differential allelic expression in the human genome: a robust approach to identify genetic and epigenetic cis-acting mechanisms regulating gene expression. PTHR1 mutations associated with Ollier disease result in receptor loss of function. Functional genetic polymorphisms and female reproductive disorders: Part I: Polycystic ovary syndrome and ovarian response. A sensitive functional assay reveals frequent loss of genomic imprinting in human placenta. Association of the GNAS locus with severe malaria. Dev...
complex; see details for increased risks
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Several susceptibilities have been linked to rs1042714, a SNP in the ADRB2 gene that is also known as the Q27E SNP. The rs1042714(C) allele encodes the glutamine (Gln; 'Q'), and the rs1042714(G) allele encodes the glutamic acid (Glu; 'E'). A study of 304 patients found that the Glu27 allele led to increased risk for idiopathic venous thromboembolism; the reported odds ratio was 1.40 (CI: 1.09-1.79, p=0.006) for carriers of at least one risk allele. A study of 334 families with at least one child with autism found that increased risk associated with the rs1042714(G;G) homozygous genotype; the odds ratio reported was between 1.33-1.60 (CI: 1.07-2.58). The risk was approximately doubled among mothers who had clinical markers for pregnancy related stress. In a study of 342 patients with type-2...
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[PharmGKB:Curated This variant in the corticotropin-releasing hormone receptor-2 gene was associated with acute bronchodilator response in the 608-participant Childhood Asthma Management Program (CAMP), but was not found to be associated in the 427-participant Sepracor study or the 152-participant LODO trial. The mean ages of the participants in the CAMP, Sepracor, and Lodo cohorts were 8.9, 32.6, and 42.9 years of age, respectively. Only Caucasians were analyzed in each of these studies.]
Frequency: 31.0%
References:6
References:6
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[PharmGKB:Curated Subjects homozygous for this genotype showed decreased response to fluvastatin]
Frequency: 31.0%
References:1
References:1
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rs2235544, was associated with the free T3 to free T4 ratio with genome-wide levels of significance (P = 3.6 x 10–13). The C-allele of this SNP was associated with increased deiodinase 1 (D1) function with resulting increase in free T3/T4 ratio and free T3 and decrease in free T4 and rT3. A common variation in deiodinase 1 gene DIO1 is associated with the relative levels of free thyroxine and triiodothyronine. Cellular and molecular basis of deiodinase-regulated thyroid hormone signaling. [GWAS:Thyroid hormone levels]
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The (C;C) genotype is linked to reduced UGT1A1 activity, and increased Bilirubin, except in people of African origin for whom the T allele is a risk factor for breast cancer. [Genetic polymorphisms of MPO, NQO1, GSTP1, UGT1A6 associated with susceptibility of chronic benzene poisoning]. The influence of metabolic gene polymorphisms on urinary 1-hydroxypyrene concentrations in Chinese coke oven workers. Low-penetrance alleles predisposing to sporadic colorectal cancers: a French case-controlled genetic association study. [Relationship between genetic polymorphisms of phase I and phase II metabolizing enzymes and DNA damage of workers exposed to vinyl chloride monomer]. Serum bilirubin levels on ICU admission are associated with ARDS development and mortality in sepsis. Pazopanib-induced hyp...
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18067C>T possibly related to non-Hodgkin lymphoma rs2040639-AG, contribute to oral cancer risk. pseudo-haplotype with AG-CC genotypes in *2.45x risk rs2040639-rs861539 *5.03x risk rs2040639-rs861539-rs2075685 *10.10x risk rs2040639-rs861539-rs2075685-rs1799782 rs4880(C;T) prostate cancer patients being treated by radiation therapy are more likely (8% compared to 0%, p=0.02) to exhibit a significant increase in grade 2 late rectal bleeding after irradiation than (C;C) or (T;T) patients, based on a study of 135 patients. The odds for this are worse if the patient also has the rs861539(C;T) genotype (14% vs 1%, p=0.002). [OMIM:?]
complex; see details
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rs1143634, also known as +3954, is a SNP in the IL-1 beta IL1B gene. A study of 556 adults in the Western Australian coronary heart disease (CHD) population concluded that rs1143634(T;T) homozygotes had larger waist circumference, by 1.8cm on average, compared to major allele (C;C) homozygotes. This association was even more pronounced in patients with higher levels of obesity or inflammatory markers. rs1143634 increases susceptibility to Alopecia Areata 2.67 times for heterozygotes (CT) and 1.13 times for homozygotes (TT) rs1143634 increases susceptibility to Alzheimer's disease 2.33 times for homozygotes (TT) rs1143634 increases susceptibility to Cervical lesions, low-grade squamous intraepithelial lesions 4.29 times for heterozygotes (CT) and 3.57 times for homozygotes (TT) rs1143634 in...
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colorectal cancer (-93G>A, rs1800734) 1,518 patients with CRC, homozygosity for the MLH1 -93A variant was associated with a significantly increased 3-fold risk of CRC negative for MLH1 protein by immunohistochemistry (odds ratio (OR): AA vs GG = 3.30, 95% CI 1.46-7.47, n = 1392, p = 0.004, MLH1 negative vs MLH1 positive CRC) and with a 68% excess of proximal CRC (OR: AA vs GG=1.68, 95% confidence interval (CI) 1.00-2.83, n = 1,518, p = 0.05, proximal vs distal CRC) [PharmGKB:Curated This promoter variant is a risk allele for the development of cancer after methylating chemotherapy for Hodgkin lymphoma.] [OMIM:MutL, E. COLI, HOMOLOG OF, 1; MLH1]
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[PharmGKB:Curated Risk or phenotype-associated allele: T Phenotype: The PPAR delta SNP rs3734254 C>T was associated with positive clincial response (partial or complete response) to treatment. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.0089 Type of association: PD; CO]
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The IL10 C627A polymorphism in the anti-inflammatory Interleukin 10 gene decreases gene transcription. Effect of Interleukin-10 Gene Polymorphisms on Clinical Outcome of Patients with Aggressive Non-Hodgkin's Lymphoma. An exploratory study with negative results. rs1800872(A) carriers were 3x more likely to have their pregnancies terminate early (<10 weeks) than (C) carriers, based on a study of ~500 pregnancies. Gene-environment interaction effects on the development of immune responses in the 1st year of life. Cytokine polymorphisms in the Th1/Th2 pathway and susceptibility to non-Hodgkin lymphoma. Asthma families show transmission disequilibrium of gene variants in the vitamin D metabolism and signalling pathway. The interferon gamma gene polymorphism +874 A/T is associated with...
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[PharmGKB:Curated Association studies with cancer, BMI, and asthma.]
0.5x decreased risk for endometriosis
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rs1800871(C) carriers are associated with a reduced endometriosis risk by approximately 2x compared with the common rs1800871(T;T) genotype in a study of 196 Chinese patients. rs2222202 (C/T) (p=0.03) and rs1800871 (C/T) (p=0.05) showed significant allelic associations with pediatric onset Crohn's disease. rs1800871(T) carriers were 3x more likely to have their pregnancies terminate early (<10 weeks) than (C) carriers, based on a study of ~500 pregnancies. In a study of 1,757 cases of Alzheimer's disease and 6,295 controls, an interaction was replicated between IL6 genotype rs2069837(A;A) and IL10 genotype rs1800871(C;C). The synergy factor (SF) was 1.63 (CI: 1.10-2.41, p = 0.01), controlling for age, gender and ApoE4 genotype. 23andMe reports that each G allele at rs1800871 is associat...
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Bladder cancer predisposition: a multigenic approach to DNA-repair and cell-cycle-control genes. Genetic susceptibility to renal cell carcinoma: the role of DNA double-strand break repair pathway. Associations between single nucleotide polymorphisms in double-stranded DNA repair pathway genes and familial breast cancer. Disease-associated mutations that alter the RNA structural ensemble. DNA repair gene and MTHFR gene polymorphisms as prognostic markers in locally advanced adenocarcinoma of the esophagus or stomach treated with cisplatin and 5-fluorouracil-based neoadjuvant chemotherapy.
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Associated with bipolar disorder in individuals of African ancestry.
Frequency: 33.6%
References:9
References:9
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[OMIM:COMPLEMENT FACTOR H-RELATED 3; CFHR3] [GWAS:Age-related macular degeneration]
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rs2234693 is a SNP upstream of the estrogen alpha receptor ESR1 gene, and is sometimes referred to as the -397T>C variation. rs2234693 rs9340799 and rs1256049 variations in ESR1 gene, in addition to the age of a woman, may predict the COH outcome in in vitro fertilization A study of 6,200+ Dutch individuals did not replicate previously reported associations between this SNP (rs2234693) and risk of ischemic stroke rs2234693(C;C)more frequent in African American schizophrenics (p=0.01 to 0.001). haplotype less common in schizophrenia rs2273206(T), rs2273207(G), rs2228480(G). Oestrogen receptor alpha gene haplotype and postmenopausal breast cancer risk: a case control study. Differential genetic effects of ESR1 gene polymorphisms on osteoporosis outcomes. Estrogen receptor alpha gene varia...
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[PharmGKB:Curated In a study of ovarian cancer patients (n=104) receiving a cisplatin-cyclophosphamide regimen, the T/T genotype of GSTA1:(-69)C>T polymorphism was associated with increased overall survival.]
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rs4410790 and rs2470893 influences habitual caffeine consumption [GWAS:None]
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rs4796793, a SNP in the 5' region of the signal transducer and activator 3 STAT3 gene, has been linked in a study of 75 Japanese patients to (successful) response to interferon-alpha immunotherapy for metastatic kidney cancer. From this paper : '... rs4796793 was the most significant predictor of IFN-alpha response (odds ratio [OR] = 2.73; 95% CI, 1.38 to 5.78). The highest OR was shown in the (C;C) genotype ... compared to the (G;G) + (G;C) genotypes (OR = 8.38, 95% CI, 1.63 to 42.96).' [PharmGKB:Curated Risk or phenotype-associated allele: C Phenotype: Metastatic renal cell carcinoma patients with the CC genotype of STAT3 rs4796793 were more likely to respond to interferon alpha therapy than those with the GC or GG genotype. Study size: 75 (29 responders and 46 non-responders). Study po...
normal
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A significant association between delusions and the rs6494223(T) allele (odds ratio 1.63, CI: 1.22-2.17, p = 0.014, ) was found in a cohort of Alzheimer's disease patients in Northern Ireland.
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[PharmGKB:Curated This study investigated aldosterone response to two antihypertensive drugs with the result that the existence of one or more variants in the KNG1gene influences interindividual variation in aldosterone response. The SNPs rs5030062 and rs698078 were significantly associated in European-American responders to the diuretic (p=0.05 and p=0.01) and European-American responders to the angiotensin receptor blocker (p=0.04 and p=0.02).]
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[PharmGKB:Curated Risk or phenotype-associated allele: GG genotype Phenotype: Using a Quantitative Transmission Disequilibrium Test (QTDT), this variant was significantly associated with increased gene expression of IL1B (P = 7 ? 10?7) and etoposide toxicity based upon IC50 values in cell lines from 30 parent-child trios. In combination, rs10018204, rs11222869, rs16965867, rs1846644, and rs6539870 were significant predictors of etoposide IC50, accounting for 55% of the etoposide IC50 variation in Caucasians. Study size: 87. Study population/ethnicity: 87 European descent Caucasians. Significance metric(s): p = 0.00002. Type of association: FA; GN.]
Frequency: 34.5%
References:8
References:8
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the T allele of SNP rs1617640 in the promoter of the EPO gene is significantly associated with Proliferative diabetic retinopathy (PDR) and end stage renal disease (ESRD). The EPO concentration in human vitreous body was 7.5-fold higher in normal subjects with the TT risk genotype than in those with the GG genotype. [PharmGKB:Curated SNP is significantly associated with proliferative diabetic retinopathy and end stage renal disease.] [OMIM:ERYTHROPOIETIN; EPO]
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rs1741981 and rs2547547 influence risk for postoperative hepatocellular carcinoma tumor recurrence up to 2.2x Detection of fetomaternal genotype associations in early-onset disorders: evaluation of different methods and their application to childhood leukemia.
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Association between ADORA2A and DRD2 polymorphisms and caffeine-induced anxiety. Adenosine A(2A) receptor gene (ADORA2A) variants may increase autistic symptoms and anxiety in autism spectrum disorder. [PharmGKB:Curated Risk or phenotype-associated allele: rs2236624 T allele. Phenotype: Carriers of 1 or 2 copies of the T allele for rs2236624 showed increased risk of any (OR = 2.73, CI 1.4-5.39, p = 0.002) or gastrointestinal-specific (OR = 2.7, CI = 1.02-7.49, p = 0.04) adverse events. Study size: 309 RA patients, including 147 good MTX responders, 101 MTX inefficacy failures, and 61 adverse event (AE) MTX failures (e.g. gastrointestinal (n = 24), abnormal liver function tests (n = 20), haematological (n = 7), skin rashes (n = 6), and other (n = 17). Study population/ethnicity: Rheumatoid...
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[PharmGKB:Curated Risk or phenotype-associated allele: T. Phenotype: This SNP was associated with increased risk of myelosuppression in cancer patients treated with irinotecan. Study size: 108. Study population/ethnicity: Japanese patients with neoplasms; Japan. Significance metric(s): p = 0.036. Type of association: PK; CO.]
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linked to blindness in old age rs3753394 carries a significantly increased risk for exudative AMD. linked to rs3753394, rs800292, rs1061147, rs1061170, rs380390, and rs1329428 Significant associations were detected for AMD with rs3753394 rs800292 rs1329428 A haplotype of rs1061170 rs3753394 rs800292 rs1329428 (TGTC) was found to confer a significantly increased likelihood of exudative AMD CFH variations appear to contribute to ARMD in Caucasians, but not in Japanese Multiple gene polymorphisms in the complement factor h gene are associated with exudative age-related macular degeneration in chinese. Plasma therapy in atypical haemolytic uremic syndrome: lessons from a family with a factor H mutation. Association analysis of CFH, C2, BF, and HTRA1 gene polymorphisms in Chinese patients with ...
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[PharmGKB:Curated SNP is associated with the onset of toxicity to methotrexate in patients with psoriasis.]
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[PharmGKB:Curated UGT1A7:-57T>G increases risk of anemia in irinotecan-treated patients.]
normal
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23andMe blog rs8034191(C;C) decreased response to alcohol rs8034191 increases susceptibility to Lung cancer 1.27 times for heterozygotes (CT) and 1.80 times for homozygotes (CC) rs8034191 increases susceptibility to Lung cancer 1.28 times for heterozygotes (CT) and 1.81 times for homozygotes (CC) [PharmGKB:Non-Curated GWAS results: Familial Aggregation of Common Sequence Variants on 15q24-25.1 in Lung Cancer. (Initial Sample Size: 194 cases, 219 controls; Replication Sample Size: 3,878 cases, 4,831 controls); (Region: 15q25.1; Reported Gene(s): LOC123688, PSMA4, CHRNA3, CHRNA5, CHRNB4; Risk Allele: rs8034191-G); (p-value= 0.00000001).This variant is associated with Lung cancer.] [OMIM:LUNG CANCER SUSCEPTIBILITY 2; LNCR2] [GWAS:Lung cancer] [GWAS:Lung cancer]
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[PharmGKB:In-Depth Associated with response to bronchodilators]
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[GWAS:Treatment response to citalopram]
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Epistatic and pleiotropic effects of polymorphisms in the fibrinogen and coagulation factor XIII genes on plasma fibrinogen concentration, fibrin gel structure and risk of myocardial infarction. Sickle cell leg ulcers: associations with haemolysis and SNPs in Klotho, TEK and genes of the TGF-beta/BMP pathway. Comparison of PrASE and Pyrosequencing for SNP Genotyping. The association between fibrinogen haplotypes and myocardial infarction in men is partly mediated through pleiotropic effects on the serum IL-6 concentration. Genetics of atherothrombotic and lacunar stroke. Use of genome-wide expression data to mine the 'Gray Zone' of GWA studies leads to novel candidate obesity genes. Pharmacogenetic aspects in therapeutic management of subfoveal choroidal neovascularisation: role of factor ...
Frequency: 35.4%
References:5
References:5
Frequency: 35.4%
References:1
References:1
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[PharmGKB:Curated Associations were found between LTC4S (rs730012) and LTA4H (rs2660845) and exacerbation rates in asthma patients treated with montelukast.] [OMIM:LEUKOTRIENE A4 HYDROLASE; LTA4H]
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[PharmGKB:Curated Risk or phenotype-associated allele: G. Phenotype: The variant 146GG genotype was associated with increased exposure to doxorubicin and its active metabolite doxorubicinol. Study size: 62. Study population/ethnicity: Patients with Breast Neoplasms receiving adjuvant doxorubicin; Asian; Singapore. Type of association: PK.]
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[PharmGKB:Curated Risk or phenotype-associated allele: G. Phenotype: There was a trend toward an association between the CBR3 V244M polymorphism and the risk of CHF. Study size: 145. Study population/ethnicity: Nested case-control study was conducted within a cohort of 1979 patients enrolled in the Childhood Cancer Survivor Study who received treatment with anthracyclines and had available DNA. Significance metric(s): OR = 8.16, p = 0.056 (G/G vs A/A); OR = 5.44, p = 0.092 (G/A vs A/A). Type of association: CO; TOX; ADR.]
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[PharmGKB:Curated This promoter variant is associated with increased risk for nasopharyngeal carcinoma in chinese population.]
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23andMe blog Influences QT interval [PharmGKB:Curated Associated with altered myocardial repolarization.] [GWAS:Electrocardiographic traits]
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rs2297404, rs2230808, and rs2020927 haplotype (CAC) was more prevalent in the Alzheimer's disease group (0.323 in AD vs. 0.202 in control); while haplotype1 (TGG) was over-represented in the healthy controls (0.595 in control vs. 0.493 in AD) ABCA1 modulates CSF cholesterol levels and influences the age at onset of Alzheimer's disease. ABCA1 polymorphisms and Alzheimer's disease. Apolipoprotein E levels in cerebrospinal fluid and the effects of ABCA1 polymorphisms. The effect of ABCA1 gene polymorphisms on ischaemic stroke risk and relationship with lipid profile. Genetic-epidemiological evidence on genes associated with HDL cholesterol levels: a systematic in-depth review. A survey of ABCA1 sequence variation confirms association with dementia. A polymorphism of the ABCA1 gene confers sus...
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[PharmGKB:Curated The C allele of this variant is associated with increased response of patients with bipolar disorder to lithium treatment relative to that observed in patients carrying two copies of the T allele. This association was seen in one cohort of 161 patients, but not in a separate cohort of 197 patients.]
depends on [[rs1801252]]
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Also known as Arg389, variation at this SNP, located in the ADRB1 gene, may encode either the amino acid glycine or arginine at amino acid position 389 of the corresponding protein, the beta-1 adrenergic receptor (hence why it is frequently called Arg389Gly). This protein is the target of beta blocker drugs, and so how well the drug works to help lower a patients high blood pressure depends in part on this SNP. The status of this SNP is often reported together with the status of SNP rs1801252, which encodes an amino acid variant at position 49 of the same (ADRB1) protein. The rs1801253(G) allele encodes the glycine. One of the best known studies of the effects of these 2 separate SNPs on the average efficacy of the beta blocker metoprolol in lowering blood pressure (BP) can be summarized f...
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Association of genetic variation in cannabinoid mechanisms and gastric motor functions and satiation in overweight and obesity. Pharmacogenetic trial of a cannabinoid agonist shows reduced fasting colonic motility in patients with nonconstipated irritable bowel syndrome. Randomized pharmacodynamic and pharmacogenetic trial of dronabinol effects on colon transit in irritable bowel syndrome-diarrhea.
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A US study of 1,172 lymphoma patients and 982 controls looked at 57 SNPs in 36 immune function genes. Five SNPs in two cytokine genes, tumor necrosis factor-alpha and lymphotoxin-alpha, were associated with a 1.31x increase in non-Hodgkin lymphoma (OR, 1.31; 95% CI, 1.06-1.63; P = 0.01) and with a 1.64x increase in the subtype known as diffuse large B cell lymphoma (OR, 1.64; 95% CI, 1.23-2.19; P = 0.0007). The other four SNPS are listed below. The cytokine genes affect inflammatory and innate immune responses. * rs1800629 * rs361525 * rs1799724 * rs2239704 [PharmGKB:Curated Risk or phenotype-associated allele, tested allele: unspecified; minor allele designation varies by ethnicity in dbSNP Phenotype: In 114 cases and 414 controls (n = 528), univariate analysis of disease association sho...
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Polymorphisms in the glutamate transporter gene SLC1A1 and obsessive-compulsive symptoms induced by second-generation antipsychotic agents. [PharmGKB:Curated Risk or phenotype-associated variant: C. Phenotype: The A/C/G haplotype at rs2228622-rs3780413-rs3780412 showed a significant association with atypical antipsychotic-induced obsessive compulsive symptoms. Study size: 94. Study population/ethnicity: Patients with schizophrenia receiving atypical antipsychotics; Asian; Korea. Significance metric(s): p = 0.04. Type of association: CO.]
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Variants in the vitamin D receptor gene and asthma. Asthma families show transmission disequilibrium of gene variants in the vitamin D metabolism and signalling pathway. Genetic and environmental determinants of 25-hydroxyvitamin D and 1,25-dihydroxyvitamin D levels in Hispanic and African Americans. Vitamin D pathway gene variants and prostate cancer risk. Association study between vitamin D receptor gene polymorphisms and asthma in the Chinese Han population: a case-control study. Overview of the Rapid Response data. Vitamin D pathway gene variants and prostate cancer prognosis. Vitamin D receptor gene polymorphisms are associated with adiposity phenotypes. [PharmGKB:In-Depth Associated with susceptibility to asthma in both children and adults.]
Frequency: 37.2%
References:1
References:1
Frequency: 37.2%
References:1
References:1
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Gene-smoking interaction associations for the ERCC1 polymorphisms in the risk of lung cancer. Genetic polymorphisms in the nucleotide excision repair pathway and lung cancer risk: a meta-analysis. A distinct ERCC1 haplotype is associated with mRNA expression levels in prostate cancer patients. Polymorphisms in DNA repair genes, smoking, and pancreatic adenocarcinoma risk. Genotypes and haplotypes of ERCC1 and ERCC2/XPD genes predict levels of benzo[a]pyrene diol epoxide-induced DNA adducts in cultured primary lymphocytes from healthy individuals: a genotype-phenotype correlation analysis. International Lung Cancer Consortium: pooled analysis of sequence variants in DNA repair and cell cycle pathways. Effects of excision repair cross-complementation group 1 (ERCC1) single nucleotide polymor...
Frequency: 37.2%
References:1
References:1
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[PharmGKB:Curated SNP is associated with clinical reponse to methotrexate in patients with psoriasis.]
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rs20455, often called Arg719 or 719Arg, is a reasonably well studied SNP in the KIF6 gene. The risk allele (encoding the arginine at position 719) is rs20455(C). An extensive 2010 meta-analysis, including over 17,000 patients, suggests this variant does not significantly influence coronary artery disease risk. This SNP is one of the 5 used by Celera's genetic risk score (GRS) for coronary heart disease (CHD). *rs20455, in the KIF6 gene *rs3900940, in the MYH15 gene *rs7439293, in the PALLD gene *rs2298566, in the SNX19 gene *rs1010, in the VAMP8 gene For each of the five variants, the GRS was increased by 1 if the subject was homozygous for the risk variant, unchanged if heterozygous, and decreased by 1 if the individual did not carry the variant. Therefore, individuals carrying all 10 pos...
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[PharmGKB:Curated This variant is in intron 4 of PICK1 and has been significantly associated with methamphetamine abusers with spontaneous relapse of psychosis.]
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[GWAS:None]
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[PharmGKB:Curated This study investigated aldosterone response to two antihypertensive drugs with the result that the existence of one or more variants in the KNG1gene influences interindividual variation in aldosterone response. The SNPs rs5030062 and rs698078 were significantly associated in European-American responders to the diuretic (p=0.05 and p=0.01) and European-American responders to the angiotensin receptor blocker (p=0.04 and p=0.02).] [GWAS:Blood metabolite levels]
normal risk of hypertension
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rs699 is a SNP in the angiotensin AGT gene that encodes a functional change. In most published literature, the name for this SNP is M235T, or perhaps Met235Thr, however its amino acid 268 (not 235) that varies based on the numbering in todays databases. rs699 is also occasionally known as C4072T. In any case, the rs699(C) allele encodes the threonine variant, which is associated with higher plasma angiotensin levels, and ultimately higher blood pressure leading to increased risk for hypertension associated disorders. This association was first reported in 1992 , and many studies, though not all, have replicated these findings. rs699 is also (generally) reported to be in tight linkage with rs5051, a neighboring SNP in the promoter of the AGT gene. rs699(C) has also been implicated as a risk...
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[PharmGKB:Curated This variant is significantly associated with the efficacy of anti-TNF treatment in rheumatoid arthritis (Adjusted P-value: 0.000006; OR: 3.6 (1.5, 9.3)). The study is a genome-wide association study using the Illumina HapMap300 SNP chip on 89 RA patients prospectively followed after beginning of anti-TNF therapy.]
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[PharmGKB:Non-Curated This variant is significantly associated with the efficacy of anti-TNF treatment in rheumatoid arthritis (Adjusted P-value: 0.000002; OR: 4.6 (1.8, 12.3)). The study is a genome-wide association study using the Illumina HapMap300 SNP chip on 89 RA patients prospectively followed after beginning of anti-TNF therapy.] [GWAS:Treatment response to TNF antagonists]
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rs2227956 in HSP70-hom, resulted in a significant association with noise-induced hearing loss [PharmGKB:Curated The C allele of this SNP is part of a haplotype that has been associated with protection from hypersensitivity to carbamazepine.] [OMIM:?]
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[GWAS:None]
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[GWAS:Response to methotrexate in rheumatoid arthritis]
more resistant to treatment for depression
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Based on a study of 256 Caucasian patients being treated for depression, carriers of a rs1049353(G) allele were less likely to respond favorably, particularly if they were females with comorbid anxiety. rs806368(C) together with rs1049353(A) or rs1049353(G) make up a haplotype associated with PTSD, with the C-A haplotype somewhat associated (p=0.04) with higher risk of PTSD and the C-G haplotype associated (p=0.01) with a lower risk of PTSD. Cannabis receptor haplotype associated with fewer cannabis dependence symptoms in adolescents. No evidence for an involvement of variants in the cannabinoid receptor gene (CNR1) in obesity in German children and adolescents. The G1422A variant of the cannabinoid receptor gene (CNR1) is associated with abdominal adiposity in obese men. No association of...
Frequency: 38.1%
References:1
References:1
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[GWAS:None]
Frequency: 38.1%
References:7
References:7
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[PharmGKB:Curated This SNP is the tagging SNP for VKORC1*4.]
Adverse reaction more likely to carbamazepine in epileptic patients
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rs2273697, also known as c1249G>A or p.V471I, is a nonsynonymous polymorphism in the ABCC2 gene. From an initial case-control study of 146 patients with epilepsy, followed by replication (p=0.001) in another 279 patients, the rs2273697(A) allele was associated with neurological adverse drug reactions from taking carbamazepine. Functional studies showed that this SNP selectively reduced carbamazepine transport across the cell membrane. [PharmGKB:Curated Risk or phenotype-associated allele: A. Phenotype: This SNP showed a strong association with the neurological adverse drug reaction caused (ADR) by carbamazepine (P=0.005). The study results indicate that the c.1249A variant is an independent risk factor of carbamazepine CNS ADR. Study size: 146 patients with epilepsy who had been prescr...
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rs4646(A) allele carriers with breast cancer being treated with letrozole are reported to do worse than rs4646(C;C) patients, based on a study of (only) 95 women. [PharmGKB:Curated A study in 67 patients with hormone receptor-positive metastatic breast cancer treated with letrozole, the presence of this SNP in the 3' untranslated region of the CYP19A1 gene is associated with improved treatment efficacy.]
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[PharmGKB:Curated No association with cardiovascular disease, breast cancer, or lipoprotein levels.]
Frequency: 38.4%
References:2
References:2
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age related macular degeneration [OMIM:COMPLEMENT FACTOR H-RELATED 3; CFHR3] [GWAS:Age-related macular degeneration]
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[PharmGKB:Curated SNP influences the efficacy of methotrexate in patients with psoriasis.]
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[PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: The PPAR delta SNP rs1883322 A>G was associated with positive clincial response (partial or complete response) to treatment. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.0061 Type of association: PD; CO]
normal
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827 males and 709 females, 606 subjects without cancer and 930 subjects with various cancers *rs1041981(A;C) (C804A, T60N) associated with lung cancer (CA + AA: CC, adjusted OR = 0.60, 95% CI = 0.37 - 0.97), in males but not in females [OMIM:MYOCARDIAL INFARCTION, SUSCEPTIBILITY TO]
Frequency: 39.8%
References:6
References:6
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[PharmGKB:Curated In a GWAS study, this SNP accounted for ~25% of the variance in log-transformed stabilized warfarin dose, and was in perfect linkage disequilibrium with rs9923231 (VKORC1:-1639).] [GWAS:Warfarin maintenance dose]
Frequency: 39.8%
References:4
References:4
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[PharmGKB:Non-Curated This variant is significantly associated with the efficacy of anti-TNF treatment in rheumatoid arthritis (Adjusted P-value: 0.0000003; OR: 4.6 (1.8, 12.3)). The study is a genome-wide association study using the Illumina HapMap300 SNP chip on 89 RA patients prospectively followed after beginning of anti-TNF therapy.] [GWAS:Treatment response to TNF antagonists]
1.2x increased risk for type-2 diabetes
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rs1470579 replicated as significant for type-2 diabetes risk in 1,900 Japanese patients, with odds ratio of 1.18 (CI: 1.07-1.31, p = 8.3 x 10e-4) T2D and normal glucose tolerant (NGT) individuals. (3,295 T2D and 3,595 NGT), strong associations with T2D were found for *CDKAL1 (OR(rs7756992) = 1.30[1.19-1.42], P = 2.3x10(-9)) *CDKN2A/2B (OR(rs10811661) = 0.74[0.66-0.82], P = 3.5x10(-8)) *IGFBP2 (OR(rs1470579) = 1.17[1.07-1.27], P = 0.0003) SNPs. T2D risk increased strongly when risk alleles, including the previously discovered T2D-associated TCF7L2 rs7903146 SNP, were combined (8.68-fold for the 14% of French individuals carrying 18 to 30 risk alleles with an allelic OR of 1.24) Neither rs4402960 or rs1470579 were found to be associated with type-2 diabetes in a study of 3,000 French Caucasi...
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[PharmGKB:Curated This SNP is the tagging SNP for VKORC1*2.]
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[GWAS:None]
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Risk alleles for multiple sclerosis identified by a genomewide study. [GWAS:None]
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Pharmacokinetics of efavirenz when co-administered with rifampin in TB/HIV co-infected patients: pharmacogenetic effect of CYP2B6 variation. The pharmacokinetics and pharmacogenomics of efavirenz and lopinavir/ritonavir in HIV-infected persons requiring hemodialysis. Polymorphisms of drug-metabolizing enzymes (GST, CYP2B6 and CYP3A) affect the pharmacokinetics of thiotepa and tepa. The impact of cytokines on the expression of drug transporters, cytochrome P450 enzymes and chemokine receptors in human PBMC. Associations between CYP2B6 polymorphisms and pharmacokinetics after a single dose of nevirapine or efavirenz in African americans. CYP2B6 (c.516G-->T) and CYP2A6 (*9B and/or *17) polymorphisms are independent predictors of efavirenz plasma concentrations in HIV-infected patients. CYP...
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[GWAS:Type 2 diabetes]
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Variants in the vitamin D receptor gene and asthma. Vitamin D receptor polymorphisms are associated with Graves' disease in German and Polish but not in Serbian patients. Asthma families show transmission disequilibrium of gene variants in the vitamin D metabolism and signalling pathway. Polymorphisms in the vitamin D receptor and their associations with risk of schizophrenia and selected anthropometric measures. Vitamin D pathway gene polymorphisms, diet, and risk of postmenopausal breast cancer: a nested case-control study. Optimization of candidate-gene SNP-genotyping by flexible oligonucleotide microarrays; analyzing variations in immune regulator genes of hay-fever samples. Vitamin D receptor gene (VDR) associations with cancer. Genome-wide association with bone mass and geometry in t...
normal
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A study of 733 breast cancer cases for 10 SNPs concluded that the rs1501299(C;C) genotype (in dbSNP orientation) was at increased risk (odds ratio 1.80, CI: 1.14 - 2.85). After categorizing individuals by adiponectin signaling status, this study found that compared with high signalers, intermediate signalers had a 4.16-fold increase in breast cancer risk (CI: 0.49-35.19), and low signalers had a 6.56x higher breast cancer risk (CI: 0.78-54.89, p(trend) = 0.001). Adiponectin signaling status was assigned as follows: rs1501299(G,G) + rs2241766(T,T) = low signaler<br> rs1501299(G,T) + rs2241766(T,T) = low signaler<br> rs1501299(G,G) + rs2241766(G,T) = low signaler<br> rs1501299(T,T) + rs2241766(T,T) = intermediate signaler<br> rs1501299(G,T) + rs2241766(G,T) = intermed...
higher blood pressure if <50
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rs8192678 encodes a SNP also known as Gly482Ser; the (A) allele encodes the Ser. Some reports have linked this SNP to risk for hypertension and systolic blood pressure (SBP). However, a meta-analysis of 13,000+ individuals did not find any such association. However, gene-age interaction was apparent. For diastolic blood pressure (DBP), p(interaction)<0.0001; for systolic BP, p(interaction)=0.026. In younger individuals (<50yrs; n=2511) the rs8192678(A) allele was associated with higher DBP (p=4.2 x 10<sup>-12</sup>) and SBP (p=7.2 x 10<sup>-12</sup>), but no association was evident for individuals over 50yrs (n=5088). Analysis of PGC-1alpha variants Gly482Ser and Thr612Met concerning their PPARgamma2-coactivation function. PPARGC1A coding variation may initiat...
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origins blog rs833070 and rs2146323. Individuals with the CC genotype at rs833070 and rs2146323 displayed smaller hippocampal volumes than T-allele and A-allele carriers, respectively. bdmh2 blog coverage of rs833070 and rs2146323
Frequency: 40.2%
Repute:Bad
References:5
Repute:Bad
References:5
1.19x increased risk for T2D
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rs11868035 is one of several SNPs associated with the SREBF1 gene that show a modest association with type-2 diabetes. A study of ~2,000 Caucasian patients (and 10,000+ controls) led to an odds ratio of 1.19 (CI: 1.07-1.33, p=0.002) for the minor (risk) allele, rs11868035(A), in the orientation as in dbSNP. type-2 diabetes rs2297508(C) and rs11868035(C) This SNP rs11868035 and rs1057217 are associated with increased risk of schizophrenia in German and Scandinavian samples. This SNP and rs6812193 are reported to affect risk of Parkinson's disease. plos Polymorphisms in the gene encoding sterol regulatory element-binding factor-1c are associated with type 2 diabetes. [PharmGKB:Curated This SNP in the SREBF1 gene was strongly associated with schizophrenia in German, Danish and Norwegian samp...
normal
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rs1042713, also known as Arg16, G16R, and 16Arg>Gly, is a SNP in the adrenergic, beta-2-, surface receptor ADRB2 gene. The rs1042713(G) allele encodes the G/glycine form that is the more common one in most populations, while rs1042713(A) encodes the R/arginine residue at this position of the ADRB2 protein. A study of 1,182 young Scottish asthma patients (age, 3-22 years) concluded that rs1042713(A) alleles are significantly associated with 'exacerbations' of their condition, regardless of treatment regimens (odds ratio 1.30, CI: 1.09-1.55, p=0.003). This didn't hold true for patients using inhalers less than once per day; and it was particularly true for those receiving daily inhaled long- or short-acting beta(2)-agonist treatment (OR, 1.64, CI: 1.22-2.20, p=.001). This may therefore in...
Normal risk for cutaneous melanoma
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rs13181 is a SNP of the XPD/ERCC2 gene. A meta-analysis of 20 studies, comprising 2,308 cases, ultimately concluded that the rs13181(G) allele is associated with increased cutaneous melanoma risk (odds ratio 1.12, CI: 1.03-1.21, p = 0.01; population attributable risk = 9.6%). Polymorphisms in XPD and TP53 and mutation in human lung cancer. Decision forest analysis of 61 single nucleotide polymorphisms in a case-control study of esophageal cancer; a novel method. ERCC1 and ERCC2 polymorphisms and adult glioma. [Correlation of genetic polymorphisms in nucleotide excision repair system to sensitivity of advanced non-small cell lung cancer patients to platinum-based chemotherapy]. Bladder cancer predisposition: a multigenic approach to DNA-repair and cell-cycle-control genes. Risk of non-Hodgk...
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risk of the development of substance dependence significantly increased with the number of 'G' alleles at rs6454674 and SNP8 (rs806368);T/T genotypes had significant interaction effects (p = .0003 for comorbid drug dependence (DD) and alcohol dependence (AD), .0002 for DD, and .007 for AD). SNP3 and SNP8 together exerted stronger genetic effects on SD (substance dependence) than either did individually. The peak delta values among all the markers were seen for SNP3 and SNP8 (rs806368) rs806368(C) together with rs1049353(A) or rs1049353(G) make up a haplotype associated with PTSD, with the C-A haplotype somewhat associated (p=0.04) with higher risk of PTSD and the C-G haplotype associated (p=0.01) with a lower risk of PTSD. Alcoholic patients with TGT haplotype (corresponding to rs6454674-r...
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[GWAS:Capecitabine sensitivity]
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per OMIM, Ma et al. (2005) found two different DDC haplotypes associated with nicotine dependence in African Americans and European Americans (with measures of smoking quantity [SQ], heaviness of smoking index [HSI], and the Fagerstrom test for ND [FTND]) *in African Americans, rs921451(T), rs3735273(G), rs1451371(T), rs2060762(G), all three measures sig. associated after correction for multiple testing *in European Americans, rs921451(T), rs3735273(G), rs1451371(T), rs3757472(G), which showed a sig. assoc. w/ the SQ and FTND score [PharmGKB:Curated In a total of 2037 smokers and non-smokers from 602 nuclear families of African- or European-American ancestry, this SNP in the DDC gene was significantly associated with two of the three adjusted nicotine dependence measures in the European-A...
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[PharmGKB:In-Depth Associated with susceptibility to asthma and bronchodilator response.]
Frequency: 41.1%
References:5
References:5
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rs12762549 and rs11045585 can be used to predict whether docetaxel will induced leukopenia/neutropenia, according to a study of ~100 Japanese patients. When patients were classified into three groups by the scoring system based on the genotypes of these two SNPs, patients with a score of 1 or 2 were shown to have a significantly higher risk of docetaxel-induced leukopenia/neutropenia as compared to those with a score of 0 (P = 0.0000057; odds ratio [OR], 7.00; 95% CI [confidence interval], 2.95-16.59). This prediction system correctly classified 69.2% of severe leukopenia/neutropenia and 75.7% of non-leukopenia/neutropenia into the respective categories. [PharmGKB:Curated In a case control study using samples from BioBank Japan, the G allele of rs12762549 was associated with docetaxel-ind...
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linked to Cardiovascular Events Several CVD risk variants were identified: In women, the combination of F5 rs7542281 × THBD rs1042580, together with three single F5 SNPs, was associated with CVD events. Among men, PROC rs1041296, when combined with either ICAM1 rs5030341 or F5 rs2269648, was associated with total mortality. As a single variant, PROC rs1401296, together with the F5 Leiden mutation, was associated with ischemic stroke events.
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Imputation-based analysis of association studies: candidate regions and quantitative traits. Genetic variants and susceptibility to neurological complications following West Nile virus infection.
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Genetic risk factors for rheumatoid arthritis differ in Caucasian and Korean populations. Association of CD40 with rheumatoid arthritis confirmed in a large UK case-control study. Overlap of disease susceptibility loci for rheumatoid arthritis and juvenile idiopathic arthritis. Genetic variants in the prediction of rheumatoid arthritis. Investigation of rheumatoid arthritis susceptibility genes identifies association of AFF3 and CD226 variants with response to anti-tumour necrosis factor treatment. Endometriosis and autoimmune disease: association of susceptibility to moderate/severe endometriosis with CCL21 and HLA-DRB1. [PharmGKB:Non-Curated GWAS Results: Common variants at CD40 and other loci confer risk of rheumatoid arthritis (Initial Sample Size: 3,393 cases, 12,460 controls; Replic...
Frequency: 41.6%
References:1
References:1
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[PharmGKB:Curated In a study of tamoxifen treated breat cancer patients, carrying the T variant of RRAS2:(-582)C>T was associated with a higher frequency of relapse.]
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obesity and type-2 diabetes *rs1121980 *rs7498665 *rs4752856 *rs17782313 *rs2815752 *rs10938397 Is the thrifty genotype hypothesis supported by evidence based on confirmed type 2 diabetes- and obesity-susceptibility variants? Common body mass index-associated variants confer risk of extreme obesity. Novel obesity risk loci do not determine distribution of body fat depots: a whole-body MRI/MRS study. From monogenic to polygenic obesity: recent advances. A strategy for analyzing gene-nutrient interactions in type 2 diabetes. Obesity and diabetes genes are associated with being born small for gestational age: results from the Auckland Birthweight Collaborative study. FTO and MC4R gene variants are associated with obesity in polycystic ovary syndrome. Genetic predictors of weight loss and weig...
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[GWAS:Asthma (bronchodilator response)]
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Associations between CYP2B6 polymorphisms and pharmacokinetics after a single dose of nevirapine or efavirenz in African americans. Univariate/multivariate genome-wide association scans using data from families and unrelated samples. CYP2B6 variants and plasma efavirenz concentrations during antiretroviral therapy in Port-au-Prince, Haiti. Tests of association for quantitative traits in nuclear families using principal components to correct for population stratification. Family-based bivariate association tests for quantitative traits. A comparative study of three methods for detecting association of quantitative traits in samples of related subjects. Family-based genome-wide association study for simulated data of Framingham Heart Study. The Genetic Analysis Workshop 16 Problem 3: simulat...
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commonly referred to as A218C rs211105, rs1800532 and rs7933505 related to schizophrenia [OMIM:TRYPTOPHAN HYDROXYLASE 1; TPH1]
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[OMIM:?] [GWAS:Systemic lupus erythematosus]
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Current limitations of SNP data from the public domain for studies of complex disorders: a test for ten candidate genes for obesity and osteoporosis. Preparation and analysis of cSNP chip on hepatocellular carcinoma-related genes. Replication of putative candidate-gene associations with rheumatoid arthritis in >4,000 samples from North America and Sweden: association of susceptibility with PTPN22, CTLA4, and PADI4. Optimization of candidate-gene SNP-genotyping by flexible oligonucleotide microarrays; analyzing variations in immune regulator genes of hay-fever samples. Genetic polymorphisms of tumour necrosis factor receptor superfamily 1A and 1B affect responses to infliximab in Japanese patients with Crohn's disease. The tumour necrosis factor receptor superfamily member 1b 676T>G p...
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rs4410790 and rs2470893 influence habitual caffeine consumption Paternal smoking, genetic polymorphisms in CYP1A1 and childhood leukemia risk. Phase I metabolic genes and risk of lung cancer: multiple polymorphisms and mRNA expression. [GWAS:None]
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associated with vulnerability to nicotine addiction in men. g2b2mh blog rs1044396 mediates effects of nicotine self-medication via parietal cortex. subjects with the (T;T) genotype showed robust brain activity in the parietal cortex while subjects with the (C;C) genotype showed very little change in activity. [PharmGKB:Curated This variant is closely linked to rs2236196 and has been associated with the intensification of nicotine dependence.] [OMIM:CHOLINERGIC RECEPTOR, NEURONAL NICOTINIC, ALPHA POLYPEPTIDE 4; CHRNA4]
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[PharmGKB:Curated A study on 50 subjects (25 patients who developed a distinct hearing loss during cisplatin therapy and in 25 patients without hearing impairment after cisplatin therapy)observed a higher frequency of the A-allele of rs2075252 in the LRP2 in the group with hearing impairment than in the group with normal hearing after cisplatin therapy.]
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[PharmGKB:Curated Risk or phenotype-associated allele: A allele. Phenotype: The A allele rs2894342, which lies in the promoter of MLN, is associated with carbamazepine (CBZ)-induced maculopapular exanthema (MPE)/ hypersensitivity syndrome (HSS). Study size: 175. Study population/ethnicity: 31 CBZ-induced MPE/HSS cases and 144 CBZ-tolerant controls of Chinese descent. Significance metric(s): p = 0.00342, OR = 2.88. Type of association: GN; PD; TOX; ADR.]
Frequency: 42.9%
References:4
References:4
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Identification of DIO2 as a new susceptibility locus for symptomatic osteoarthritis. A common variation in deiodinase 1 gene DIO1 is associated with the relative levels of free thyroxine and triiodothyronine. Cellular and molecular basis of deiodinase-regulated thyroid hormone signaling. The -258A/G (SNP rs12885300) polymorphism of the human type 2 deiodinase gene is associated with a shift in the pattern of secretion of thyroid hormones following a TRH-induced acute rise in TSH.
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rs7569963 is directly adjacent to CREB1. Associated with significantly (p = 0.005) increased chance of suicide in a study of 1447 citalopram users (male only subgroup, 539 in total). Two haplotypes (see below) also showed significant association with suicidality in the male subgroup. *rs2709376(C),rs2253206(A),rs7569963(A),rs7594560(T),rs4675690(C) - common haplotype, reduced chance of suicide in males, p = 0.004 *rs2709376(C),rs2253206(A),rs7569963(G),rs7594560(T),rs4675690(T) - increased chance of suicide in males, p = 0.009 [PharmGKB:Curated In a nested case-control study derived from the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) study this SNP in the CREB1 gene was associated with treatment-emergent suicidality among men with depression.]
complex; see details
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rs1800795 is a SNP in the promoter of the interleukin-6 IL6 gene, affecting the levels made of this important cytokine. In the literature, it is almost universally referred to as the IL6 '-174' polymorphism. It tends to be quite polymorphic in Caucasians, but Asian and African populations are almost monomorphic (for the (G) allele). It was first described in 1998, when it was shown that the rs1800795(C) allele produces less IL6 than the (G) allele, which supported the hypothesis that a protective genotype against systemic onset juvenile rheumatoid arthritis would be rs1800795(C;C), and indeed, few juvenile RA patients had that genotype. Studies on rs1800795 now include potential associations with heart disease, Kaposi's sarcoma, type-2 diabetes, stroke, obesity, Hodgkin's lymphoma, sudden ...
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rs1800797, rs1800796 and rs1800795 have been shown to affect both the transcription and secretion of IL-6, to symptomatic distal interphalangeal osteoarthritis based on 535 women. the G alleles of two promoter single-nucleotide polymorphisms (SNP) G-597A and G-174C were more common among the subjects with symptomatic DIP OA than among those with no disease (p-values corrected for multiple testing 0.020 and 0.024). Also, the carriage of at least one G allele in these positions increased the risk of disease (p=0.006 and, p=0.008, respectively). Carrying a haplotype with the G allele in all three promoter SNPs increased the risk of symptomatic DIP OA more than four-fold (OR 4.45, p=0.001). Carriage of the G-G diplotype indicated an increased risk of both symmetrical DIP OA (OR 1.52 95% CI 1.0...
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may influence Parkinson's disease abstract may influence brain structure [OMIM:GLYCOGEN SYNTHASE KINASE 3-BETA; GSK3B]
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Data-mining analysis suggests an epigenetic pathogenesis for type 2 diabetes. Genetic prediction of future type 2 diabetes. Interaction between the UCP2-866G/A, mtDNA 10398G/A and PGC1alpha p.Thr394Thr and p.Gly482Ser polymorphisms in type 2 diabetes susceptibility in North Indian population. Association between obesity and insulin resistance with UCP2-UCP3 gene variants in Spanish children and adolescents. Association of genetic variants with chronic kidney disease in Japanese individuals. Polymorphisms of the UCP2 gene are associated with proliferative diabetic retinopathy in patients with diabetes mellitus. Interaction between the UCP2 -866 G>A polymorphism, diabetes, and beta-blocker use among patients with acute coronary syndromes. Effect of the common -866G/A polymorphism of the u...
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[PharmGKB:Curated This variant is associated with end-of-induction minimal risidual disease (MRD) in childhood acute lymphoblastic leukemia (ALL) from 2 independent cohorts (GWAS result). Risk Allele: A, MAF= 0.25, combined P value= 1.28E-04. It is also associated with greater methotrexate clearance.]
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Polymorphisms in inflammation-related genes are associated with susceptibility to major depression and antidepressant response. A comparison of classification methods for predicting Chronic Fatigue Syndrome based on genetic data. [PharmGKB:Curated This variant is associated with response to escitalopram and nortriptyline in a study of 760 adult patients with moderate-to-severe depression.]
Intermediate risk of low bone mineral density disorders
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rs1544410, also known as the BsmI polymorphism, is a SNP in the Vitamin D receptor (VDR). Multiple studies examining bone mineral density (BMD) in women have associated the A allele with increased risk of low BMD , , & . Additionally, A meta-analysis of 26 studies estimated a decreased risk of osteoporosis associated with the G;G genotype with an odds ratio of 0.61, 95% CI, 0.40-0.92 . rs1544410 increases susceptibility to Shorter stature for carriers of the A allele [PharmGKB:Curated This variant is associated with etidronate response in Caucasian (Slovenian) postmenopausal women (24 patients), with bb genotype associated with lower increase in bone mineral density (BMD) after bisphosphonate treatments.]
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[PharmGKB:Curated SNP is significantly associated with the incidence of biopsyproven acute rejection in the first year post-transplantation in kidney transplant patients.]
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rs731236 protection from breast cancer (OR=0.80, 95%CI=0.64-0.99; p= 0.047) [PharmGKB:Curated This variant was significantly associated with acquired resistance to clodronate treatment in Caucasian patients with Paget's disease of the bone]
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[PharmGKB:Curated This variant in the corticotropin-releasing hormone receptor-2 gene was associated with acute bronchodilator response in the 608-participant Childhood Asthma Management Program (CAMP), but was not found to be associated in the 427-participant Sepracor study or the 152-participant LODO trial. The mean ages of the participants in the CAMP, Sepracor, and Lodo cohorts were 8.9, 32.6, and 42.9 years of age, respectively. Only Caucasians were analyzed in each of these studies.]
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rs1367117 (C711T/711C>T) is a SNP within APOB (Apolipoprotein B). among 97 hypertensive subjects, C allele carriers responded to irbesartan with an average blood pressure reduction of 19 mmHg, however, they did not respond to atenolol associated with apoB levels [PharmGKB:Curated The APOB:711C>T, C allele was associated with reduction of blood pressure in response to irbesartan treatment but not atenolol treatment.] [OMIM:?] [GWAS:None]
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[PharmGKB:Curated lower response allele: C; phenotype: change in interocular pressure; study size: 100; study population: healthy Japanese subjects with no history of eye disease; description: change in interocular pressure: CC, 20.3%±1.5%; CT + TT, 15.6%±1.2%; P = 0.0316; T allele associate with lower transcriptional activity; type of association: CO]
Frequency: 44.0%
References:1
References:1
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[PharmGKB:Curated A study in 121 acutely psychotic patients with DSM-IV schizophrenia receiving treatment with typical antipsychotic medication alone or plus risperidone showed that this variant in the NEF3 gene was associated with early response to the medication.]
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Gene variants associated with deep vein thrombosis. Updated analysis of gene variants associated with deep vein thrombosis. Explaining variability in ciclosporin exposure in adult kidney transplant recipients. Polymorphisms in NF-kappaB, PXR, LXR, PPARgamma and risk of inflammatory bowel disease. Pregnane X receptor (PXR/NR1I2) gene haplotypes modulate susceptibility to inflammatory bowel disease. Variants of the human NR1I2 (PXR) locus in chronic periodontitis.
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[PharmGKB:Curated Associated with several different conditions, particularly among women.]
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Linkage disequilibrium blocks, haplotype structure, and htSNPs of human CYP7A1 gene. Cholesterol 7alpha-hydrolase (CYP7A1) c.-278A>C promoter polymorphism in gallstone disease patients. CYP7A1 (-204 A>C; rs3808607 and -469 T>C; rs3824260) promoter polymorphisms and risk of gallbladder cancer in North Indian population. Promoter variant -204A > C of the cholesterol 7alpha-hydroxylase gene: association with response to plant sterols in humans and increased transcriptional activity in transfected HepG2 cells.
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Comprehensive analysis of the impact of SNPs and CNVs on human microRNAs and their regulatory genes. Tissue effect on genetic control of transcript isoform variation. Fine-scale variation and genetic determinants of alternative splicing across individuals.
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[GWAS:Crohn's disease]
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New atypical antipsychotics for schizophrenia: iloperidone. [PharmGKB:Non-Curated GWAS Results: Whole genome association study identifies polymorphisms associated with QT prolongation during iloperidone treatment of schizophrenia (Initial Sample Size: 183 individuals; Replication Sample Size: NR; Risk Allele: rs993648-T). This variant is associated with Response to iloperidone treatment (QT prolongation).] [GWAS:Response to iloperidone treatment (QT prolongation)]
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Influences ABO blood group ABO Blood Type
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[OMIM:?]
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[PharmGKB:Curated Risk or phenotype-associated allele: not stated Phenotype: Using a Quantitative Transmission Disequilibrium Test (QTDT), this variant was significantly associated with etoposide toxicity based upon IC50 values in cell lines from 30 parent-child trios. Study size: 176. Study population/ethnicity: 87 European descent Caucasians and 89 Yorubans. Significance metric(s): p = 0.00005. Type of association: FA; GN.]
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[PharmGKB:Curated This SNP on chromosome 1 was associated with the susceptibility to daunorubicin-induced cytotoxicity in the YRI population using International HapMap cell lines.]
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[GWAS:Age-related macular degeneration]
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[GWAS:None]
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[GWAS:Metabolite levels]
possibly increased risk for Alzheimers
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rs669 is a SNP in the alpha-2-macroglobulin A2M gene. In dbSNP orientation, the rs669(A) allele encodes an isoleucine, and the rs669(G) allele encodes a valine; the SNP is also known as the Ile/Val variant. On its own, rs669 was not seen to reproducibly and independently increase risk for Alzheimer's disease in several studies of ~200 Italian patients. However, the T-C-A haplotype of rs12316150-rs1050283-rs669 was associated with both early- and late-onset Alzheimer's disease. The majority of the disease risk from this haplotype was based on rs1050283. The original 2004 study of 148 Italian sporadic AD patients yielded an odds ratio for the rs669(G;G) genotype (as oriented in dbSNP orientation) of 3.81 (CI: 1.66-8.75). The presence of rs2333227(C;C), in addition to rs669(G;G), appears to s...
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rs1208 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The risk allele for this SNP is rs1208(G). [PharmGKB:Curated in vitro study; PK: 20-fold reduction in Vmax vs wild type] [OMIM:?]
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[PharmGKB:Non-Curated GWAS results: Genome-wide Linkage and Association Anaylses to Identify Genes Influencing Adiponectin Levels: The GEMS Study. (Initial Sample Size: 997 cases, 989 controls; Replication Sample Size: NR); (Region: 3q27.3; Reported Gene(s): ADIPOQ; Risk Allele: rs6773957-A); (p-value= 0.00000005).This variant is associated with Adiponectin Levels.] [OMIM:?] [GWAS:Adiponectin Levels]
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Identification of genes and haplotypes that predict rheumatoid arthritis using random forests. Polymorphisms in the VEGF-A in polypoidal choroidal vasculopathy in a Korean population.
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Mutational spectrum of the succinate semialdehyde dehydrogenase (ALDH5A1) gene and functional analysis of 27 novel disease-causing mutations in patients with SSADH deficiency. Reduced SSADH activity with T variant (83% of normal). A 77-kilobase region of chromosome 6p22.2 is associated with dyslexia in families from the United Kingdom and from the United States. Comparative genomics of aldehyde dehydrogenase 5a1 (succinate semialdehyde dehydrogenase) and accumulation of gamma-hydroxybutyrate associated with its deficiency.
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Epigenetic regulation of human gamma-glutamyl hydrolase activity in acute lymphoblastic leukemia cells.
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intelligence related [PharmGKB:Curated Several studies showed an associaction of this SNP in DTNBP1 with schizophrenia and other psychotic disorders, including substance-induced psychosis]
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[PharmGKB:Curated Risk or phenotype-associated allele: None. Phenotype: Variants identified in a screen of 13 genes involved in the gemcitabine drug metabolic pathway. For the non-synonymous SLC28A2:283A>C (R75S) SNP, the C (75Ser) allele was at frequency was 0.34 and 0.08 in Europeans and Africans, respectively. There was a significant difference between ethnic groups in genotype frequency distribution (p < 0.001). Study size: 187. Study population/ethnicity: Healthy, unrelated blood donors of European (n = 95) and African (n = 92) descent. Significance metric(s): p < 0.001. Type of association: GN.]
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rs1946518 and rs1946519 may influence cervical cancer
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[GWAS:None]
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rs1051740, also known as Tyr113His, is a SNP in the microsomal epoxide hydrolase EPHX1 gene. severe hypersensitivity syndrome, triggered by carbamazepine in the presence of a concomitant active human herpes virus (HHV) 6 and 7 infection with the allele HLA-A*3101 and rs1051740(C;C) [PharmGKB:Curated Risk or phenotype-associated allele: T. Phenotype: In a logistic regression model adjusted for history of phenytoin use during the first trimester and maternal epilepsy, the maternal EPHX1 113 H (rs1051740 T/C) allele was associated with craniofacial abnormalities in the child. Study size: 157 pregnancies. Study population/ethnicity: phenytoin use during the first trimester and maternal epilepsy. metric(s): per rare allele OR: 2.43, 95% confidence interval (CI): 1.16-5.10, P=0.02. Type of asso...
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[PharmGKB:Curated Risk or phenotype-associated allele: undetermined. Phenotype: The variant allele was not associated with warfarin maintenance dose variability (p = 0.7123). Study size: 283. Study population/ethnicity: Hospitalized Caucasian patients aged 75 years or older, recruited Sep 2002-Nov 2004 in Ivry, France, and Oct 2005-Mar 2008 from 14 French centers. Significance metric(s): not significant. Type of association: GN; PK.]
1.4x increased gastric cancer risk. Increased risk of Acute Graft-Versus-Host Disease after Unrelated Bone Marrow Transplantation
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rs2275913, also known as G-197A, is a SNP in the IL17A gene. A study of 811 Japanese subjects (524 without gastric cancer and 287 with gastric cancer) reported an odds ratio of 1.42 (CI: 1.09-1.85, p=0.01) for the rs2275913(A) allele, and 3.02 (CI: 1.86-4.91, p<0.0001) for the (A;A) genotype, with gastric cancer. This 'A'-allele of this SNP is also functionally associated with acute Graft-Versus-Host Disease after unrelated bone marrow transplantation
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Gene expression and association analyses of LIM (PDLIM5) in bipolar disorder and schizophrenia. A polymorphism in the PDLIM5 gene associated with gene expression and schizophrenia. Genetic correlates of brain aging on MRI and cognitive test measures: a genome-wide association and linkage analysis in the Framingham Study. Positive association between PDLIM5 and schizophrenia in the Chinese Han population. A major single nucleotide polymorphism of the PDLIM5 gene associated with recurrent major depressive disorder. PDLIM5 and susceptibility to bipolar disorder: a family-based association study and meta-analysis. A case-control association study of the PDLIM5 gene and bipolar disorder in a Sardinian sample.
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G-protein-coupled receptor kinase 4 polymorphisms and blood pressure response to metoprolol among African Americans: sex-specificity and interactions.
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This is one of the SNPs reported by NutraHacker.
multiple associations, see details
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rs4680 (Val158Met) is a well studied SNP in the COMT gene. 23andMe blog summarizes them as *rs4680(A) = Worrier. Met, more exploratory, lower COMT enzymatic activity, therefore higher dopamine levels; lower pain threshold, enhanced vulnerability to stress, yet also more efficient at processing information under most conditions *rs4680(G) = Warrior. Val, less exploratory, higher COMT enzymatic activity, therefore lower dopamine levels; higher pain threshold, better stress resiliency, albeit with a modest reduction in executive cognition performance under most conditions Roughly speaking, the predominant wisdom (known colloquially as the warrior/worrier hypothesis; summary at ) posits that people with Val alleles have increased COMT activity and lower prefrontal extracellular dopamine compar...
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[PharmGKB:Non-Curated GWAS Results: Whole genome association study identifies polymorphisms associated with QT prolongation during iloperidone treatment of schizophrenia (Initial Sample Size: 183 individuals; Replication Sample Size: NR; Risk Allele: rs4799915-T). This variant is associated with Response to iloperidone treatment (QT prolongation).] [GWAS:Response to iloperidone treatment (QT prolongation)]
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rs5182 (573C/T) is a SNP within the AGTR1 (Angiotensin II receptor type 1). among 4,096 hypertensive subjects, the CT/CC genotypes were associated with reduced risk of heart attack among those treated with ACE inhibitors [PharmGKB:Curated Risk or phenotype-associated allele: T. Phenotype: Homozygotes for the minor allele (TT) had reduced HR for cardiac events while treated with perindopril. Study size: 8907. Study population/ethnicity: PERGENE study; EUROPA trial; European; White. Significance metric(s): p = 0.054. Type of association: CO]
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A allele associated with better response to treatment of ADHD with atomoxetine.
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associated with ankylosing spondylitis risk of Helicobacter pylori infection. Children carrying IL1A-889T had a lower risk of H. pylori positivity, compared to those carrying -889C, with each T allele associated with 43% risk reduction (OR = 0.57, 95% CI = 0.33-0.99, p-trend = .05) upregulation of pro-inflammatory cytokines may protect against persistent H. pylori colonization. Association study of functional genetic variants of innate immunity related genes in celiac disease. Prognostic significance of host immune gene polymorphisms in follicular lymphoma survival. Association of common polymorphisms in inflammatory genes with risk of developing cancers of the upper aerodigestive tract. Potential influence of IL1B haplotype and IL1A-IL1B-IL1RN extended haplotype on hand osteoarthritis ris...
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SNPs nominally associated with schizophrenia (rs3787283, rs3746544) were the same as those previously demonstrated to be associated with ADHD but with the opposite alleles, allowing the intriguing hypothesis that genetic variation at SNAP25 may be differentially associated with both schizophrenia and ADHD When comparing pooled results of multiple ADHD studies, only rs3746544(A) was found to have a significant association (p=0.028) with slightly increased risk (OR 1.15 at 95%) of ADHD. Support for the MnlI polymorphism of SNAP25; a Korean ADHD case-control study. Investigation of variation in SNAP-25 and ADHD and relationship to co-morbid major depressive disorder. Biased paternal transmission of SNAP-25 risk alleles in attention-deficit hyperactivity disorder.
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news three SNPs that appear to have different effects in men and women rs3846662 rs2304130 rs2083637 journal LDL-Cholesterol minor allele was associated with up to 2.2-fold lower expression Common SNPs in HMGCR in micronesians and whites associated with LDL-cholesterol levels affect alternative splicing of exon13. The HMG-CoA reductase gene and lipid and lipoprotein levels: the multi-ethnic study of atherosclerosis. Genetic loci associated with plasma concentration of low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, triglycerides, apolipoprotein A1, and Apolipoprotein B among 6382 white women in genome-wide analysis with replication. Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip. Analysis of recently identifie...
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Genetic variants in the UCP2-UCP3 gene cluster and risk of diabetes in the Women's Health Initiative Observational Study.
Frequency: 46.4%
References:1
References:1
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[GWAS:Major depressive disorder]
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rs1799929 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The risk allele for this SNP is rs1799929(T). When this SNP is indicative of carrying a NAT2*5A allele, the following may be relevant: A study (based on only 42 patients) found that women with the NAT2*5A slow genotype (which presumably means rs1799929(T;T)) had a significantly higher risk of cervical cancer compared with individuals with the NAT2*5A fast genotype (i.e. carriers of only one rs1799929(T) allele), with a reported odds ratio of 7.469 (CI: 1.6-33.3, p=0.008). [PharmGKB:Curated in vitro study; PK: 20-fold reduction...
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Association testing of the positional and functional candidate gene SLC1A1/EAAC1 in early-onset obsessive-compulsive disorder. Association of the SLC1A1 glutamate transporter gene and obsessive-compulsive disorder. A haplotype containing quantitative trait loci for SLC1A1 gene expression and its association with obsessive-compulsive disorder. Family-Based Association Testing of OCD-associated SNPs of SLC1A1 in an autism sample. Polymorphisms in the glutamate transporter gene SLC1A1 and obsessive-compulsive symptoms induced by second-generation antipsychotic agents. [PharmGKB:Curated Risk or phenotype-associated variant: G. Phenotype: The A/C/G haplotype at rs2228622-rs3780413-rs3780412 showed a significant association with atypical antipsychotic-induced obsessive compulsive symptoms. Stud...
Frequency: 46.8%
References:8
References:8
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[PharmGKB:Curated Risk or phenotype-associated variant: A. Phenotype: The A/C/G haplotype at rs2228622-rs3780413-rs3780412 showed a significant association with atypical antipsychotic-induced obsessive compulsive symptoms. Study size: 94. Study population/ethnicity: Patients with schizophrenia receiving atypical antipsychotics; Asian; Korea. Significance metric(s): p = 0.04. Type of association: CO.]
slower responder
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This SNP in the ACE gene, also known as G12269A, is reported to influence how quickly African Americans respond to the anti-hypertensive drug ramipril. rs4344(A;A) and rs4344(G;G) homozygotes are able to reach lower blood pressure levels upon treatment with ramipril sooner than rs4344(A;G) heterozygotes. The odds ratio reported for this study, comparing both homozygotes to heterozygotes, is 1.86 (CI: 1.32-3.23). Note that this SNP is in almost complete linkage disequilibrium with the insertion/deletion ACE gene SNP.
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[GWAS:None]
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[GWAS:Response to methotrexate in rheumatoid arthritis]
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[PharmGKB:Non-Curated GWAS Results: Whole genome association study identifies polymorphisms associated with QT prolongation during iloperidone treatment of schizophrenia (Initial Sample Size: 183 individuals; Replication Sample Size: NR; Risk Allele: rs7142881-A). This variant is associated with Response to iloperidone treatment (QT prolongation).] [GWAS:Response to iloperidone treatment (QT prolongation)]
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[PharmGKB:Curated Risk or phenotype-associated allele (s): A/A and A/G. Phenotype: Carriers of the FPGS rs1544105 AA and AG genotypes [OR (95% CI) = 3.47 (1.19-10.12)] were predictors of poor response to methotrexate among rheumatoid arthritis patients Study size: 281. Study population/ethnicity: Indian metric(s): OR (95% CI) = 3.47 (1.19-10.12). Type of association: GN.]
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rs2306283 (Asn130Asp/N130D, A388G/388A>G) is a SNP within SLCO1B1 (Solute carrier organic anion transporter family member 1B1). A G at this location denotes the SLCO1B1*1B allele. among 8 healthy volunteers with *1B/*1B genotypes and 16 with the *1A/*1A genotype, *1B/*1B genotype associated with reduced plasma concentrations of repaglinide (but not nateglinide) consistent with increased hepatic uptake by SLCO1B1 (but w/ limited effects on nateglinide pharmacokinetics) news rs2306283 influences statin-related myopathy risk Genotyping panel for assessing response to cancer chemotherapy. Common variants in the SLCO1B3 locus are associated with bilirubin levels and unconjugated hyperbilirubinemia. Pazopanib-induced hyperbilirubinemia is associated with Gilbert's syndrome UGT1A1 polymorphism...
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A polymorphism in the PDLIM5 gene associated with gene expression and schizophrenia. Genetic correlates of brain aging on MRI and cognitive test measures: a genome-wide association and linkage analysis in the Framingham Study. Positive association between PDLIM5 and schizophrenia in the Chinese Han population. A case-control association study of the PDLIM5 gene and bipolar disorder in a Sardinian sample.
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[PharmGKB:Curated This SNP at chromosome 9 is significantly associated with HNRPD expression (located on chromosome 4), and daunorubicin IC50 in CEU population using International HapMap cell lines.]
Frequency: 47.3%
References:1
References:1
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[PharmGKB:Curated This intronic variant is moderately associated with olanzapine-induced median weight gain and significantly associated with extreme weight gain in schizophrenia subjects from north India.This variant alters the binding of a transcription factor (zinc finger 5) using in silico analysis.]
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[PharmGKB:Curated Risk or phenotype-associated allele: A Phenotype: This SNP was associated with a greater reduction in total cholesterol after at least 1 week of statin use. This was not replicated in a second cohort. Study size: 546 (original cohort); 100 (replication cohort). Study population/ethnicity: People taking statins; age 55 or older; Rotterdam Study; Netherlands. Significance metric(s): p = 0.05 (original); p = 0.975 (replication) Type of association: PD.]
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associated with bronchodilator response among a sample of 209 children and their parents participating in the Childhood Asthma Management Program, the minor allele was associated with lower BDR compared to the homozygous major allele [PharmGKB:Curated This variant is associated with acute response to inhaled ? agonists in both childhood and adult asthmatic patients.]
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Rs2237717 (major: C, minor: T) is located in intron 11 within the MET proto-oncogene. The MET gene is primarily known to be involved in tumor metastasis . However, MET has also been shown to have roles in general neurodevelopment and in the development of autism . Rs2237717 has been linked to schizophrenia, ability to recognize facial emotion, and chronic rhinosinusitis. ==Association with schizophrenia and cognitive ability== Given that schizophrenic patients have a lower incidence of cancer despite more exposure to risk factors and relatives without schizophrenia appear to also have a protective effect on cancer incidence, it has been hypothesized that alterations in cancer genes (like MET, containing rs2237717) may be involved in the pathogenesis of schizophrenia . ===Schizophrenia=== I...
normal
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rs6749447 is a SNP in the serine threonine kinase 39 STK39 gene. A study of ~1,000 Amish originally identified rs6749447 and another SNP also in the STK39 gene, rs3754777, as being significantly associated with hypertension. This association was then found to also hold in patient data analyzed from the Framingham Heart Study and the Diabetes Genetics Initiative. On average, each minor allele, in this case rs6749447(G), is associated with 2.0 mmHg higher systolic blood pressure and a 1.0 mm Hg higher diastolic pressure. [PharmGKB:Non-Curated GWAS results: Whole-genome association study identifies STK39 as a hypertension susceptibility gene. (Initial Sample Size: 542 individuals; Replication Sample Size: 6,583 individuals); (Region: 2q24.3; Reported Gene(s): STK39; Risk Allele: rs6749447-G)...
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[PharmGKB:Curated Minor allele G is associated with LQTS1(tagging SNP for QTL haplotype block).]
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[PharmGKB:Curated Risk or phenotype-associated allele: not given. Phenotype: In lymphoblastoid cell lines, this SNP was significantly associated with the IC-50 of cisplatin. Study size/population/ethnicity: lymphoblastoid cell lines from 100 healthy Caucasian-American subjects. Significance metric(s): P = 0.019. Type of association: FA. Also, suggestive, but not significant, evidence was found for association of this SNP with survival of lung cancer patients treated with cisplatin.]
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[PharmGKB:Curated Risk or phenotype-associated allele: rs2267076 T allele Phenotype: Carriers of 1 or 2 copies of the T allele for rs2267076 showed increased risk of any (OR = 2.1, CI 1.05-4.27, p = 0.02) or gastrointestinal-specific (OR = 1.77, CI = 0.65-5.77, p = 0.22) adverse events. Study size: 309 RA patients, including 147 good MTX responders, 101 MTX inefficacy failures, and 61 adverse event (AE) MTX failures (e.g. gastrointestinal (n = 24), abnormal liver function tests (n = 20), haematological (n = 7), skin rashes (n = 6), and other (n = 17). Study population/ethnicity: Rheumatoid arthritis (RA) patients aged over 18 yrs, of White Caucasian ethnic origin, classified as having RA according to ARA criteria that were retrospectively recruited from University Hospital of North Staffor...
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rs394581, a SNP cited to be associated with the risk of Rheumatoid Arthritis (RA), is situated on 6q25.3 in the 5' untranslated region of the TAGAP gene , which encodes the T-cell Activation Rho GTPase activating protein . This gene is highly expressed in immune cells such as B-lymphocytes, T-lymphocytes, dendritic cells, natural killer cells, and monocytes, yet its specific role in immune function is still unclear . Meta-analysis of GWAS in RA with validation in independent samples identified the TAGAP as an RA susceptibility locus . ==Rheumatoid Arthritis and Genetics== RA is an autoimmune disease that is characterized by chronic and systemic inflammation . At least half the variance in RA risk is estimated to be genetic based on family studies . A twin study with nationwide British and ...
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[GWAS:Response to irinotecan and platinum-based chemotherapy in non-small-cell lung cancer]
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[PharmGKB:Curated Risk or phenotype-associated allele(s): G/G. Phenotype:the GG-genotype carriers were 2.5 times less likely to be overweight/obese (i.e. having a BMI above the 85th percentile). Study population/ethnicity: Children and adolescents, aged 7-17 years, treated with risperidone for 6 months or more.]
normal
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rs2228001, also known as Lys939Gln, K939Q, and K940Q, is a SNP in the DNA nuclear excision repair gene xeroderma pigmentosum complementation group C XPC gene. The Lys (K) allele is encoded by the rs2228001(A) allele. A meta-analysis of 16 studies with 6797 cancer cases and 9018 controls concluded that rs2228001(C;C) homozygotes had an increased overall cancer risk (odds ratio of 1.16, CI: 1.05-1.28) compared with (A;A) homozygotes. This was primarily a risk for lung cancer. [PharmGKB:Curated Risk or phenotype-associated allele: Not specified. Phenotype: This SNP was associated with clearance of docetaxel. Study size: 31. Study population/ethnicity: Patients with Non-Small-Cell Lung Carcinoma. Significance metric(s): p = 0.0045 (ANOVA); p = 0.052 (QMIS); p = 0.0004 (KW) Type of association...
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[PharmGKB:Curated Risk or phenotype-associated allele: T. Phenotype: The C allele was correlated with increased overall survival (CC vs. CT vs. TT: 15.4, 7.3, 4.8 months) given combined pemetrexed/bevacizumab treatment (p = 0.04), and lymphopenia as an adverse drug effect (p <= 0.05). Study size: from a study using 48 patients with metastatic or stage IIIB nonsquamous non-small-cell lung cancer patients. Significance metric(s): log-rank p = 0.04, p <= 0.05. Type of association: CO, GN]
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[PharmGKB:In-Depth May be associated with a higher warfarin dose phenotype]
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Polymorphisms within the C-reactive protein (CRP) promoter region are associated with plasma CRP levels. Genetic variation is associated with C-reactive protein levels in the Third National Health and Nutrition Examination Survey. Common variants in the CRP gene in relation to longevity and cause-specific mortality in older adults: the Cardiovascular Health Study. C-reactive protein (CRP) gene polymorphisms, CRP levels, and risk of incident coronary heart disease in two nested case-control studies. Genetic determinants of basal C-reactive protein expression in Filipino systemic lupus erythematosus families. Fine-mapping the genetic basis of CRP regulation in African Americans: a Bayesian approach. C-reactive protein, interleukin-6, and prostate cancer risk in men aged 65 years and older. I...
Frequency: 48.6%
References:7
References:7
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[PharmGKB:Curated A study, investigating the response of SSRI in 137 Japanese major depression subjects, observed a significant association of better response to antidepressant in rs10042486 (P < 0.0001), rs6295 (P < 0.0001) and rs1364043 (P = 0.018) genotype carriers (minor allele homozygotes), independently from clinical variables. The rs6295 variant has been found to affect the expression and function of HTR1A. rs6295 is in strong linkage disequilibrium with other polymorphisms of HTR1A.]
slightly less drug dependence, decreased effectiveness of analgesics
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Genome-wide association study identifies a potent locus associated with human opioid sensitivity rs2952768(C) was associated with more analgesic requirements ... exhibited less vulnerability to severe methamphetamine or alcohol dependence, fewer eating disorders, and a lower ‘Reward Dependence’ score on a personality questionnaire. The (C;C) genotype was significantly associated with the elevated expression of a neighboring gene, CREB. SNPs in this locus are the most potent genetic factors associated with human opioid sensitivity known to date, affecting both the efficacy of opioid analgesics and liability to severe substance dependence. Our findings provide valuable information for the personalized treatment of pain and drug dependence. [GWAS:Opioid sensitivity]
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rs1047840, also known as K589E, is a SNP in the EXO1 gene. A study of 1,272 breast cancer Taiwanese patients concluded that the rs1047840(A) allele conferred a significantly (p=0.000025) increased risk of breast cancer.
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Complement component 3 polymorphisms interact with polyunsaturated fatty acids to modulate risk of metabolic syndrome.
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A and G alleles of rs4343 are strongly associated marking insertion and deletion alleles of ACE I/D respectively. For those looking for the ACE Alu Insertion/Deletion, this is a very good substitute for people searching for ACE Del16. G would mean deletion. A haplotype of rs4311, rs4343, rs699 increases risk of diabetic nephropathy 4x. [PharmGKB:Curated While the ACE:I/D has dbSNP identifiers rs1799752, rs4340, rs13447447 and rs4646994, measurement of a single base at these positions does not give an informative genotype. In Europeans, rs4343 is in complete LD with the ACE:I/D, with the A and G alleles of rs4343 marking the insertion and deletion alleles of ACE:I/D respectively.] [GWAS:Angiotensin-converting enzyme activity]
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[PharmGKB:Curated This variant is associated with end-of-induction minimal risidual disease (MRD) in childhood acute lymphoblastic leukemia (ALL) from 2 independent cohorts (GWAS result). Risk Allele: G, MAF= 0.44, combined P value= 2.08E-04. It is also associated with greater methotrexate clearance.]
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[PharmGKB:Curated This variant is significantly associated with the efficacy of anti-TNF treatment in rheumatoid arthritis (Adjusted P-value: 0.000003; OR: 8.5 (2.6, 36.5)). The study is a genome-wide association study using the Illumina HapMap300 SNP chip on 89 RA patients prospectively followed after beginning of anti-TNF therapy.]
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[GWAS:None]
normal risk
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rs6166, also known as Asn680Ser, is a SNP in the follicle stimulating hormone receptor FSHR gene. rs6166(G) is the risk allele encoding the Ser amino acid, at least based on one study in which less fecund women were found to be disproportionately Ser/Ser homozygotes (i.e. rs6166(G;G) homozygotes; p=0.0035). [OMIM:OVARIAN RESPONSE TO FSH STIMULATION]
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rs6275/DRD2 and rs4680/COMT useful in predicting disease risk among schizophrenia patients See also rs6277. [PharmGKB:Curated Risk or phenotype-associated allele: T. Phenotype: The average and maximum daily methadone doses were significantly associated with the DRD2 rs6275C>T SNP (P=0.016 and 0.005 for average and maximum dose, respectively). Carriers of the variant rs6275T allele needed higher methadone doses than noncarriers. Study size: 85. Study population/ethnicity: Caucasian. Type of association: GN.]
metabolic consequences
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rs780094, a SNP in the GCKR gene encoding the glucokinase regulatory protein, contributes to the risk of type-2 diabetes and dyslipidaemia in mulitple populations. The effect on type 2 diabetes is probably mediated through impaired beta cell function rather than through obesity. The rs780094(A) risk allele is associated with the following traits : * higher levels of fasting serum triacylglycerol * impaired fasting and OGTT-related insulin release * dyslipidemia * somewhat reduced risk of type-2 diabetes There may also be an additive effect between this SNP and a SNP known as 'GCK -30A', rs1799884, at least on fasting serum insulin levels. rs780094 influences severe hypertriglyceridemia. 132 patients of European ancestry with severe HTG (fasting plasma TG>10 mmol/L), and 351 matched norm...
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Lack of replication of genetic predictors for the rheumatoid arthritis response to anti-TNF treatments: a prospective case-only study. [PharmGKB:Non-Curated This variant is significantly associated with the efficacy of anti-TNF treatment in rheumatoid arthritis (Adjusted P-value: 0.000004; OR: 4.6 (1.8, 12.3)). The study is a genome-wide association study using the Illumina HapMap300 SNP chip on 89 RA patients prospectively followed after beginning of anti-TNF therapy.] [GWAS:Treatment response to TNF antagonists]
Frequency: 49.2%
References:6
References:6
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Association of warfarin dose with genes involved in its action and metabolism. [PharmGKB:Curated Risk or phenotype-associated allele: G. Phenotype: The multimarker composed of rs2461823/A-rs7643645/G was significantly associated with severity of nonalcoholic fatty liver disease (NAFLD) (P<6.9x10, beta: 0.45). In univariate analysis rs7643645/G was significantly associated with fatty liver disease (P<0.04), with an odds ratio of 1.457 (95% confidence interval: 1.018-2.086). Study size: 290. Study population/ethnicity: 188 NAFLD patients with different stages of disease severity and 102 healthy individuals. Type of association: GN.]
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[PharmGKB:Curated Risk or phenotype-associated allele: A. Phenotype: This variant was associated with higher clearance of docetaxel. Study size: 31. Study population/ethnicity: Patients with Non-Small-Cell Lung Carcinoma. Significance metric(s): Type of association: PK.]
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[OMIM:CHOLINERGIC RECEPTOR, MUSCARINIC, 2; CHRM2]
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[OMIM:CHOLINERGIC RECEPTOR, MUSCARINIC, 2; CHRM2]
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[PharmGKB:Curated Risk or phenotype-associated allele: TT genotype. Phenotype: Patients with the GGH 401TT genotype were 4.8-fold (p = 0.002) more likely to have methotrexate polyglutamate (MTXPG3-5) levels below the group median compared to patient carriers of the 401CC or CT genotype. Study size: 226. Study population/ethnicity: Adult rheumatoid arthritis patients from Tennessee and Florida who received low-dose MTX therapy for at least 3 months. Significance metric(s): OR = 4.8; p = 0.002. Type of association: PD, GN]
Frequency: 49.6%
References:1
References:1
Frequency: 49.6%
References:6
References:6
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[OMIM:COMPLEMENT FACTOR H-RELATED 3; CFHR3] [GWAS:None]
Frequency: 49.6%
References:8
References:8
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[OMIM:?] [GWAS:Rheumatoid arthritis]
Frequency: 49.6%
References:2
References:2
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23andMe blog blood pressure Confirmation of top polymorphisms in hypertension genome wide association study among Han Chinese. Pharmacogenetic implications for eight common blood pressure-associated single-nucleotide polymorphisms. [GWAS:Diastolic Blood Pressure]
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[GWAS:None]
1.3x risk of [[type-2 diabetes]]
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rs1111875 is a SNP of the HHEX homeobox gene. In several studies, it has been associated with risk for type-2 diabetes (T2D). In a study of 500 unrelated Caucasian T2D patients, the rs1111875(G) allele was overrepresented; the odds ratio was 1.68 (CI: 1.19-2.35, p=0.003). In this population, the population attributable risk for this allele was estimated to be 36%. In a study of ~400 Japanese, rs1111875(G) was also associated with type-2 diabetes (odds ratio 1.42, CI: 1.13-1.78, p=0.0024). Heterozygous and homozygous carriers of the risk allele had odds ratios of 1.31 (CI: 0.97-1.77, p=0.0810) and 2.40 (CI: 1.34-4.32, p=0.0028) relative to non-carriers. And in a third study, 1,630 Japanese patients were also found to have this SNP significantly overrepresented (p=0.0064). rs1111875 replicat...
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escitalopram response [GWAS:Response to antidepressants]
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Physiogenomic analysis of weight loss induced by dietary carbohydrate restriction. Physiogenomic comparison of human fat loss in response to diets restrictive of carbohydrate or fat. Genetic-epidemiological evidence on genes associated with HDL cholesterol levels: a systematic in-depth review. TagSNP transferability and relative loss of variability prediction from HapMap to an admixed population. Analysis of recently identified dyslipidemia alleles reveals two loci that contribute to risk for carotid artery disease. Polymorphism in the CETP gene region, HDL cholesterol, and risk of future myocardial infarction: Genomewide analysis among 18 245 initially healthy women from the Women's Genome Health Study. Genetics and beyond--the transcriptome of human monocytes and disease susceptibility. ...
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[PharmGKB:Curated A study in 243 children with ADHD and their parents suggests a role for the promoter region of the SLC6A3 gene in ADHD susceptibility. In the DSM-IV combined subtype, results showed a preferential transmission of the haplotype A/C/C/C/A derived from five SNPs (rs2550948, rs11564750, rs261759, rs2652511, rs2975223) in 5' region of the SLC6A3 gene.]
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(Associated with ADHD.)
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23andMe blog psoriasis Europeans *rs610604(G) 1.19x risk [PharmGKB:Non-Curated GWAS results: Genome-wide scan reveals association of psoriasis with IL-23 and NF-kappaB pathways. (Initial Sample Size: 1,359 cases, 1,400 controls; Replication Sample Size: 5,048 cases, 5,041 controls); (Region: 6q23.3; Reported Gene(s): TNFAIP3; Risk Allele: rs610604-G); (p-value= 0.000000000009).This variant is associated with Psoriasis.] [GWAS:Psoriasis]
Frequency: 50.0%
References:1
References:1
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risk of the development of substance dependence significantly increased with the number of 'G' alleles at rs6454674 and SNP8;T/T genotypes had significant interaction effects (p = .0003 for comorbid DD and AD, .0002 for DD, and .007 for AD). SNP3 and SNP8 together exerted stronger genetic effects on SD than either did individually. The peak delta values among all the markers were seen for SNP3 and SNP8 (rs806368) rs806377(C) together with rs6454674(G) make up a haplotype associated (p=0.008) with higher risk of ADHD. In addition, the haplotype was more associated (p=0.03) with ADHD in males than in females with the risk haplotype. Cannabis receptor haplotype associated with fewer cannabis dependence symptoms in adolescents. No association of CNR1 gene variations with susceptibility to schi...
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[PharmGKB:Curated Risk or phenotype-associated allele: heterozygote CT bears the greatest genotypic risk. Phenotype: A significant difference in 3-month progression-free survival was associated with the rs1051298 genotype (CC vs. CT vs. TT: 57%, 29%, 78%) (p = 0.01); and median progression-free survival was associated with the rs1051298 genotype (CC vs. CT vs. TT: 5.7, 2.8, 4.7 months) (p = 0.05). Study size: from a study using 48 patients with metastatic or stage IIIB nonsquamous non-small-cell lung cancer patients given combined pemetrexed/bevacizumab treatment. Significance metric(s): p = 0.01, p = 0.05. Type of association: CO, GN]
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[PharmGKB:Curated Phenotype : In a meta-analysis of 21 GWAS cohorts followed by analysis in additional individuals, this SNP was found to be associated with fasting glucose level. Study size: 116,882. Significance metric(s): p = 6.6 x 10(-12). Study population/ethnicity: Non-diabetic Individuals of European descent. Type of association: CO;GN.] [GWAS:Fasting glucose-related traits]
Frequency: 50.4%
References:2
References:2
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'''rs11264359''' is an intronic SNP located 4125 base pairs from the translation start site of the ''FDPS'' (Farnesyl diphosphate synthase) gene. The ''FDPS'' gene encodes an enzyme that converts isopentenyl pyrophosphate and dimethylallyl pyrophosphate into geranyl pyrophosphate and farnesyl pyrophosphate as part of the mevalonate pathway. This pathway is known to be important in cholesterol and sterol biosynthesis [NCBI Gene ID: 2224]. This enzyme is essential in the bone remodeling process. Particularly, it is necessary for the survival and function of osteoclasts, which are bone cells important in the breakdown of bone tissue (bone resorption). This is the first step of the bone remodeling process, where bone tissue is first broken down by osteoclasts and then reformed by osteoblasts. ...
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Genome bioinformatic analysis of nonsynonymous SNPs. Physiogenomic analysis of localized FMRI brain activity in schizophrenia. HTR3B is associated with alcoholism with antisocial behavior and alpha EEG power--an intermediate phenotype for alcoholism and co-morbid behaviors. Pharmacogenetics of antidepressant response. Are serotonin 3A and 3B receptor genes associated with suicidal behavior in schizophrenia subjects? [OMIM:5-@HYDROXYTRYPTAMINE RECEPTOR 3B; HTR3B]
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CYP2B6 polymorphisms influence the plasma concentration and clearance of the methadone S-enantiomer.
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[OMIM:INSULIN-LIKE GROWTH FACTOR-BINDING PROTEIN 3; IGFBP3]
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Mutation analysis and the correlation between genotype and phenotype of Arg778Leu mutation in chinese patients with Wilson disease.
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[PharmGKB:Curated In a Chinese population, this SNP was significantly associated with blood pressure response to nifedipine treatment.]
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QT interval rs3807375 rs2880058 [PharmGKB:Curated QT prolongation] [GWAS:Electrocardiographic traits]
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[GWAS:Hematological and biochemical traits]
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Synergistic association of mitochondrial uncoupling protein (UCP) genes with schizophrenia. A genetic association analysis of cognitive ability and cognitive ageing using 325 markers for 109 genes associated with oxidative stress or cognition. Ala55Val polymorphism on UCP2 gene predicts greater weight loss in morbidly obese patients undergoing gastric banding. Lack of association between uncoupling protein-2 Ala55Val polymorphism and incident diabetes in the atherosclerosis risk in communities study. Ser1369Ala variant in sulfonylurea receptor gene ABCC8 is associated with antidiabetic efficacy of gliclazide in Chinese type 2 diabetic patients. Human uncoupling protein 2 and 3 genes are associated with obesity in Japanese. Physiogenomic comparison of edema and BMI in patients receiving ros...
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Association of single-nucleotide polymorphisms in JAK3, STAT4, and STAT6 with new cardiovascular events in incident dialysis patients. An association study of the signal transducer and activator of transcription 6 gene with periodic psychosis.
Frequency: 50.8%
References:4
References:4
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23andMe blog blood pressure [GWAS:Diastolic Blood Pressure]
Frequency: 50.8%
References:1
References:1
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rs1801280, also known as T341C, is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The allele associated with slow NAT2 metabolization for this SNP is rs1801280(C). Genosets gs154 and gs156 evaluate predicated NAT2 metabolizer phenotype based on rs1041983 and rs1801280. [PharmGKB:Curated in vitro study; PK: 20-fold reduction in Vmax vs wild type] [OMIM:?]
1.6x risk for ICP
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rs3740066, a SNP in the ABCC2 gene, is reported to be associated with a higher risk of developing intrahepatic cholestasis of pregnancy (ICP) based on a study of ~70 Argentinian patients. ICP is associated with increased fetal risks such as premature birth or intrauterine death. The risk allele is rs3740066(A), and the odds ratio for homozygous rs3740066(A;A) mothers is 4.44 (CI: 1.83 - 10.78), and for heterozygous mothers 1.65 (CI: 0.76 - 3.64), compared to rs3740066(G;G) mothers. [PharmGKB:Curated The AUCs of irinotecan, SN-38, SN-38 glucuronide, and APC are influenced by rs3740066, rs2306283, rs35605, rs10276036, and rs717620 .]
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rs1799864(G), rs3025058(A) and rs662 were associated with increased risk, and rs1800775(A) with reduced risk of recurrent venous thromboembolism [PharmGKB:Curated Meta-analysis showed weak inverse association with coronary risk for the CETP:-629C>A, A allele.] [OMIM:HIGH DENSITY LIPOPROTEIN CHOLESTEROL LEVEL QUANTITATIVE TRAIT LOCUS] [GWAS:HDL cholesterol]
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A PAI-1 (SERPINE1) polymorphism predicts osteonecrosis in children with acute lymphoblastic leukemia: a report from the Children's Oncology Group. SNP combinations in chromosome-wide genes are associated with bone mineral density in Taiwanese women.
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per OMIM, Ma et al. (2005) found two different DDC haplotypes associated with nicotine dependence in African Americans and European Americans (with measures of smoking quantity [SQ], heaviness of smoking index [HSI], and the Fagerstrom test for ND [FTND]) *in African Americans, rs921451(T), rs3735273(G), rs1451371(T), rs2060762(G), all three measures sig. associated after correction for multiple testing *in European Americans, rs921451(T), rs3735273(G), rs1451371(T), rs3757472(G), which showed a sig. assoc. w/ the SQ and FTND score [PharmGKB:Curated A study on 2037 smokers and non-smokers from 602 nuclear families of African- or European-American ancestry found first evidence for the involvement of DDC in the susceptibility to nicotine dependence. This variant in the DDC gene is part of t...
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[GWAS:Coronary artery disease]
Frequency: 52.2%
References:2
References:2
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[GWAS:None]
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[PharmGKB:Non-Curated GWAS results: Genome-wide association study of acute post-surgical pain in humans. (Initial Sample Size: 60 females, 52 males; Replication Sample Size: NR); (Region: 19p12; Reported Gene(s): LOC400680, ZNF429; Risk Allele: rs2562456-?); (p-value= 0.0000000002).This variant is associated with Pain.] [GWAS:Pain]
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The rs2832407(C) allele has inconsistently been linked to alcoholism and its treatment. Nonetheless, a 2014 report based on 138 patients concludes that rs2832407(C;C) individuals show a greater decrease than non-carriers (of a rs2832407(C) allele) in the number of heavy drinking days per week when taking topiramate at a dose of 200 mg/daily. A follow-up study done 3 and 6 months after treatment seemed to mostly confirm the topiramate benefit preferentially to rs2832407(C;C) individuals.
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Influences blood volume and platelet count Determinants of platelet count in humans. [PharmGKB:Curated GWAS results: A novel variant on chromosome 7Q22.3 associated with mean platelet volume, counts and function. (Initial Sample Size: 1,221 individuals; Replication Sample Size: 7,365 individuals); (Region: 7q22.3; Reported Gene(s): Intergenic; Risk Allele: rs342293-G); (p-value= 1E-24).This variant is associated with Mean platelet volume.] [GWAS:MPV]
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Lack of replication of genetic predictors for the rheumatoid arthritis response to anti-TNF treatments: a prospective case-only study. [PharmGKB:Non-Curated This variant is significantly associated with the efficacy of anti-TNF treatment in rheumatoid arthritis (Adjusted P-value: 0.0000005; OR: 4.9 (1.8, 14.0)). The study is a genome-wide association study using the Illumina HapMap300 SNP chip on 89 RA patients prospectively followed after beginning of anti-TNF therapy.] [GWAS:Treatment response to TNF antagonists]
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[PharmGKB:Curated This variant is significantly associated with the efficacy of anti-TNF treatment in rheumatoid arthritis (Adjusted P-value: 0.0000005; OR: 4.9 (1.8, 14.0)). The study is a genome-wide association study using the Illumina HapMap300 SNP chip on 89 RA patients prospectively followed after beginning of anti-TNF therapy.]
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Lack of replication of genetic predictors for the rheumatoid arthritis response to anti-TNF treatments: a prospective case-only study. [PharmGKB:Curated This variant is significantly associated with the efficacy of anti-TNF treatment in rheumatoid arthritis (Adjusted P-value: 0.00003; OR: 5.5 (1.8, 20.2)). The study is a genome-wide association study using the Illumina HapMap300 SNP chip on 89 RA patients prospectively followed after beginning of anti-TNF therapy.]
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[PharmGKB:Curated Risk or phenotype-associated allele: None. Phenotype: Variants identified in a screen of 13 genes involved in the gemcitabine drug metabolic pathway. For the non-synonymous SLC28A1:1576T>C (N521D) SNP, the C (521Asp) allele was at frequency was 0.47 and 0.00 in Europeans and Africans, respectively. There was a significant difference between ethnic groups in genotype frequency distribution (p < 0.001). Study size: 185. Study population/ethnicity: Healthy, unrelated blood donors of European (n = 94) and African (n = 91) descent. Significance metric(s): p < 0.001. Type of association: GN.]
higher risk for RA
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rs6313, also known as T102C, is part of a 4-SNP haplotype in the serotonin 2A receptor gene HTR2A that has been associated with rheumatoid arthritis in a study of 1800 European patients. The risk allele is rs6313(C). The overall risk for the haplotype CTCC of SNPs rs6311-rs1328674-rs6313-rs6314 is 1.68 (CI: 1.20 - 2.34, p = 0.02). Note: the orientation of rs1328674 in dbSNP is opposite that cited by this publication; therefore, with respect to dbSNP, the haplotype of risk as cited above is CACC rather than CTCC. see also gs108 and gs226 Polymorphisms in the serotonin receptor gene HTR2A are associated with quantitative traits in panic disorder. [PharmGKB:Curated Risk or phenotype-associated allele (s): T/T. Phenotype: Patients, with a diagnosis of probable Alzheimer's disease, carryi...
Frequency: 52.3%
References:6
References:6
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Clinically relevant UGT1A10 variant. [PharmGKB:Curated *93 is a common variant of UGT1A1 in Caucasian and African-American populations. It is located in the Phenobarbital Response Enhancer Module (an upstream regulatory sequence) and may be important in predicting irinotecan response.]
Frequency: 52.3%
References:9
References:9
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[PharmGKB:Curated Phenotype: This variant is associated with null virological response (NVR) in Janapese patients with hepatitis C virus infection treated with PEG-INF-alpha plus ribavirin. Study size: Initial sample:154; Replication Sample: 172. Study population/ethnicity: Japanese. Significance metric(s): P=2.84 x 10(-31) (NVR). Type of association: GN; CO]
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[PharmGKB:Non-Curated GWAS Results: Newly identified loci that influence lipid concentrations and risk of coronary artery disease (Initial Sample Size: 8,656 individuals; Replication Sample Size: 11,399 individuals; Risk Allele: rs2144300-T). This variant is associated with HDL cholesterol levels.] [GWAS:Circulating myeloperoxidase levels (serum)] [GWAS:HDL cholesterol]
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RGS4 mRNA expression in postmortem human cortex is associated with COMT Val158Met genotype and COMT enzyme activity. RGS4 is not a susceptibility gene for schizophrenia in Japanese: association study in a large case-control population. Allelic variation in RGS4 impacts functional and structural connectivity in the human brain. Ethnic stratification of the association of RGS4 variants with antipsychotic treatment response in schizophrenia. RGS4 polymorphism and response to electroconvulsive therapy in major depressive disorder. Interaction between interleukin 3 and dystrobrevin-binding protein 1 in schizophrenia. Association of RGS4 variants with schizotypy and cognitive endophenotypes at the population level. Executive function, neural circuitry, and genetic mechanisms in schizophrenia. La...
Frequency: 52.5%
References:2
References:2
Frequency: 52.7%
References:2
References:2
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[OMIM:G30 GENE]
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[PharmGKB:Curated Risk or phenotype-associated allele: A. Phenotype: CBR3 11G>A variant was associated with lower doxorubicinol AUC, lower CBR3 expression in breast tumor tissue, greater tumor reduction, and greater percentage reduction of leukocyte and platelet counts at nadir. Study size: 101 Study population/ethnicity: Asian; patients with Breast Neoplasms; Chinese; Malay; Indian Significance metric(s): p = 0.009 (AUC); p = 0.001 (expression); p = 0.015 (tumor reduction); p = 0.03 (leukocyte and platelet counts). Type of association: PK; TOX]
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RGS4 mRNA expression in postmortem human cortex is associated with COMT Val158Met genotype and COMT enzyme activity. RGS4 is not a susceptibility gene for schizophrenia in Japanese: association study in a large case-control population. Association of RGS2 and RGS5 variants with schizophrenia symptom severity. Association of RGS4 variants with schizotypy and cognitive endophenotypes at the population level. Persistence criteria for susceptibility genes for schizophrenia: a discussion from an evolutionary viewpoint. [PharmGKB:Curated Results from a study in patients with acutely exacerbated schizophrenia suggest that this variant in the RGS4 gene influences clinical manifestations of schizophrenia as well as the treatment response to risperidone.]
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[GWAS:None]
lower TGF-β1 levels, higher risk for COPD? This normal C version significantly reduces TGF-β1 levels by allowing AP1 to downregulate TGF-β1 production.
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rs1800469, also known as -509 C>T or −1347 C > T, is an SNP in the promoter region of the transforming growth factor beta1 TGFB1 gene. That means it doesn't change the nature of the TGF-β1 protein, but it does change the amount produced. The T version increases the amount of TGF-β1 produced, by preventing AP1 from binding to this region where in the C version it would normally downregulate production. That increased TGF-β1 production with the T version is probably what causes all the health effects of this SNP. Whether increased TGF-β1 is good or bad probably depends on the disease you are interested in. It has been associated with increased risk for chronic obstructive pulmonary disease (COPD). Although smoking is the main risk factor, smokers with a rs1800469(C) allele (or 2 other ...
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obesity Q223R rs1137101 may be associated with obesity in women with a psychotic disorder treated with atypical antipsychotic drugs Gln223Arg polymorphism could be considered a disease susceptibility modulating factor both in ischemic heart disease or dilated cardiomyopathy patients. [OMIM:LEPTIN RECEPTOR POLYMORPHISM]
This is the genotype of User:Watson
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This snp influences obesity however * the most strongly linked neighboring snp is rs9939609 * some evidence suggests rs1421085 may be the true causative snp This plos genetics paper reports rs9930506 showed the strongest association with BMI (p = 8.6 *10-7), hip circumference (p = 3.4 * 10-8) and weight (p = 9.1 * 10-7). homozygotes for the rare 'G' allele were were 1.3 BMI units heavier than homozygotes for the common 'A' allele. This SNP did not show any association with obesity, type-2 diabetes or any other related traits in a study of 3,210 Chinese subjects. Furthermore, the minor allele frequency was much lower in Chinese populations compared to populations of European descent. rs9930506 (A;A) showed decreased levels of methylated PPARGC1A in comparison with AG + GG genotypes, suggest...
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rs4675690 is in close proximity to CREB1, and adjacent to LOC151194. g2b2mh blog individuals with the TT genotype at rs4675690 (C/T) showed less disgust, but not happiness, desire or fear. T allele associated with increased chance of suicide (OR = 2.3, 95% CI 1.3-2.9, TT homozygotes vs CC homozygotes?) during the first 30 days (p > 0.05 after the first month) of citalopram treatment, in a study of 1447 citalopram users (male only subgroup, 539 in total). Two haplotypes (see below) also showed significant association with suicidality in the male subgroup. *rs2709376(C),rs2253206(A),rs7569963(A),rs7594560(T),rs4675690(C) - common haplotype, reduced chance of suicide in males, p = 0.004 *rs2709376(C),rs2253206(A),rs7569963(G),rs7594560(T),rs4675690(T) - increased chance of suicide in males...
Frequency: 54.0%
References:8
References:8
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[GWAS:None]
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rs9296158 rs3800373 rs1360780 rs9470080 linked with the severity of child abuse to predict level of adult PTSD symptoms after correcting for multiple testing. [PharmGKB:Curated This variant is associated with higher chance of response to anti-depressant drugs.]
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Polymorphisms in the vascular endothelial growth factor gene and breast cancer in the Cancer Prevention Study II cohort. Large-scale evaluation of candidate genes identifies associations between VEGF polymorphisms and bladder cancer risk. Vascular endothelial growth factor (VEGF) gene (VEGFA) polymorphism can predict the prognosis in acute myeloid leukaemia patients. VEGF polymorphisms and survival in early-stage non-small-cell lung cancer. Vascular endothelial growth factor gene polymorphisms in age-related macular degeneration. Polymorphisms in the vascular endothelial growth factor gene and the risk of familial endometriosis. Genetic polymorphisms of VEGF, interactions with cigarette smoking exposure and esophageal adenocarcinoma risk. Functional genetic polymorphisms and female reprodu...
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rs4810485 is a SNP associated with rheumatoid arthritis (RA), a chronic autoimmune disease characterized by joint inflammation. At this locus, the minor allele, T, protects against RA. The SNP is located on chromosome 20q13 in the second intron of the CD40 gene, which encodes a receptor that is expressed on the surface of multiple immune cells. CD40 binds the ligand CD154 which is expressed by activated T cells, and this interaction plays a critical role in T cell helper activity in the immune system. rs4810495 is closely linked with another SNP, rs1883832, that appears to lesson translation of the CD40 gene, affecting this critical signaling pathway that leads to B cell proliferation . Mouse model knockouts of CD40 have been shown to alleviate arthritis . The association between rs4810485...
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common trait being optimism [GWAS:Common traits (Other)]
Frequency: 54.9%
References:26
References:26
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23andMe blog rs8099917(C) less likely to respond to Hepatitis C treatment. rs12979860(C;C) better able to become naturally Hepatitis C virus-free. rs12980275(A) usually corresponds to the rs12979860(C) Variants in IL28B in liver recipients and donors correlate with response to peg-interferon and ribavirin therapy for recurrent hepatitis C. Importance of IL28B gene polymorphisms in hepatitis C virus genotype 2 and 3 infected patients. Predictive value of the IL28B polymorphism on the effect of interferon therapy in chronic hepatitis C patients with genotypes 2a and 2b. Peginterferon and ribavirin treatment for hepatitis C virus infection. IL28B polymorphisms predict reduction of HCV RNA from the first day of therapy in chronic hepatitis C. IL28B polymorphisms, IP-10 and viral load predict v...
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The association between type-1 diabetes and rs5215 is mentioned as being replicated in ; there is also a 90% correlation between rs5215 and rs5219. [GWAS:Type 2 diabetes]
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rs10935838, rs2046934, rs5853517, and rs6809699 venous thromboembolism lower risk of incident DVT/PE as compared to the reference haplotype H1 (odds ratio=0.50, 95% CI=0.27-0.93, p=0.028) [PharmGKB:Curated This SNP was used to tag the H2 haplotype to show association with peripherial arterial disease and coronary artery disease.]
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[PharmGKB:Curated This variant is associated with differential antipsychotic treatment response in individuals of african descent. Patient with rs2842030 TT genotype responded better to perphenazine treatment than by quatiapine, risperidone or ziprasidone. Patient with European descent and rs2842030 GG genotype responded better to risperidone than those with TT genotype.No association was found between this variant and increased susceptibility to the etiology of schizophrenia in Han Chinese.]
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rs1051266 (Arg27Cys, 80G>A) is a snp within SLC19A1 (Solute carrier family 19 (folate transporter), member 1). Cys (A) allele associated with reduced plasma folate women with GA and AA genotypes had higher red blood cell folate concentrations, not significantly associated with serum folate or homocysteine levels methotrexate (antifolate drug) uptake lowest in individuals with GG genotype than those with GA or AA genotypes [PharmGKB:Curated Risk or phenotype-associated allele: SLC19A1 80GG (27Arg/Arg) and GA (27His/Arg)>AA (27His/His) genotypes. Phenotype: A composite pharmacogenetic index (additive from zero to five) was calculated using the following values: ATIC 347CC or TSER*3/*3 or SLC19A1 80GG or SLC19A1 80GA genotypes were valued as 0, ATIC 347CG or TSER*2/*3 or SLC19A1 80AA g...
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[GWAS:Homocysteine levels]
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[GWAS:None]
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showed that rs947267 was significantly associated with schizophrenia rs778294 and rs947267 associated with the risk of schizophrenia, however rs947267, showed an opposite direction of genetic effect on schizophrenia risk here than in a previous study
Frequency: 56.6%
References:3
References:3
Frequency: 56.6%
References:3
References:3
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[PharmGKB:Non-Curated The AUCs of irinotecan, SN-38, SN-38 glucuronide, and APC are influenced by rs3740066, rs2306283, rs35605, rs10276036, and rs717620 .]
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[PharmGKB:Curated The C allele of this variant is associated with increased response of patients with bipolar disorder to lithium treatment relative to that observed in patients carrying two copies of the T allele. This association was observed in two separate cohorts: one of 188 patients, and one of 151 patients.]
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[PharmGKB:Curated This variant is associated with triglyceride lowering response after fibrate treatment in patients with hypertriglyceridemia. Individuals with the G/G genotype had a significantly lower triglyceride lowering reponse than those with wild type.]
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An in silico functional analysis using FASTSNP predicts that this rs4974081 (-3624 A/G) could be a potential transcription factor binding site. This finding suggests that rs4974081 could be a good candidate SNP for association studies with immunosuppressive and chemotherapeutic therapy outcomes.
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Brain-derived neurotrophic factor does not influence age at neurologic onset of Huntington's disease. The influence of serotonin- and other genes on impulsive behavioral aggression and cognitive impulsivity in children with attention-deficit/hyperactivity disorder (ADHD): Findings from a family-based association test (FBAT) analysis. Evidence of association between brain-derived neurotrophic factor gene and bipolar disorder. Brain-derived neurotrophic factor ( BDNF) gene: no major impact on antidepressant treatment response. Molecular differentiation of schizoaffective disorder from schizophrenia using BDNF haplotypes. The role of BDNF genetic polymorphisms in bipolar disorder with psychiatric comorbidities. Pharmacogenetics of antidepressant response. Linkage and association study of neur...
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[PharmGKB:Curated This variant is significantly associated with the efficacy of anti-TNF treatment in rheumatoid arthritis (Adjusted P-value: 0.0000006; OR: 5.4 (1.9, 17.3)). The study is a genome-wide association study using the Illumina HapMap300 SNP chip on 89 RA patients prospectively followed after beginning of anti-TNF therapy.] [GWAS:Amyotrophic lateral sclerosis]
may require more methadone during heroin withdrawal
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rs1128503 is a SNP in the transporter P-glycoprotein (P-gp) 170, encoded by the ABCB1 (also known as MDR1) gene. Methadone is a substrate of this protein, so variants may affect the efficacy and optimal dosage of this drug as used for treating opiate dependence. A study of 98 methadone-maintaining patients concluded that the higher (>150 mg/day) and lower (< or =150 mg/day) methadone dose groups differed significantly in their rs1128503 status (experiment-wise p = 0.0325). Furthermore, individuals with the 3-locus genotype pattern (T;T)-(T;T)-(T;T) for SNPs rs1045642, rs2032582 and rs1128503, respectively, had an approximately 5-fold chance of requiring the 'higher' methadone dose, while individuals heterozygous for these three SNPs have an approximately 3-fold chance of stabilizing ...
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associated with bipolar disorder
Frequency: 56.9%
References:1
References:1
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Nicotine Dependence the minor allele of rs2072660 increased the mean score
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[PharmGKB:Curated This variant in the SCNN1B gene showed the most significant association with fluid retention/oedema in participants diagnosed with T2DM receiving farglitazar plus insulin or glyburide combination therapies. But this association has low penetrance in the fluid retention/oedema case population reflecting that SCNN1B variation may be only one of the covariates that contribute to the development of PPAR[gamma]-induced fluid retention.]
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Bipolar I disorder and schizophrenia: a 440-single-nucleotide polymorphism screen of 64 candidate genes among Ashkenazi Jewish case-parent trios. RGS4 mRNA expression in postmortem human cortex is associated with COMT Val158Met genotype and COMT enzyme activity. RGS4 is not a susceptibility gene for schizophrenia in Japanese: association study in a large case-control population. Association of RGS2 and RGS5 variants with schizophrenia symptom severity. Interaction between interleukin 3 and dystrobrevin-binding protein 1 in schizophrenia. Association of RGS4 variants with schizotypy and cognitive endophenotypes at the population level. A genome-wide investigation of SNPs and CNVs in schizophrenia. [PharmGKB:Curated This variant is associated with differential antipsychotic treatment respon...
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rs1176713 is a SNP, also known as g.14396A>G, in the 5-hydroxytryptamine (serotonin) receptor 3A HTR3A gene. rs1176713 may be a useful predictor of therapeutic response to risperidone treatment in Chinese schizophrenia patients
Frequency: 58.4%
References:3
References:3
Frequency: 58.4%
References:11
References:11
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Alzheimer's disease risk for non ApoE4 carriers is affected by the heterozygous form of rs6265, as well as the diplotypes of rs6265, rs11030104, and rs2049045. [GWAS:Body mass index]
Frequency: 58.4%
References:1
References:1
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per OMIM, Ma et al. (2005) found two different DDC haplotypes associated with nicotine dependence in African Americans and European Americans (with measures of smoking quantity [SQ], heaviness of smoking index [HSI], and the Fagerstrom test for ND [FTND]) *in African Americans, rs921451(T), rs3735273(G), rs1451371(T), rs2060762(G), all three measures sig. associated after correction for multiple testing *in European Americans, rs921451(T), rs3735273(G), rs1451371(T), rs3757472(G), which showed a sig. assoc. w/ the SQ and FTND score [PharmGKB:Curated A study on 2037 smokers and non-smokers from 602 nuclear families of African- or European-American ancestry found first evidence for the involvement of DDC in the susceptibility to nicotine dependence. This variant in the DDC gene is part of t...
1.4x higher schizophrenia risk
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rs6277 (957C>T, Pro319Pro) is one of several SNPs in the dopamine receptor DRD2 gene. In a study of 300+ Russian patients with schizophrenia, the rs6277(C) allele was associated with higher risk. From a pooled meta-study (total of 4 other reports plus this one) the allelic odds ratio is 1.42 (CI: 1.26-1.61, p<0.00005), and the genotypic odds ratio for the (C;C) genotype was 1.6 (CI: 1.32-1.95, p<0.00005). Note that rs6275 and rs6277 are only 18bp apart, hence their very tight linkage (r<sup>2</sup>=1). gs278 reflects a gene-gene interaction between this SNP and a NR3A SNP, rs10989591, in which older adults with a particular combination of genotypes at these two (independent) loci are reported to exhibit better episodic memory. C allele associated significantly (p = 0.0...
Frequency: 58.9%
References:3
References:3
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[PharmGKB:Curated This variant is significantly associated with the efficacy of anti-TNF treatment in rheumatoid arthritis (Adjusted P-value: 0.000004; OR: 6.8 (1.7, 40.3)). The study is a genome-wide association study using the Illumina HapMap300 SNP chip on 89 RA patients prospectively followed after beginning of anti-TNF therapy.] [GWAS:Treatment response to TNF antagonists]
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[GWAS:None]
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A Danish case-control study comprising 373 Crohn's disease and 541 ulcerative colitis patients (and 796 healthy controls) concluded that carriers of the homozygous COX-2 and MDR1 intron 3 variant (rs3789243) had a relatively high risk of CD, odds ratio (95% CI) (OR (95% CI))=2.86 ((1.34-5.88) p=0.006) and 1.39 ((0.99-1.92) p=0.054), respectively, and for UC of 2.63 ((1.33-5.26) p=0.005) and 1.28 ((0.96-1.51) p=0.093), respectively, assuming complete dominance. [PharmGKB:Curated This variant maybe associated with drug resistance in chinese epilepsy patients. Sample size: 464 chinese epilepsy patients (270 drug responsive, 194 drug resistant).] [OMIM:ATP-BINDING CASSETTE, SUBFAMILY B, MEMBER 1; ABCB1]
Frequency: 59.1%
References:10
References:10
3.4x risk of gout
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rs16890979 has been found to be associated with gout in several independent studies. It may be a variation in the SLC2A9 gene, which is more commonly known as GLUT9. In a study of Old Order Amish, rs16890979 - which is also known as the missense mutation Val253Ile - was found as the most significantly associated SNP during a follow-up study based on a genome wide association study. Each copy of the minor allele, rs16890979(T), was associated with a decrease of 0.47 mg/dl in the uric acid level (CI: 0.31-0.63, p = 1.43 x 10e-11). See also: 23andMe blog gout Independently, a large study totaling 7,699 participants in the Framingham cohort and 4,148 participants in the Rotterdam cohort was conducted, with genome-wide significant SNPs then replicated in 11,000+ Caucasian and ~4,000 African-Ame...
Frequency: 59.3%
References:1
References:1
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[PharmGKB:Curated SNP is associated with clinical reponse to methotrexate in patients with psoriasis.]
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Rs1062613 (C178T, Pro16Ser) is located within the 5' UTR of HTR3A and may effect HTR3A expression. reporter constructs containing the T allele showed increased HTR3A expression compared to the C allele CC and CT carriers associated with higher harm avoidance (p = 0.04) scores in 2 sample groups of Swedish women (366 in total), and non-conformity in 1 sample no significant association between treatment-resistant schizophrenia and Rs1062613, however, maintenance neuroleptic dose was significantly higher for TT carriers (p = 0.041) [PharmGKB:Curated This promoter variant regulates expression of the gene. The T allele is associated with increased expression.]
Frequency: 59.8%
References:1
References:1
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[PharmGKB:Curated In a GWAS of 3497 Dutch subjects from the Netherlands Study of Depression and Anxiety or from the Netherlands Twin Registry, this SNP was found to be associated with Current Smoking (p = 0.00009556;OR for minor allele C:1.277).]
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[PharmGKB:Curated This SNP was significantly associated with response to therapy in 182 patient who received treatment for major depression.]
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Association study between the serotonin 1A receptor (HTR1A) gene and neuroticism, major depression, and anxiety disorders. SSRI response in depression may be influenced by SNPs in HTR1B and HTR1A. Pharmacogenetics of antidepressant response. Sertraline (Zoloft) response in major depressive disorder is not associated with three 5-HT1A receptor gene polymorphisms (rs6295, rs10042486, or rs1364043) in Chinese-Han patients. [PharmGKB:Curated A study, investigating the response of SSRI in 137 Japanese major depression subjects, observed a significant association of better response to antidepressant in rs10042486 (P < 0.0001), rs6295 (P < 0.0001) and rs1364043 (P = 0.018) genotype carriers (minor allele homozygotes), independently from clinical variables. The rs6295 variant has been found...
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Associated with at least one 'mortality outcome' in a study of ~10,000 individuals. Separately, a meta-analysis of 10 case-control studies, including over 2,200 Graves' disease cases, concluded that rs1799964(C) carriers were associated with the disease. [PharmGKB:Curated Haplotype tagging SNP.] [GWAS:Crohn's disease]
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Candidate gene association studies of genes involved in neuronal cholinergic transmission in Alzheimer's disease suggests choline acetyltransferase as a candidate deserving further study. Genetic variation in the choline acetyltransferase (CHAT) gene may be associated with the risk of Alzheimer's disease. ApoE-epsilon 4-dependent association of the choline acetyltransferase gene polymorphisms (2384G>A and 1882G>A) with Alzheimer's disease. Choline acetyltransferase variants and their influence in schizophrenia and olanzapine response. Combining fMRI and SNP data to investigate connections between brain function and genetics using parallel ICA. Replication and extension of association of choline acetyltransferase with nicotine dependence in European and African American smokers.
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[PharmGKB:Curated SNP is significantly associated with the incidence of biopsyproven acute rejection in the first year post-transplantation in kidney transplant patients.]
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Genetic variation in the choline acetyltransferase (CHAT) gene may be associated with the risk of Alzheimer's disease. A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease. ApoE-epsilon 4-dependent association of the choline acetyltransferase gene polymorphisms (2384G>A and 1882G>A) with Alzheimer's disease. Choline acetyltransferase variants and their influence in schizophrenia and olanzapine response. Combining fMRI and SNP data to investigate connections between brain function and genetics using parallel ICA. Regional association-based fine-mapping for sodium-lithium countertransport on chromosome 10. Identification of pharmacogenetic markers in smoking cessation therapy. Replication and extension of association of choline a...
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Implicated as part of a haplotype of the dopamine D1 receptor DRD1 gene associated with autism spectrum disorders in families having only affected males. The haplotype is rs265981(C)-rs4532(A)-rs686(T) as published, though not necessarily as oriented in dbSNP.
Frequency: 61.1%
References:6
References:6
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[PharmGKB:Curated Risk or phenotype-associated allele: C . Phenotype: In a meta-analysis of nine genome-wide association studies (n = 15,234 nondiabetic individuals) and a follow-up of 29 independent loci (n = 6,958-30,620), this SNP was found to be associated with 2-h glucose level (a clinical measure of glucose tolerance). Effect (s.e.m.) = 0.08(0.01) mmol/l per C allele. Study size/population/ethnicity: 15,234 plus 6,958-30,620 nondiabetic individuals of European descent. Significance metric(s): p = 4.23 x 10(-10). Type of association: CO;GN.] [GWAS:Two-hour glucose challenge]
normal
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rs1554973 is a SNP near the toll-like receptor 4 TLR4 gene. A study of 109 pregnant women focusing on TLR4 SNPs associated with chorionic plate inflammation concluded that rs1554973 was associated with increased risk when present in the fetal genome. The risk allele's increased odds ratio for clinically significant inflammation was 4.95 (CI: 3.0-5.6, p = .005). No evidence of major effects in several Toll-like receptor gene polymorphisms in rheumatoid arthritis. Traffic-related air pollution, oxidative stress genes, and asthma (ECHRS). Sequence variants in the TLR4 and TLR6-1-10 genes and prostate cancer risk. Results based on pooled analysis from three independent studies. Role of polymorphic variants as genetic modulators of infection in neonatal sepsis. Interaction between interleukin-1...
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Implicated as part of a haplotype of the dopamine D1 receptor DRD1 gene associated with autism spectrum disorders in families having only affected males. The haplotype is rs265981(C)-rs4532(A)-rs686(T) as published, though not necessarily as oriented in dbSNP. [OMIM:DOPAMINE RECEPTOR D1; DRD1]
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[GWAS:Rheumatoid arthritis]
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Implicated as part of a haplotype of the dopamine D1 receptor DRD1 gene associated with autism spectrum disorders in families having only affected males. The haplotype is rs265981(C)-rs4532(A)-rs686(T) as published, though not necessarily as oriented in dbSNP. Significant association of DRD1 with nicotine dependence. A haplotype of the DRD1 gene is associated with alcohol dependence. The influence of serotonin- and other genes on impulsive behavioral aggression and cognitive impulsivity in children with attention-deficit/hyperactivity disorder (ADHD): Findings from a family-based association test (FBAT) analysis. Differential allelic expression of dopamine D1 receptor gene (DRD1) is modulated by microRNA miR-504. Heroin addiction in African Americans: a hypothesis-driven association study....
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rs2230806, also known as Arg219Lys or R219K, is a SNP in the ABCA1 ATP-binding cassette, sub-family A (ABC1), member 1 gene. The rs2230806(G) allele encodes the arginine (R), and the (A) allele encodes the lysine (K). A meta-analysis published in 2011 comprising 22 studies with 6597 cases and 15,369 controls studied the association between the rs2230806 and risk for coronary artery disease. Overall, rs2230806(A) significantly associated with a higher HDL-C level in Asians and does lower the risk (odds ratio 0.76, CI: 0.68-0.85, p=3.78e-07) of coronary artery disease in Asians and Caucasians. ABCA1 modulates CSF cholesterol levels and influences the age at onset of Alzheimer's disease. Gender-specific association of ATP-binding cassette transporter 1 (ABCA1) polymorphisms with the risk of l...
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[GWAS:None]
Frequency: 62.8%
References:11
References:11
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Genome-wide association with bone mass and geometry in the Framingham Heart Study. Vitamin D receptor gene polymorphisms and epithelial ovarian cancer risk. CDX2 VDR polymorphism and colorectal cancer. Vitamin D receptor gene haplotypes and susceptibility to HIV-1 infection in injection drug users. Vitamin D receptor gene polymorphisms and haplotypes and postmenopausal breast cancer risk. Association of vitamin D receptor gene variants, adiposity and colon cancer. Modification of the inverse association between dietary vitamin D intake and colorectal cancer risk by a FokI variant supports a chemoprotective action of Vitamin D intake mediated through VDR binding. Circulating 25-hydroxyvitamin D, VDR polymorphisms, and survival in advanced non-small-cell lung cancer. Colon tumor mutations an...
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A common variant of the ABO gene protects against hypertension in a Spanish population. Pharmacogenetic predictors of angiotensin-converting enzyme inhibitor-induced cough: the role of ACE, ABO, and BDKRB2 genes. Genome-wide association identifies the ABO blood group as a major locus associated with serum levels of soluble E-selectin. Genome-wide association study identifies variants in the ABO locus associated with susceptibility to pancreatic cancer. [PharmGKB:Curated Risk or phenotype-associated allele: C Phenotype: Mean angiotensin converting enzyme activity among subjects with the CC genotype at ABO-rs495828 was higher than the CA or AA. Carriage of the A allele is associated with the A blood group antigen. The mean ACE activity of the blood type A subjects was significantly lower th...
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[PharmGKB:Curated This study investigated aldosterone response to two antihypertensive drugs with the result that the existence of one or more variants in the KNG1gene influences interindividual variation in aldosterone response. SNP rs4686799 was associated in African-American and European-American responders to the diuretic (p=0.04 and p=0.07 respectively).]
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[PharmGKB:Curated This SNP located on chromosomes 22q13 is associated with susceptibility to rheumatoid arthritis in a validation study of 4,106 individuals with rheumatoid arthritis and an expanded reference group of 11,238 subjects.]
Frequency: 63.7%
References:1
References:1
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[GWAS:None]
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[PharmGKB:Curated In a GWAS study, this SNP was modestly associated with warfarin dose, and was in perfect linkage disequilibrium with rs4086116.]
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[PharmGKB:Curated Phenotype: This variant is associated with null virological response (NVR) in Janapese patients with hepatitis C virus infection treated with PEG-INF-alpha plus ribavirin. Study size: Initial sample:154; Replication Sample: 172. Study population/ethnicity: Japanese. Significance metric(s): P=1.98 x 10(-31) (NVR). Type of association: GN; CO]
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Association of the multidrug-resistance-associated protein gene (ABCC2) variants with intrahepatic cholestasis of pregnancy. Polymorphisms of MRP2 (ABCC2) are associated with susceptibility to nonalcoholic fatty liver disease. MRP2 and GSTP1 polymorphisms and chemotherapy response in advanced non-small cell lung cancer. Genetic polymorphisms influence mycophenolate mofetil-related adverse events in pediatric heart transplant patients. ADME pharmacogenetics: investigation of the pharmacokinetics of the antiretroviral agent lopinavir coformulated with ritonavir. Interindividual variability in hepatic expression of the multidrug resistance-associated protein 2 (MRP2/ABCC2): quantification by liquid chromatography/tandem mass spectrometry. A comprehensive study of polymorphisms in ABCB1, ABCC2...
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[PharmGKB:Non-Curated This variant is significantly associated with the efficacy of anti-TNF treatment in rheumatoid arthritis (Adjusted P-value: 0.000005; OR: 10.2 (2.6, 59.2)). The study is a genome-wide association study using the Illumina HapMap300 SNP chip on 89 RA patients prospectively followed after beginning of anti-TNF therapy.] [GWAS:Treatment response to TNF antagonists]
normal
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rs1611115 (C-1021T) is a SNP near the dopamine beta-hydroxylase (DBH) gene. per OMIM, the T allele is associated with lower DBH expression in plasma (16 of TT genotype had DBH activity of 4.1, 46 of CT genotype had DBH activity of 25.2, and 112 of CC genotype had DBH activity of 48.1 nmol/min/ml) Association tests related to affective disorders such as ADHD were performed using four independent samples, healthy volunteers (N = 387), patients with affective disorders (N = 182), adult attention deficit hyperactivity disorder (ADHD) patients (N = 407), and patients with personality disorders (N = 637). Personality disorder patients carrying the DBH TT genotype exhibited higher neuroticism and novelty seeking scores as compared to individuals with the (C;C) or (C;T) genotype. Analyses on the l...
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[GWAS:Treatment response to citalopram]
Frequency: 66.4%
References:1
References:1
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[PharmGKB:Curated Risk or phenotype-associated allele: A. AA homozygotes had reduced HR for cardiac events while treated with perindopril. Study size: 8907. Study population/ethnicity: PERGENE study; EUROPA trial; European; White. Significance metric(s): HR = 0.64 (0.55-0.78), p = 0.012. Type of association: CO]
Normal risk of adverse drug reations from cyclophosphamide treatments
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rs9561778 is a SNP in the ATP-binding cassette, sub-family C (CFTR/MRP), member 4 ABCC4 gene. A stepwise case-control study of ~400 breast cancer Japanese patients receiving cyclophosphamide-based combination chemotherapy, roughly divided equally between those having or not having serious adverse drug reactions (ADRs), concluded that carriers of rs9561778(T) allele had a ~2x higher risk of ADRs. The ADRs for these patients tended to be gastrointestinal toxicity and leukopenia/neutropenia. [PharmGKB:Curated Risk or phenotype-associated allele: T. Phenotype: In a stepwise case-control association study of breast cancer patients receiving cyclophosphamide combination therapy, rs9561778 in ABCC4 was associated with cyclophosphamide-induced ADRs. Study size: 403. Study population/ethnicity: Ja...
Possibly more 'Insistence on Sameness' on ADI-R test.Possibly increased FTND nicotine dependence.[http://www.ncbi.nlm.nih.gov/pubmed/22309839?dopt=Abstract
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rs167771 was significantly associated with autism spectrum disorder in a study of 144 patients. G allele associated with increased extra-pyramidal symptom risk as a result of risperidone treatment in a study of 321 psychiatric inpatients (81 presenting with EPS and 189 without) [PharmGKB:Curated Risk or phenotype-associated allele: G. Phenotype: The G variant of rs167771 was associated with increased risk for extrapyramidal symptoms in psychiatric patients receiving risperidone. Study size: 132. Study population/ethnicity: Patients with Schizophrenia or Bipolar disorder receiving antipsychotics; Caucasians; Spain; Catalonia. Significance metric(s): OR = 3.3; p = 0.00013. Type of association: PD.]
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Association study of the genetic polymorphisms of the transcription factor 7-like 2 (TCF7L2) gene and type 2 diabetes in the Chinese population. Association of TCF7L2 polymorphisms with susceptibility to type 2 diabetes in 4,087 Japanese subjects. Exon sequencing and association analysis of polymorphisms in TCF7L2 with type 2 diabetes in a Chinese population. Meta-analysis of the association between SNPs in TCF7L2 and type 2 diabetes in East Asian population. Investigation of type 2 diabetes risk alleles support CDKN2A/B, CDKAL1, and TCF7L2 as susceptibility genes in a Han Chinese cohort. [PharmGKB:Curated Risk or phenotype-associated allele: T allele. Phenotype: Body mass index was significantly lower (p < 0.030), and cholesterol levels (p < 0.012)) were significantly higher in T2D...
Frequency: 68.1%
References:5
References:5
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Common variants in the SLCO1B3 locus are associated with bilirubin levels and unconjugated hyperbilirubinemia. [PharmGKB:Curated Risk or phenotype-associated allele: T allele, with additive genotypic effect. Phenotype: Genome-wide analysis of 398,699 germline SNPs showed association of the rs11045879 T allele increased methotrexate (MTX) plasma clearance, with additive effect per T allele (increase of 13.1 mL/min/m(2) per allele in 434 subjects), after adjusting for age, race, sex, and MTX regimen. Variants rs11045879 and rs4149081 were in linkage disequilibrium (r(2) = 1). The T allele was associated with increased risk of gastrointestinal toxicity (mucositis) (OR = 16.4, p = 0.004). Pharmacokinetics differed by ethnicity (MTX clearance: African>Caucasian). Study size: 434 (discovery ...
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[PharmGKB:Curated Risk or phenotype-associated allele: G allele, with additive genotypic effect. Phenotype: Genome-wide analysis of 398,699 germline SNPs showed association of the rs4149081 G allele with increased methotrexate (MTX) plasma clearance, with an additive effect per G allele (increase of 12.7 mL/min/m(2) per allele in 434 subjects), after adjusting for age, race, sex, and MTX regimen. Variants rs11045879 and rs4149081 were in linkage disequilibrium (r(2) = 1). The G allele was associated with increased risk of gastrointestinal toxicity (mucositis) (OR = 15.3, p = 0.03). Pharmacokinetics differed by ethnicity (MTX clearance: African>Caucasian). Study size: 434 (discovery cohort), 206 (independent validation cohort), 640 (combined cohort). Study population/ethnicity: Multiethn...
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[PharmGKB:Curated This variant is significantly associated with the efficacy of anti-TNF treatment in rheumatoid arthritis (Adjusted P-value: 0.000003; OR: 11.1 (2.5, 103.3)). The study is a genome-wide association study using the Illumina HapMap300 SNP chip on 89 RA patients prospectively followed after beginning of anti-TNF therapy.] [GWAS:Treatment response to TNF antagonists]
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[PharmGKB:Curated The G allele of this SNP is associated with increased incidence of medium-severe nausea or vomiting, and with reduced leukocyte counts in gastric carcinoma and colon carcinoma patients treated with 5-fluorouracil. The elimination constant (Ke) for 5-fluorouracil was significantly lower in patients homozygous for the G allele.]
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[PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: The GG (Gly/Gly) genotype was associated with lower risk for colorectal cancer. This risk was further lowered in men with low alcohol intake. Study size: Study population/ethnicity: Patients with colorectal cancer from the Physicians' Health Study (PHS) and the Health Professional Follow-up Study (HPFS). Significance metric(s): OR = 0.59 (95% CI, 0.27-1.27); OR = 0.27 (95% CI, 0.09-0.81)(interaction with alcohol) Type of association: CO]
Frequency: 69.9%
References:1
References:1
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(T;T) associated with a higher risk of osteonecrosis of the jaw in am small study of multiple myeloma patients under bisphosphonate therapy [PharmGKB:Non-Curated This variant was associated with bisphosphonate-related osteonecrosis of the jaw (ONJ) in a GWAS study. Individuals homozygous for the T allele had an increased risk for developing ONJ.] [OMIM:MYELOMA, MULTIPLE] [GWAS:Osteonecrosis of the jaw]
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[PharmGKB:Curated This variant is significantly associated with the efficacy of anti-TNF treatment in rheumatoid arthritis (Adjusted P-value: 0.000003; OR: 7.6 (1.9, 44.6)). The study is a genome-wide association study using the Illumina HapMap300 SNP chip on 89 RA patients prospectively followed after beginning of anti-TNF therapy.]
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imputed via rs3897584 and rs2471854 in http://www.pnas.org/content/early/2011/01/07/1011687108.full.pdf+html
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[PharmGKB:Curated This variant is in intron 5, and T allele shifts mRNA splicing from the short form (D2S) to the long form (D2L). The T allele carriers are also associated with reduced working memory and attension perfermance.]
Frequency: 71.7%
References:2
References:2
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[PharmGKB:Curated This variant is associated with differences in clinical efficacy of antidepressants, most likely by influencing their access to the brain.]
Frequency: 71.7%
Repute:Bad
References:3
Repute:Bad
References:3
normal (lower) response to certain antidepressants
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rs12720067 is a SNP in the ABCB1 gene (also known as the MDR1 gene), which encodes a protein that transports certain molecules across the blood-brain barrier. SNPs in ABCB1 may thus influence the intracerebral concentrations of certain drugs and thus their efficacy or potential for adverse side effects. rs12720067 is one of 9 SNPs found within a tight linkage block (r<sup>2</sup> >= 0.8 ) such that the minor allele at any one of them predicts (with ~80%+ accuracy) that the other SNPs will also be the minor allele. The list of the 9 SNPs is shown below. When treated for depression with substrates of the protein encoded by ABCB1, carriers of one or two minor alleles at these ABCB1 SNPs have been reported to respond better than non-carriers. The antidepressant drugs that are kn...
Frequency: 71.7%
References:3
References:3
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[PharmGKB:Curated Risk or phenotype-associated allele: T Phenotype: The SLC10A2:rs2301159 T variant was associated with toxicity in response to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.01 Type of association: CO; TOX]
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[PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: The SPG7:rs12960 G variant was associated with toxicity in response to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.004 Type of association: CO; TOX]
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[PharmGKB:Curated Risk or phenotype-associated allele: SLCO1B3: T334. Phenotype: The metabolic ratio of glucuronidated mycophenolic acid (MPAG) to mycophenolic acid (MPA) showed a very significant decrease in carriers of the SLCO1B3 T334 allele (p = 0.0001). Carriers of at least one SLCO1B3 T334 allele (n = 22) had a 1.42-fold higher (p = 0.0003) MPA AUC(0-12 hours) and a 1.38-fold higher (p = 0.0010) Cmax as compared with carriers of the 334GG genotype (n = 48). Patients carrying 334 TT or TC genotypes (n = 22) had significantly higher MPA AUC(4-9 hours) than patients carrying the CC genotype (n = 48; p = 0.0027). However, they also had higher AUC(0-4 h) (p = 0.0008), resulting in an unchanged AUC(4-9 h)/AUC(0-9 h) ratio (p = 0.4945). In the subgroups of patients cotreated with sirolimus ...
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influences warfarin dose [PharmGKB:Non-Curated This intronic variant in the membrane calcium-channel gene CACNA1C was correlated with warfarin dose (p = 9.2 × 10−5) in the index population (n = 181) from a GWAS study of white patients undergoing anticoagulation therapy. Combined analysis of the index and replication populations (n = 374) yielded a p value of 8.6 × 10−7. "However, this variant did not reach established significance threshold independently in the replication population (P = .002), nor did it achieve significance after multiple testing correction in multivariate modeling (uncorrected P = .003)".] [GWAS:Warfarin maintenance dose]
1.12x risk on diuretic; if hypertensive, better outcome when treated with calcium channel blocker than with diuretic
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rs5065, also known as T2238C, is a SNP in the atrial natriuretic precursor A NPPA gene. A large study has been conducted in which 42,418 hypertensive participants 55 or older were followed for several years while on one of four medications: a diuretic, a calcium antagonist, an angiotensin-converting enzyme inhibitor, or an alpha-blocker. The primary endpoint was either fatal heart disease or a heart attack. The blood pressure after six months of rs5065(G;G) patients (note: genotype is in dbSNP orientation, not as published) was lower if the patients were treated with diuretics compared to other medications, with smaller variation seen for (A;A) genotypes. The authors noted that none of the findings retained statistical significance after correction for multiple comparisons, but since the t...
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In a survey that scanned 80 genes, no SNPs with a large effect were found to be associated with bipolar disorder. However, the SNP with the largest association was rs1170191, in first intron of the diacylglycerol kinase eta DGKH gene. The odds ratio for the risk allele of this SNP is 1.59 (p = 1.5x10e-8, experiment-wide p<0.01).
Frequency: 73.5%
References:2
References:2
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Association between liver X receptor alpha gene polymorphisms and risk of metabolic syndrome in French populations. Functional and genetic analysis in type 2 diabetes of liver X receptor alleles--a cohort study. Genetic variation within the NR1H2 gene encoding liver X receptor beta associates with insulin secretion in subjects at increased risk for type 2 diabetes. Associations between common genetic polymorphisms in the liver X receptor alpha and its target genes with the serum HDL-cholesterol concentration in adolescents of the HELENA Study. Liver X receptor alpha gene polymorphisms and variable cardiovascular outcomes in patients treated with antihypertensive therapy: results from the INVEST-GENES study.
greater relative benefit of iloperidone to schizophrenics
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rs1800169 is a SNP in the ciliary neurotrophic factor CNTF gene. In a study of 417 patients with schizophrenia, 279 were treated with iloperidone while 138 were treated with placebo. Iloperidone significantly improved in 6 clinical scores versus placebo. rs1800169(G;G) homozygotes showed greater improvement with iloperidone compared to placebo for 3 of the clinical scores compared to carriers of a rs1800169(A) allele. [PharmGKB:Curated Schizophrenia patients with homozygous G/G for the rs1800169 show better response to iloperidone.]
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No genetic association between dopamine D1 receptor gene and (early onset) schizophrenia.
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rs568408(A) and rs3212227(C) variant genotypes were associated with a significantly increased risk of cervical cancer [adjusted odds ratio, 1.43; 95% confidence interval (CI), 1.06-1.93; and adjusted odds ratio, 1.30; 95% CI, 0.97-1.75, respectively]. subjects carrying variant genotypes of both loci had a 1.82-fold (95% CI, 1.28-2.57) increased risk of cervical cancer
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rs3813928 (-995G>A / G-995A) is a SNP upstream of HTR2C. in a small sample of 45 autistic patients taking risperidone for up to one year, HTR2A Rs6311 (-1438G>A), DRD3 rs6280 (Ser9Gly), HTR2C rs3813928 (995G>A) and ABCB1 rs1128503) (1236C>T) were predictive of risperidone response Identification of functional SNPs in the 5-prime flanking sequences of human genes. The association between HTR2C polymorphisms and obesity in psychiatric patients using antipsychotics: a cross-sectional study. The association between HTR2C gene polymorphisms and the metabolic syndrome in patients with schizophrenia. [PharmGKB:Curated Risk or phenotype-associated allele: A Phenotype: Carriers of the A variant of HTR2C:(-995)G>A had higher Autism Treatment Evaluation Checklist (ATEC) scores, indica...
Frequency: 74.3%
References:4
References:4
normal risk
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rs140504, a SNP in the BCR gene on chromosome 22, has been associated with increased risk for bipolar disorder. The odds ratio for carriers of the minor allele (G) are reported as 1.45 (CI:1.11 - 1.84, p=0.0054) based on a study of 171 Japanese patients. [OMIM:MAJOR AFFECTIVE DISORDER 1; MAFD1]
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[PharmGKB:Curated Risk or phenotype-associated allele: SCLO1B3 haplotype formed by 112Ser>Ala (rs4149117, 334T>G) and 223Met>Ile (rs7311358, 699G>A). Phenotype: HEK293 cells transiently expressing the SCLO1B3 334G-699A haplotype or reference haplotype were incubated in the presence of increasing concentrations of mycophenolic acid phenyl-glucuronide (MPAG) for 10 min. The uptake of MPAG according to the SCLO1B3 334G-699A haplotype was markedly lower than in cells expressing the reference sequence 334T-669G. Type of association: GN; FA; PK]
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[PharmGKB:Curated Risk or phenotype-associated allele: C Phenotype: Patients homozygous for the rs4436578-C allele were at increased risk of body weight gain as compared with the heterozygotes and those of the rs4436578-TT genotype after atypical antipsychotics treatment Study size: 479 chronic inpatients with schizophrenia Study population/ethnicity: Chinese Significance metric(s): OR = 3.36 (95% confidence interval=1.62 approximately 7.00) Type of association: GN]
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[GWAS:None]
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[GWAS:None]
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[PharmGKB:Curated patients with ref CC genotype had significantly higher clearance of doxorubicin compared to CT patients, 24.07 CL/BSA vs 20.13 CL/BSA (P=0.028); patients with CC genotype had trend toward lower exposure levels vs CT patients, 15.44 AUC/dose/BSA vs 20.36 AUC/dose/BSA (P=0.066); patients with ref CC genotype had lower peak plasma concentration of doxorubicinol compared to CT patients 0.32 Cmax/dose/BSA vs 0.49 Cmas/dose/BSA (P=0.030) ; study population: patients with invasive breast cancer; study size=62; ethnicity Chinese (74%), Malays (18%) and Indians (8%)]
Frequency: 76.1%
References:1
References:1
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An association analysis of Alzheimer disease candidate genes detects an ancestral risk haplotype clade in ACE and putative multilocus association between ACE, A2M, and LRRTM3. Disease-associated mutations that alter the RNA structural ensemble.
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[PharmGKB:Curated This variant is found to be a risk marker for statin induced myalgia]
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[GWAS:Response to serotonin reuptake inhibitors in major depressive disorder (plasma drug and metabolite levels)]
Frequency: 76.9%
References:2
References:2
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rs1042114 increases susceptibility to Substance dependence, Opioid 3.56 times for carriers of the G allele [OMIM:OPIOID RECEPTOR, DELTA-1; OPRD1]
Frequency: 77.0%
References:8
References:8
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[PharmGKB:Curated Lymphocytes carrying the C allele of the IMPDH2:IVS7+10T>C variant had less of a response to mycophenolic acid treatment compared to cells from TT individuals.]
The rs2243093 locus is located in the platelet glycoprotein (1bα) gene. This locus is associated with an increase risk for coronary heart disease and ischemic stroke. However, individuals who possess (T;T) are believed to be less at risk than those who possess a (C;C) genotype.
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Resides within the platelet glycoprotein (1bα) gene. The rs2243093 variant (C;C) was found to increase the odds of coronary heart disease in a clinical Chinese Han population. The (C;C) genotype is also associated with a risk of ischemic stroke. Rs2243093 is also classified in the literature as the -5T/C, Kozak sequence polymorphism. A case-control study of 246 Chinese Han patients (with preexisting coronary heart disease) reported that in comparison to the '(T;T)' genotype, the '(C;C)' genotype is associated with an increased risk for coronary heart disease with an odds ratio of 3.41 (CI: 1.19-9.75, p<0.029). A meta-analysis was performed in order to test the hypothesis that genetic variation of the platelet glycoprotein 1bα gene(which includes rs2243093 Kozak variant (n=1984...
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[PharmGKB:Curated Phenotype: This variant is associated with null virological response (NVR) in Janapese patients with hepatitis C virus infection treated with PEG-INF-alpha plus ribavirin. Study size: Initial sample:154; Replication Sample: 172. Study population/ethnicity: Japanese. Significance metric(s): P=1.8 x 10(-30) (NVR). Type of association: GN; CO]
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[PharmGKB:Curated This variant in the corticotropin-releasing hormone receptor-2 gene was associated with acute bronchodilator response in the 427-participant Sepracor study, but not in the 608-participant Childhood Asthma Management Program (CAMP) or the 152-participant LODO trial. The mean ages of the participants in the CAMP, Sepracor, and Lodo cohorts were 8.9, 32.6, and 42.9 years of age, respectively. Only Caucasians were analyzed in each of these studies.]
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rs1386494 is a SNP in the tryptophan hydroxylase 2 (TPH2) gene on chromosome 12. It is located about 20,000 bp from the 5' end of the gene. This SNP has been found to be associated with various mental health disorders. TPH1 and TPH2 are two isoforms of the rate-limiting enzyme for the biosynthesis of 5-HT (serotonin), a neurotransmitter involved in many neurological processes. Both isoforms have been studied extensively as genetic markers of mental health. Many association studies have linked the TPH1 gene to suicidality, alcoholism and depression. However, the second TPH isoform was not discovered until more recently, when it was observed that TPH1 knockout mice were still able to produce normal levels of 5-HT. It has been shown to be expressed exclusively in the brain, suggesting that it...
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Single nucleotide polymorphisms of microRNA machinery genes modify the risk of renal cell carcinoma. Genetic variations in microRNA-related genes are novel susceptibility loci for esophageal cancer risk. Black carbon exposures, blood pressure, and interactions with single nucleotide polymorphisms in MicroRNA processing genes.
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[GWAS:Capecitabine sensitivity]
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[PharmGKB:Curated patients with ref GG genotype had significantly higher clearance of doxorubicin compared to GA patients, 24.42 CL/BSA vs 20.43 CL/BSA (P=0.009); patients with GG genotype hadlower exposure levels vs GA patients, 15.62 AUC/dose/BSA vs 22.43 AUC/dose/BSA (P=0.024); patients with ref GG genotype had lower peak plasma concentration of doxorubicinol compared to GA patients 0.32 Cmax/dose/BSA vs 0.48 Cmas/dose/BSA (P=0.030) ; study population: patients with invasive breast cancer; study size=62; ethnicity Chinese (74%), Malays (18%) and Indians (8%);]
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Tryptophan hydroxylase 2 (TPH2) gene variants associated with ADHD. Preferential transmission of paternal alleles at risk genes in attention-deficit/hyperactivity disorder. The analysis of 51 genes in DSM-IV combined type attention deficit hyperactivity disorder: association signals in DRD4, DAT1 and 16 other genes.
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[GWAS:None]
7x less likely to respond to certain antidepressants
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rs4148740 is a SNP in the ABCB1 gene (also known as the MDR1 gene), which encodes a protein that transports certain molecules across the blood-brain barrier. SNPs in ABCB1 may thus influence the intracerebral concentrations of certain drugs and thus their efficacy or potential for adverse side effects. rs4148740 is one of 9 SNPs found within a tight linkage block (r<sup>2</sup> >= 0.8 ) such that the minor allele at any one of them predicts (with ~80%+ accuracy) that the other SNPs will also be the minor allele. The list of the 9 SNPs is shown below. When treated for depression with substrates of the protein encoded by ABCB1, carriers of one or two minor alleles at these ABCB1 SNPs have been reported to respond better than non-carriers. The antidepressant drugs that are know...
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[GWAS:Response to haloperidol in psychosis]
Frequency: 80.5%
References:2
References:2
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[PharmGKB:Curated Based on an study on 284 Mexican Americans, this variant in the 3' UTR of TBX21 is significantly associated with major depressive disorder (MDD). The results implicate that the specific UTR variation increases the risks for a T-cell dysfunction in MDD in the studied population.]
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[PharmGKB:Curated Risk or phenotype-associated allele: None. Phenotype: Variants identified in a screen of 13 genes involved in the gemcitabine drug metabolic pathway. For the SLC28A1:1383C>T SNP, the T allele was at frequency was 0.08 and 0.05 in Europeans and Africans, respectively. There was no significant difference between ethnic groups in genotype frequency distribution (p > 0.05). Study size: 185. Study population/ethnicity: Healthy, unrelated blood donors of European (n = 91) and African (n = 94) descent. Significance metric(s): Not significant, p > 0.05. Type of association: GN.]
Frequency: 81.2%
References:4
References:4
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Role of the PXR gene locus in inflammatory bowel diseases. Polymorphisms in NF-kappaB, PXR, LXR, PPARgamma and risk of inflammatory bowel disease. Pregnane X receptor (PXR/NR1I2) gene haplotypes modulate susceptibility to inflammatory bowel disease. Variants of the human NR1I2 (PXR) locus in chronic periodontitis.
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[OMIM:DYSTROBREVIN-BINDING PROTEIN 1; DTNBP1]
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rs3740065 is a SNP in the ATP-binding cassette, sub-family C (CFTR/MRP), member 2 ABCC2 gene. A study of 282 hormone receptor-positive, invasive breast cancer Japanese patients receiving tamoxifen found a significant association with shorter recurrence-free survival (p = .00017; hazard ratio 10.64, CI: 1.44 - 78.88) in rs3740065(T;T) patients; the hazard ratio for carriers of one (T) allele was 3.5 (CI: 0.5-26). Curiously, no significant difference in plasma levels of the tamoxifen metabolites endoxifen or 4-hydroxytamoxifen were seen. This same study of tamoxifen users concluded that rs3740065(T;T) patients who also had two CYP2D6 risk alleles had a 45 fold higher risk of recurrence than patients with zero or one (out of the possible four) risk alleles. The overall average recurrence risk...
Frequency: 84.6%
References:1
References:1
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In a study of 1,757 cases of Alzheimer's disease and 6,295 controls, an interaction was replicated between IL6 genotype rs2069837(A;A) and IL10 genotype rs1800871(C;C). The synergy factor (SF) was 1.63 (CI: 1.10-2.41, p = 0.01), controlling for age, gender and ApoE4 genotype.
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Gemcitabine and arabinosylcytosin pharmacogenomics: genome-wide association and drug response biomarkers. [PharmGKB:Curated Risk or phenotype-associated allele: None. Phenotype: Variants identified in a screen of 13 genes involved in the gemcitabine drug metabolic pathway. For the intronic DCK:IVS1-1110T>C SNP, the C allele was not observed among the Europeans and Africans interrogated in this study. There was no significant difference between ethnic groups in genotype frequency distribution (p > 0.05). Study size: 179. Study population/ethnicity: Healthy, unrelated blood donors of European (n = 90) and African (n = 89) descent. Significance metric(s): Not significant, p > 0.05. Type of association: GN.]
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Genetic variation in insulin-like growth factor signaling genes and breast cancer risk among BRCA1 and BRCA2 carriers. No association of the IRS1 and PAX4 genes with type I diabetes. Overview of the Rapid Response data.
Frequency: 86.7%
References:1
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Frequency: 87.6%
References:1
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[GWAS:Asthma (bronchodilator response)]
Frequency: 89.1%
References:3
References:3
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A study of 12,854 Japanese subjects replicated the association between rs3093059 and serum CRP levels (p = 3.5 x 10e-21). Association study of CRP gene polymorphisms with serum CRP level and cardiovascular risk rs3093059 rs3091244 A prospective assessment of the Y402H variant in complement factor H, genetic variants in C-reactive protein, and risk of age-related macular degeneration. C-reactive protein gene variation and type 2 diabetes mellitus: a case-control study. Genetic determinants of basal C-reactive protein expression in Filipino systemic lupus erythematosus families. Bayesian meta-analysis of genetic association studies with different sets of markers. Loci related to metabolic-syndrome pathways including LEPR,HNF1A, IL6R, and GCKR associate with plasma C-reactive protein: the Wom...
Frequency: 92.9%
References:1
References:1
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[GWAS:Blood metabolite levels]
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[PharmGKB:Curated Risk or phenotype-associated allele: T allele. Phenotype: The T allele of rs3130690 (36 kb telomeric to HLA-B), which is strongly associated with the HLA-B*1502 allele, shows strong association with carbamazepine (CBZ)-induced Stevens-Johnson syndrome (SJS)/Toxic Epidermal Necrolysis (TEN, Lyell's syndrome) (OR = 254.6 for TT/TG genotype versus GG genotype; T allele only: p = 4.66x10(-42), Pc = 1.29x10(-39), OR = 45.65). Also, an extended haplotype with rs3130690 T, HLA-B*1502, and other alleles of major histocompatibility complex genes (A*1101-Cw*0801-HLABC-CA*119-rs3130690T-B*1502-MICA*019-DRB1*1202) was in strong association with CBZ-induced SJS/TEN. Study size: 204. Study population/ethnicity: 60 CBZ-induced SJS/TEN cases and 144 CBZ-tolerant controls of Chinese desce...
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[PharmGKB:Curated In a case-control study (258 cases; 774 controls) performed in patients residing in the mainland U.S. or Puerto Rico and who had hypertension and stable coronary artery disease, this SNP was found to be related to primary outcome of atenolol vs. verapamil SR - based treatment. AA genotype was associated with 46% reduction in primary outcome for patients on verapamil SR-based treatment compared to atenolol-based treatment (odds ratio 0.54; 95% CI 0.32 to 0.92), AG genotype showed no difference in primary outcome between the two strategies (odds ratio 1.47; 95% CI 0.86 to 2.53), and GG subjects had more than 4 fold increased risk of primary outcome on verapamil SR-based treatment as opposed to atenolol-based treatment (odds ratio 4.59; 95% CI 1.67 to 12.67). Study size: 258...
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rs1801030 (Met223Val) is a snp within SULT1A1 (Sulfotransferase 1A1) and defines the SULT1A1*3 allele. [PharmGKB:In-Depth SULT1A1*3 is the second most common SULT1A1 SNP.]
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Common variation in the SERPING1 gene is not associated with age-related macular degeneration in two independent groups of subjects. [PharmGKB:Curated This variant is associated with age-related macular degeneration.]
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rs1007888(C;C) was associated with an increased risk of type-2 diabetes in women [hazard ratio (95% CI) 1.74 (1.02-2.97)], but not in men [1.17 (0.75-1.81)]. Macrophage migration inhibitory factor in acute lung injury: expression, biomarker, and associations. Gene variants influencing measures of inflammation or predisposing to autoimmune and inflammatory diseases are not associated with the risk of type 2 diabetes. The macrophage migration inhibitory factor (MIF) gene polymorphism in Czech and Russian patients with myocardial infarction. Macrophage migration inhibitory factor: critical role in obesity, insulin resistance, and associated comorbidities. Usefulness of Mendelian randomization in observational epidemiology.
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rs1019385 ( -200G/T ) is a SNP in close proximity to GRIN2B (Glutamate [NMDA] receptor subunit epsilon-2). significant effect of rs1019385 genotype on habituation after acoustic stimulus noted small preliminary study (consisting of 16 psychotropic-naive pediatric patients) observed a significant association between rs1019385 genotype and anterior cingulate cortex (ACC) glutamatergic concentration (but not occipital glutamatergic concentration)
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[PharmGKB:Curated This variant is a noncoding SNP within 5' UTR of ADRB2, in amino acid residue 19 of the 19 amino acid beta upstream peptide (BUP) affecting ADRB2 expression at the translational level. Arg-19 allele was associated with lower receptor expression.]
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[PharmGKB:Curated A haplotype of RRM1 (2455 A>G and 2464 G>A) was associated with a lower frequency of neutropenia in advanced breast cancer patients treated with gemcitabine.]
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[GWAS:None]
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[OMIM:CHOLINERGIC RECEPTOR, NEURONAL NICOTINIC, ALPHA POLYPEPTIDE 4; CHRNA4]
References:1
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[PharmGKB:Curated This variant is associated with response to escitalopram and nortriptyline in a study of 760 adult patients with moderate-to-severe depression.]
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This SNP is part of the HNMT gene known as C939T (or 939A>G) that regulates histamine. According to the lack of a C allele for this gene indicates an increase in ADHD behavior for children age 3 and 8/9 when they have been exposed to certain food additives: sunset yellow, carmoisine, tartrazine, ponceau 4R, quinoline yellow, allura red AC and sodium benzoate
normal
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rs1057868, also known as A503V, is a relatively common variant defining the POR*28 allele of the P450 (cytochrome) oxidoreductase POR gene. The POR gene encodes a protein involved in electron transport of cytochrome p450 enzymes such as CYP3A4, CYP3A5 and CYP3A7. A study of 251 individuals from two independent studies (182 patients treated with methadone and 69 patients with clozapine) for CYP3A activity found that CYP3A SNPs themselves did not predict particularly well inter-individual variability in overall CYP3A activity. However, rs1057868(T;T) individuals had a 1.6x increased CYP3A activity compared to rs1057868(C) carriers (n=182, p=0.004), and the finding was replicated in a second independent dataset. The authors conclude that this POR gene SNP is a better predictor of overall CYP3...
References:38
normal
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rs10757274 is a SNP located in chromosomal region 9p21; to date (2009), it is the strongest genetic predictor of early myocardial infarction (heart attack) discovered so far. SNPs in this region are also associated with increased risk of stroke, abdominal aortic aneurysm (AAA), and intracranial aneurysm. Based on a large (20,000+) study primarily of Caucasian females, it appears that on its own, this single SNP does not improve on the discrimination or classification of predicted heart disease risk achieved by traditional risk factors, high-sensitivity C-reactive protein, and a family history of premature myocardial infarction. rs10757274 and rs2383206 can double the risk of heart diseaseAbout one in every four Caucasians are thought to carry the gene variants. rs10757278] in the same regi...
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[PharmGKB:Curated Risk or phenotype-associated allele: C. Phenotype: The C allele was associated with weight gain of at least 7% in schizophrenia patients treatment with clozapine or olanzapine. Study size: 206. Study population/ethnicity: European american; African American; German; Schizophrenia. Significance metric(s): OR = 3.44 (CI: 1.46-8.11). Type of association: PD.]
References:3
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[PharmGKB:Curated Risk or phenotype-associated allele: C Phenotype: Individuals that were CC homozygotes for CAT c.66 + 78C>T had increased risk of cardiac damage after anthracyline exposure. Study size: 76 Study population/ethnicity: Survivors of childhood leukemia (Precursor Cell Lymphoblastic Leukemia-Lymphoma), Slovenia Significance metric(s): p = 0.02 Type of association: CO; TOX; ADR]
References:7
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[PharmGKB:Curated Results from a study in patients with acutely exacerbated schizophrenia suggest that this variant in the RGS4 gene influences clinical manifestations of schizophrenia as well as the treatment response to risperidone.]
References:4
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[PharmGKB:Curated Risk or phenotype-associated allele: C. Phenotype: In a study of patients with major depressive disorder, individuals with the CC genotype had poorer response to paroxetine than those with the A variant. Study size: 111. Study population/ethnicity: Individuals with a major depressive disorder treated with paroxetine. Significance metric(s): OR = 0.075 (95% CI 0.019-0.295); p < 0.001. Type of association: PD.]
References:3
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[PharmGKB:Curated Risk or phenotype-associated allele: T Phenotype: The CYP2C19*17 allele was associated with significantly increased metabolism of imipramine. Study size: 178 Study population/ethnicity: Psychiatric patients aged 18-65 with a score of greater than or equal to 17 on the Hamilton Rating Scale for Depression. Significance metric(s): p = 0.035 Type of association: PK]
References:2
References:6
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rs1169288 (Ile27Leu) is a SNP in located within the HNF1A (Hepatocyte nuclear factor 1 homeobox A) gene. The C allele encodes for the Leu variant. among 356 unrelated Japanese men, lower HDL cholesterol was observed in those with the Ile/Ile genotype (and higher in the Leu/Leu genotype) minor alleles of rs1169288, rs1169286, rs2464196, rs1169310 constitutes a common haplotype (freq. 30%) associated with lower CRP levels [PharmGKB:Curated In a candidate gene-based association analysis of 4333 European-descended, age 65 or older, subjects from the CHS (Cardiovascular Health Study), this was one of the SNPs most strongly associated with plasma C-reactive protein levels. The minor allele is part of a haplotype of frequency 30% which was associated with lower levels of CRP.] [OMIM:INSULIN RESI...
References:2
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[PharmGKB:Curated Associated with femoral BMD in men and left ventricular mass and left ventricular wall thickness in women.]
References:6
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[PharmGKB:Curated Risk or phenotype-associated allele: undetermined. Phenotype: The variant allele was not associated with warfarin maintenance dose variability (p = 0.7669). Study size: 283. Study population/ethnicity: Hospitalized Caucasian patients aged 75 years or older, recruited Sep 2002-Nov 2004 in Ivry, France, and Oct 2005-Mar 2008 from 14 French centers. Significance metric(s): not significant. Type of association: GN; PK.]
References:1
normal
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This position is referred to as the -1154 position in many VEGF-associated publications. The normal (or wild type) form of this SNP is a (G). The (A) form reduces the activity of this gene, resulting in less VEGF protein. Individuals with one or more rs1570360(A) alleles are reported to be at about a 3 fold higher risk of developing Sudden Infant Death Syndrome . A functional variant of vascular endothelial growth factor is associated with severe ischemic complications in giant cell arteritis. Analysis of vascular endothelial growth factor (VEGF) functional variants in rheumatoid arthritis. Association between functional haplotypes of vascular endothelial growth factor and renal complications in Henoch-Schonlein purpura. Polymorphisms in the vascular endothelial growth factor gene and brea...
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anxiety-related personality traits, ADHD, schizophrenia part of a three marker haplotype rs737865-rs4680-rs165599 epistasis between SNPs in COMT (rs2097603, Val158Met (rs4680), rs165599) and polymorphisms in other schizophrenia susceptibility genes popular in pubmed is associated with bipolar disorder and influences prefrontal aspects of verbal memory in bipolar patients and healthy controls. [PharmGKB:Curated In a study of 78 African American and 65 white patients diagnosed with schizophrenia or schizoaffective disorder, this SNP in the COMT gene was found to have significant associations with response to risperidone over 2-12 weeks in both African-American and white patients.] [OMIM:CATECHOL-O-METHYLTRANSFERASE; COMT]
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[PharmGKB:Curated Risk or phenotype-associated allele: undetermined. Phenotype: The variant allele was not associated with warfarin maintenance dose variability (p = 1). Study size: 283. Study population/ethnicity: Hospitalized Caucasian patients aged 75 years or older, recruited Sep 2002-Nov 2004 in Ivry, France, and Oct 2005-Mar 2008 from 14 French centers. Significance metric(s): not significant. Type of association: GN; PK.]
References:4
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[PharmGKB:Curated In a study of ovarian cancer patients (n=104) receiving a cisplatin-cyclophosphamide regimen, the AGG/AGG genotype (insertion) of GSTM3 intron 6 insertion/deletion was associated with decreased incidence of thrombocytopenia, anemia and neuropathy.]
normal
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rs1800012(T;T) was significantly (p=0.031, OR=0.08, 95%CI <0.01 to 1.46) under-represented in South African participants with anterior cruciate ligament ruptures, based on a study of ~100 patients vs ~100 controls. [PharmGKB:Curated This promoter variant affects an Sp1 binding site within a key regulatory region of COL1A1. It is associated with reduced bone mineral density (BMD) and increased susceptibility to osteoporotic fracture, particularly vertebral fractures in women.] [OMIM:COLLAGEN, TYPE I, ALPHA-1; COL1A1]
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rs1800693 is a SNP in the tumor necrosis factor receptor superfamily, member 1A TNFRSF1A gene. A large study (~5,000 patients) found two SNPs in the TNFRSF1A gene that each (independently) increase risk for multiple sclerosis, rs1800693 and rs4149584. This SNP, rs1800693, is more common but increases risk less; the odds ratio is reported as 1.2 (CI: 1.10-1.31, p=1.6x10(-11)). [OMIM:?] [GWAS:Multiple sclerosis]
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rs1801262 increases susceptibility to Type II Diabetes 1.15 times for carriers of the A allele Mutation of CERKL, a novel human ceramide kinase gene, causes autosomal recessive retinitis pigmentosa (RP26). NeuroD1 gene and interleukin-18 gene polymorphisms in type 1 diabetes in Dalmatian population of Southern Croatia. Identification of type 2 diabetes-associated combination of SNPs using support vector machine.
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[PharmGKB:Curated Risk or phenotype-associated allele: undetermined. Phenotype: The variant allele was not associated with warfarin maintenance dose variability (p = 0.7024). Study size: 283. Study population/ethnicity: Hospitalized Caucasian patients aged 75 years or older, recruited Sep 2002-Nov 2004 in Ivry, France, and Oct 2005-Mar 2008 from 14 French centers. Significance metric(s): not significant. Type of association: GN; PK.]
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[PharmGKB:Curated This variant is associated with success rate of smoking cessation. Individuals carrying the minor allele have substantially decreased odds of quitting (OR = 0.31; 95% CI 0.18-0.55). This variant is in the 3' UTR region of CHRNB2 genes, and may have a role in the time to relapse and an impact on withdrawal symptoms at target quit date.]
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[PharmGKB:Curated The G allele of this polymorphism is associated with the intensification of nicotine dependence in a genetic association study in three large samples from the German general population (N1=1412; N2=1855; N3=2294). This variant is in the 3'-untranslated region of CHRNA4 gene.] [OMIM:CHOLINERGIC RECEPTOR, NEURONAL NICOTINIC, ALPHA POLYPEPTIDE 4; CHRNA4]
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nature type-2 diabetes *rs2237895, P = 7.3 times 10-9; OR = 1.32, 95% CI = 1.20–1.45 SNPs in KCNQ1 are associated with susceptibility to type 2 diabetes in East Asian and European populations. Meta-analysis in genome-wide association studies. Genetic variation in KCNQ1 associates with fasting glucose and beta-cell function: a study of 3,734 subjects comprising three ethnicities living in Singapore. Common variants in KCNQ1 are associated with type 2 diabetes and impaired fasting glucose in a Chinese Han population. Polymorphisms in KCNQ1 are associated with gestational diabetes in a Korean population. KCNQ1 gene polymorphisms are associated with lipid parameters in a Chinese Han population. Variants in KCNQ1 increase type II diabetes susceptibility in South Asians: a stu...
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[PharmGKB:Non-Curated Haplotypes containing the variant showed decreased luciferase activity in reporter assays in cells and in vivo assay.]
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[OMIM:CHOLINERGIC RECEPTOR, NEURONAL NICOTINIC, ALPHA POLYPEPTIDE 4; CHRNA4]
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rs2279343, also known as Lys262Arg, is a SNP within the CYP2B6 gene. variants including the Arg allele include CYP2B6*4, CYP2B6*6, and CYP2B6*7 Pharmacokinetics of efavirenz when co-administered with rifampin in TB/HIV co-infected patients: pharmacogenetic effect of CYP2B6 variation. Polymorphisms of drug-metabolizing enzymes (GST, CYP2B6 and CYP3A) affect the pharmacokinetics of thiotepa and tepa. Associations between CYP2B6 polymorphisms and pharmacokinetics after a single dose of nevirapine or efavirenz in African americans. CYP2B6 variants and plasma efavirenz concentrations during antiretroviral therapy in Port-au-Prince, Haiti. Cyclophosphamide-metabolizing enzyme polymorphisms and survival outcomes after adjuvant chemotherapy for node-positive breast cancer: a retrospective cohort s...
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FcepsilonRIalpha gene (FCER1A) promoter polymorphisms and total serum IgE levels in Japanese atopic dermatitis patients.
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rs2494732 is a SNP in the AKT1 gene, encoding one of three serine/threonine-protein kinases regulating numerous processes such as cell survival, growth and angiogenesis. Medical conditions that may be linked to the rarer (minor) rs2494732(C) allele include drug response, schizophrenia, and drug-related psychoses, in particuler, cannabis-related psychosis. A case-control study of 489 first-episode psychosis patients concluded that while rs2494732 was not associated with an increased risk of a psychotic disorder, with lifetime cannabis use, or with frequency of use, there was a significant association between psychosis and cannabis use. rs2494732(C;C) individuals with a history of cannabis use had an increased likelihood of a psychotic disorder (odds ratio 2.18, CI: 1.1 - 4.3) when compared ...
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577 testicular germ cell tumors cases (254 seminoma, 323 nonseminoma) and 707 controls. inversely associated with nonseminoma: *rs4886605 OR = 0.75 (95% CI = 0.54-1.04) among the heterozygotes and OR = 0.37, 95% CI = 0.12-1.11 among the homozygotes with a p-value for trend = 0.02; *rs2606345 OR = 0.69 (95% CI = 0.51-0.93) among heterozygotes and OR = 0.70 (95% CI = 0.42-1.17) among homozygotes, with a p-value for trend = 0.02.
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[PharmGKB:Curated This variant is associated with enhanced agonist-induced platelet aggragation and response to aspirin in both whites and african americans. The C allele was associated with increased aggregation of native platelets to collagen, epinephrine. The C allele was also associated with reduced platelet responsiveness to aspirin. (N=1486)]
References:3
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rs28360521 is a SNP in the vicinity of the CYP2D6 gene. Little is known of the significance of either allele.
References:5
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[PharmGKB:Curated This variant is associated with severe exacerbations with asthma in both white and african american childen. This variant also leads to decreased FEER2 expression and may be used to predict treatment outcome in asthma.]
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[PharmGKB:Curated This promoter variant is associated with hyperlipidemia (elevated triglyceride levels) for HIV-infected individuals treated with ritonavir.] [OMIM:?]
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[PharmGKB:Curated This promoter variant is associated with hyperlipidemia (elevated triglyceride levels) for HIV-infected individuals treated with ritonavir.] [OMIM:?]
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This is a triallelic SNP - note that the sidebar (currently) only shows 3 of the 6 possible genotypes. ====CRP==== claims that this SNP does not affect the serum concentration of CRP, while older resources seem to disagree. However, they do report an association between CRP levels and risk of abdominal aortic aneurysm (AAA). rs3091244 serum CRP level and cardiovascular risk in the NHLBI Family Heart Study. the AA genotype of the triallelic SNP rs3091244 in the gene C-reactive protein was associated with prevalent coronary heart disease in the non-Hispanic white population Association study of CRP gene polymorphisms with serum CRP level and cardiovascular risk in the NHLBI Family Heart Study. rs3093059 rs3091244 Weaker linkage disequilibrium in this region in African Americans allows the co...
References:1
possible weight gain if taking olanzapine
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rs3813929, also known as -759C/T, is a SNP in the 5-hydroxytryptamine (serotonin) receptor 2C HTR2C gene. A study of 107 patients with schizophrenia being treated with olanzapine reported a protective effect against weight-gain from the (T) allele of this SNP; zero patients (of 28) with a rs3813929(T) allele had a body mass index increase of >=10% (p=0.002), whereas (C;C) homozygotes did. This effect may also involve nearby SNP rs518147. T allele showed borderline significant association with higher BMI and incidence of lifetime major depressive disorder among 4978 persons from the European Prospective Investigation into Cancer (EPIC)-Norfolk study, however, only the association with BMI remained borderline significant within the full EPIC-Norfolk cohort (20,981 persons) The association...
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[PharmGKB:Curated Associated with significantly lower AUC ratio of SN38G/SN38, high incidence of severe diarrhea, but not tumor response.]
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Optimization of candidate-gene SNP-genotyping by flexible oligonucleotide microarrays; analyzing variations in immune regulator genes of hay-fever samples. Genetic polymorphisms of tumour necrosis factor receptor superfamily 1A and 1B affect responses to infliximab in Japanese patients with Crohn's disease. Genome-wide association scan identifies candidate polymorphisms associated with differential response to anti-TNF treatment in rheumatoid arthritis. Polymorphisms in apoptosis-related genes and survival of patients with early-stage non-small-cell lung cancer. Genetic variants in inflammation-related genes are associated with radiation-induced toxicity following treatment for non-small cell lung cancer.
>3x increased risk for Alzheimer's; 1.4x increased risk for heart disease
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This SNP, located in the fourth exon of the ApoE gene, affects the amino acid at position 130 of the resulting protein. The more common rs429358 allele is (T). If the allele is (C) and the same chromosome also harbors the rs7412(C) allele, the combination is known as an APOE-ε4 allele. The APOE-ε4 allele has a strong influence on the risk of Alzheimer's disease. Both deCODEme and 23andMe (v3 chip) test for this SNP. Many studies have estimated the level of risk, and it varies depending on age, sex, ethnicity, and other factors. One meta-analysis estimated the odds ratios for homozygous rs429358(C;C) individuals compared to the more common ApoE3/ApoE3 homozygotes to be 12x for late-onset Alzheimer's and 61x for early-onset disease. Meta-analyses have also supported the association between t...
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[PharmGKB:Curated Risk or phenotype-associated allele: GG. Phenotype:Increased risk of diabetes associated with thiazide use, this risk was more increased for ACE GG subjects Study size: 497 incident cases of type 2 diabetes and 2,633 controls. metric(s): SI 1.70 (95% CI: 1.08-2.66). Type of association: GN.]
slower responder
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This SNP in the ACE gene, also known as C17888T, is reported to influence how quickly African Americans respond to the anti-hypertensive drug ramipril. rs4359(C;C) and rs4359(T;T) homozygotes are able to reach lower blood pressure levels upon treatment with ramipril sooner than rs4359(C;T) heterozygotes. The odds ratio reported for this study, comparing both homozygotes to heterozygotes, is 1.49 (CI: 1.01-2.13).
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http://papers.ssrn.com/sol3/papers.cfm?abstract_id=1915939 Born to Lead? A Twin Design and Genetic Association Study of Leadership Role Occupancy leadership role occupancy is associated with rs4950 residing on a neuronal acetylcholine receptor gene (CHRNB3). rs4950(G;G) less likely to be in a leadership role http://www.sciencedaily.com/releases/2013/01/130115111553.htm https://www.23andme.com/you/community/thread/16689/
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The (-) form of this SNP, representing a deletion of one nucleotide, causes a frameshift such that the resulting CYP2D6 protein is nonfunctional. The associated allele is also known as CYP2D6*6, and there are several subtypes but they are all nonfunctional. If two copies of this (or similar) changes are inherited, CYP2D6 poor metabolism ('PM') is observed. CYP2D6 poor metabolism may affect the efficacy or degree of side effects of drugs metabolized by CYP2D6, such as dextromorphan, sparteine, nortriptyline, venlafaxine and codeine. Response to serotonin reuptake inhibitors in OCD is not influenced by common CYP2D6 polymorphisms. [PharmGKB:Curated This variant is part of the CYP2D6*6 PM haplotype. Plasma concentrations of metoprolol were shown to be were 4.9-fold higher in the PMs, with gr...
more likely to gain weight if taking olanzapine
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rs5092 is a SNP in the apolipoprotein A4 APOA4 gene. In a study of 67 mostly Caucasian patients prescribed the atypical antipsychotic olanzapine, carriers of a rs5092(G) allele were less likely to gain significant weight compared to rs5092(A;A) carriers, as assessed by physiogenomic analysis of corresponding weight profiles. Two other SNPs, rs4765623 and rs7412, were also significantly associated with weight profiles in these patients.
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[PharmGKB:Curated Risk or phenotype-associated allele: A. Phenotype: The AA homozygote was associated with lower clearance of docetaxel. Study size: 31. Study population/ethnicity: Patients with Non-Small-Cell Lung Carcinoma. Significance metric(s): Type of association: PK.]
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[PharmGKB:Curated A study in a cohort of 192 patients receiving azathioprine for inflammatory bowel disease found that this SNP in the AOX1 gene predicted lack of azathioprine response (p=0.035, OR 2.54, 95%CI 1.06-6.13).]
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[PharmGKB:Curated The T allele of this SNP is associated with protection from early onset nicotine addiction, i.e., daily smoking commencing at or before age 16. Haplotype C, which is defined by the T allele of this SNP and the A allele of rs578776, is similarly associated with protection from early onset nicotine dependence.]
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identifies a region associated with nicotine dependence in this particular study (1,050 dependents, 879 non-dependent controls, all of European descent), noted as distinct from the loci which rs16969968 defines Cholinergic nicotinic receptor genes implicated in a nicotine dependence association study targeting 348 candidate genes with 3713 SNPs. Variants in nicotinic receptors and risk for nicotine dependence. Systematic biological prioritization after a genome-wide association study: an application to nicotine dependence. Genetic variability in nicotinic acetylcholine receptors and nicotine addiction: converging evidence from human and animal research. Familial aggregation of common sequence variants on 15q24-25.1 in lung cancer. Association of a single nucleotide polymorphism in neuronal...
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[PharmGKB:Curated Risk or phenotype-associated allele: C. Phenotype: This variant is statistically correlated with the mean of maximum transaminase values (ALT) in patients from Mozambique, with higher ALT mean value for C genotype carriers. Study size: 156. Study population/ethnicity: HIV infected patients from Mozambique. Significance metric(s): p= 0.01. Type of association: GN; CO]
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[PharmGKB:Curated This variant in the 5' untranslated region of BDNF was associated with antidepressant response after adjusting for age, sex, medication, and baseline score on the 21-item Hamilton Depression Rating Scale in a study of 264 controls and 272 Mexican Americans with major depressive disorder.]
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[PharmGKB:Curated On the basis of subjects' pain responsiveness, haplotypes involving rs6269 (A/G), rs4633 (C/T), rs4818 (C/G), and rs4680 (G/A) were designated as low (low pain sensitivity (LPS) haplotype; GCGG), average (average pain sensitivity (APS) haplotype; ATCA), or high (high pain sensitivity (HPS) haplotype; ACCG) pain sensitive.]
References:4
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Polymorphisms in the epidermal growth factor receptor gene and the risk of primary lung cancer: a case-control study. EGFR-targeted therapies in lung cancer: predictors of response and toxicity. A two-stage case-control study of EGFR polymorphisms and breast cancer risk. [PharmGKB:Curated The T allele of -216G/T was associated with improved progression free survival in gefitinib-treated non-small-cell lung cancer patients. It was also associated with significantly higher rates of stable disease/partial response and a significantly higher risk of treatment-related rash/diarrhea.]
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[PharmGKB:Curated In a study of 78 African American and 65 white patients diagnosed with schizophrenia or schizoaffective disorder, this SNP in the GRM3 gene was found to have significant associations with response to risperidone over 2-12 weeks in both African-American and white patients.]
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association of the rs7483 SNP with late-onset Alzheimer's disease
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linked to Cardiovascular Events Several CVD risk variants were identified: In women, the combination of F5 rs7542281 × THBD rs1042580, together with three single F5 SNPs, was associated with CVD events. Among men, PROC rs1041296, when combined with either ICAM1 rs5030341 or F5 rs2269648, was associated with total mortality. As a single variant, PROC rs1401296, together with the F5 Leiden mutation, was associated with ischemic stroke events.
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g2b2mh blog In a population of healthy individuals, those that carry common variants (such as rs760761, rs1018381, rs2619522) located in the dysbindin (DTNBP1) gene, a risk factor for schizophrenia, show minor cognitive impairments such as decreased attentional capacity, worse performance on memory tasks, and alterations in schizotypal beliefs and experiences. The association between several SNPs in the DTNBP1 gene, most especially rs760761, and schizophrenia was confirmed in a new sample of 1021 cases and 626 controls from Ireland. Genetic variation in the 6p22.3 gene DTNBP1, the human ortholog of the mouse dysbindin gene, is associated with schizophrenia. Support for association of schizophrenia with genetic variation in the 6p22.3 gene, dysbindin, in sib-pair families with linkage and i...
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ARG1 is a novel bronchodilator response gene: screening and replication in four asthma cohorts. [PharmGKB:Curated Risk or phenotype-associated allele: T Phenotype: The T variant of CRHR2 rs7793837 was associated with reduced acute bronchodilation response to short-acting beta2-agonist treatment in the CAMP and LODO studies but not the Sepracor study. Study size: 607 (CAMP); 152 (LODO); 427 (Sepracor) Study population/ethnicity: Caucasian children with asthma with a mean age of 8.83 years enrolled in the Childhood Asthma Management Program (CAMP); Adult Caucasian participants with asthma enrolled in the Clinical Trial of Low-Dose Theophylline and Montelukast conducted by the American Lung Association Asthma Clinical Research Centers (LODO); Adult Caucasian participants with asthma enrolled...
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[PharmGKB:Curated Risk or phenotype-associated allele: C. Phenotype: This variant was associated with higher clearance of docetaxel. Study size: 31. Study population/ethnicity: Patients with Non-Small-Cell Lung Carcinoma. Significance metric(s): Type of association: PK.]
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may be associated with haloperidol response in treatment-resistant schizophrenic patients [PharmGKB:Curated Patients with diplotype ACCCTC/GCCGCC, genotype A/G, or allele A of marker rs909706 have better response to haloperidol (0.007</=P</=0.080) in a study of patients with refractory schizophrenia.]
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rs9332131, also known as 818delA, 10601delA or 273Frame shift, is a SNP in the CYP2C9 gene. The rs9332131(-) allele defines the CYP2C9*6 variant, which is inactive. [PharmGKB:Curated Phenotype: In African Americans patients, weekly warfarin dose requirements were lower in those with the CYP2C9*8 allele (34 (30-47) mg; P = 0.023) and the CYP2C9 *2, *3, *5, *6, or *11 allele (33(28-40 mg); P < 0.001) as compared with those with the CYP2C9*1/*1 genotype (43 (35-56) mg). Adding the *5,*6,*8 and *11 alleles to a model containing the *2 and *3 alleles plus the VKORC1 -1639 G>A allele (along with clinical variables) explained 36% vs. 30% of the variability in dose requirements. Study size: 226 . Study population/ethnicity: African-American . Type of association: PD;GN;CO]
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[PharmGKB:Curated A haplotype of RRM1 (2455 A>G and 2464 G>A) was associated with a lower frequency of neutropenia in advanced breast cancer patients treated with gemcitabine.]
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GPX1 Pro198Leu polymorphism, interactions with smoking and alcohol consumption, and risk for lung cancer. Gene x Gene interaction between MnSOD and GPX-1 and breast cancer risk: a nested case-control study. Genetic association of glutathione peroxidase-1 with coronary artery calcification in type 2 diabetes: a case control study with multi-slice computed tomography. Do genetic factors protect for early onset lung cancer? A case control study before the age of 50 years. A prospective study of genetic polymorphism in MPO, antioxidant status, and breast cancer risk. Oxidative response gene polymorphisms and risk of adult brain tumors. The Mn-superoxide dismutase single nucleotide polymorphism rs4880 and the glutathione peroxidase 1 single nucleotide polymorphism rs1050450 are associated with ...
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a variation in CYP2D6
References:1
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[PharmGKB:Curated Risk or phenotype-associated allele: T. Phenotype: The T allele was marginally associated with increased overall survival (CC vs. TC: 6.5, 14.1 months) given combined pemetrexed/bevacizumab treatment. Study size: from a study using 48 patients with metastatic or stage IIIB nonsquamous non-small-cell lung cancer patients. Significance metric(s): p = 0.06 Type of association: CO, GN]
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commonly referred to as A779C Only for Hispanics, individuals who have a genoset composed of rs1799913(C;C) and rs7963720(T;T) are reported to be at 14x higher risk for developing heroin addiction (CI:0.83-244.63, p=0.012). Again, only for Hispanics, individuals having a genoset composed of rs1799913(C;C) and rs4290270(T;T) are reported to be at 9x higher risk for developing heroin addiction (CI:0.5-153, p=0.063). Association between 5-HT2A, TPH1 and GNB3 genotypes and response to typical neuroleptics: a serotonergic approach. Tryptophan hydroxylase gene 1 (TPH1) variants associated with cerebrospinal fluid 5-hydroxyindole acetic acid and homovanillic acid concentrations in healthy volunteers. [OMIM:TRYPTOPHAN HYDROXYLASE 1; TPH1]
hypertension not a risk factor for sudden cardiac death
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rs187238, also known as -137 G/C, is a SNP in the interleukin 18 IL18 gene. Based on studying autopsies of 700 men in the Helsinki Sudden Death Study, there was a significant interaction between IL-18 genotype and hypertension impacting on the risk of sudden cardiac death (SCD) due to coronary heart disease (CHD). Among rs187238(G;G) homozygotes, hypertension was a major risk factor for SCD due to CHD (adjusted odds ratio 3.75, CI:1.78-7.91, p < 0.001) and hypertension also associated with larger coronary atherosclerotic plaque areas (p = 0.002) and the occurrence of complicated plaques (adjusted OR 8.38, CI: 2.39-29.33, p < 0.001). Among rs187238(C) allele carriers, hypertension was not a significant risk factor for CHD-related SCD or CAD and did not associate with the development o...
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A case-control study of 471 Italian late-onset Alzheimer's disease patients aged 60 years or older, and 254 subjects with no neurodegenerative disorders serving as the control group, found that the rs2177369(G;G) genotype (in dbSNP orientation) a risk factor with an odds ratio of 1.56 (CI: 1.10-2.22, p = 0.01). Refreshingly, the authors call their results 'far from definitive'.
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[PharmGKB:In-Depth Associated with susceptibility to asthma and with IgE levels.]
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[GWAS:Response to dabigatran etexilate treatment]
Increased risk for Crohn's Disease
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rs2631367, a SNP in the promoter region of the SLC22A5 gene, has been associated with an autoimmune disease, in this case, Crohn's disease, odds ratio = 2.1 (CI = 1.31–3.39, p = 0.002), based on a study of 203 cases and 200 controls. The risk allele is the more rare allele, which appears to be rs2631367(C).[Note: this orientation has not been confirmed relative to dbSNP.] A nearby SNP (rs1050152) in the coding region of the SLC22A4 gene defines a haplotype along with rs2631367, with odds ratio reported as similar for either SNP or the haplotype. Referring to the TC risk haplotype, the population risk attributable to heterozygotes was 19%, and for homozygous haplotype carriers, 27%. [PharmGKB:Non-Curated No appreciable effect of this variant on carnitine disposition]
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[PharmGKB:Curated Risk or phenotype-associated allele: None. Phenotype: Variants identified in a screen of 13 genes involved in the gemcitabine drug metabolic pathway. For the synonymous DCTD:315T>C (V105V, V116V) SNP, the C allele was at frequency 0.25 and 0.48 in Europeans and Africans, respectively. There was a significant difference between ethnic groups in genotype frequency distribution (p < 0.001). Study size: 186. Study population/ethnicity: Healthy, unrelated blood donors of European (n = 92) and African (n = 94) descent. Significance metric(s): p < 0.001. Type of association: GN.]
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[PharmGKB:Curated Risk or phenotype-associated allele(s): G/G. Phenotype: This SNP was strongly associated with response to treatment, in which 20 subjects with the GG genotype showed minimal changes in panic attack frequency with a relative risk of no response of 4.73. Study size: 102. Study population/ethnicity: patients with a diagnosis of panic disorder receiving sertraline or paroxetine.]
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[PharmGKB:Curated Risk or phenotype-associated allele: C allele. Phenotype: The C allele of rs750332 shows strong association with carbamazepine (CBZ)-induced Stevens-Johnson syndrome (SJS)/Toxic Epidermal Necrolysis (TEN, Lyell's syndrome). Study size: 204. Study population/ethnicity: 60 CBZ-induced SJS/TEN cases and 144 CBZ-tolerant controls of Chinese descent. Significance metric(s): p = 3.04x10(-14), Pc = 8.45x10(-12), OR = 6.41. Type of association: GN; PD; TOX; ADR.]
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Norepinephrine transporter and catecholamine-O-methyltransferase gene variants and attention-deficit/hyperactivity disorder symptoms in adults. Further evidence of association between two NET single-nucleotide polymorphisms with ADHD. Lack of association between response of OROS-methylphenidate and norepinephrine transporter (SLC6A2) polymorphism in Korean ADHD. Genetic influences on attention deficit hyperactivity disorder symptoms from age 2 to 3: a quantitative and molecular genetic investigation. Support for association between ADHD and two candidate genes: NET1 and DRD1.
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[GWAS:Response to statin therapy]
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[PharmGKB:Curated Risk or phenotype-associated allele: undetermined. Phenotype: The variant allele was not associated with warfarin maintenance dose variability (p = 0.7223). Study size: 283. Study population/ethnicity: Hospitalized Caucasian patients aged 75 years or older, recruited Sep 2002-Nov 2004 in Ivry, France, and Oct 2005-Mar 2008 from 14 French centers. Significance metric(s): not significant. Type of association: GN; PK.]
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[PharmGKB:Curated Risk or phenotype-associated allele: ATIC 347CC (116Thr/Thr) > GC (116Thr/Ser) > GG (116Ser/Ser) Phenotype: A composite pharmacogenetic index (additive from zero to five) was calculated using the following values: ATIC 347CC or TSER*3/*3 or SLC19A1 80GG or SLC19A1 80GA genotypes were valued as 0, ATIC 347CG or TSER*2/*3 or SLC19A1 80AA genotypes were valued as 1, and ATIC 347GG or TSER*2/*2 genotypes were valued as 2. The sum originating from each component (ATIC + TSER + SLC19A1) was calculated and constitutes the pharmacogenetic index for the patient. There was a significant association between smaller pharmacolgical index and greater number of tender joints (p = 0.002), swollen joints (p = 0.003), greater physician's global assessment of disease activity (p = 0.0...
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rs2631372 increases susceptibility to Crohn's disease 1.28 times for carriers of the C allele
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This SNP, located in the 3' UTR of the CSNK1E gene, has been associated with sensitivity to the acute effects of d-amphetamine. Sensitivity to psychoactive drugs has been associated with potential to develop drug abuse. The more sensitive allele is rs135745(C). However, in a separate study, this SNP did not affect susceptibility to methamphetamine dependence or psychosis, at least in a Japanese population. Note: orientation relative to dbSNP needs to be confirmed/checked.
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No significant association was found between this CHRM2 gene SNP and diverse measures of cognitive ability in two population based cohorts - one Scottish aged over 50 years (N = 2,091) and the other English comprising non-demented elderly participants (N = 758)- nor in a family-based Australian adolescent sample (N = 1,537). No evidence for association between 19 cholinergic genes and bipolar disorder. A genetic association analysis of cognitive ability and cognitive ageing using 325 markers for 109 genes associated with oxidative stress or cognition. Exploring the functional role of the CHRM2 gene in human cognition: results from a dense genotyping and brain expression study. Uncovering genes for cognitive (dys)function and predisposition for alcoholism spectrum disorders: a review of hum...
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[PharmGKB:Curated Several studies showed an associaction of this SNP in DTNBP1 with schizophrenia and other psychotic disorders, including substance-induced psychosis. A study in bipolar samples could not find a major contribution of the variation at the SNP to susceptibility to bipolar disorder.] [OMIM:DYSTROBREVIN-BINDING PROTEIN 1; DTNBP1]
less weight gain if taking olanzapine
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rs518147, also known as -697G/C, is a SNP in the 5-hydroxytryptamine (serotonin) receptor 2C HTR2C gene. A study of 107 patients with schizophrenia being treated with olanzapine reported a protective effect against weight-gain from the (C) allele of this SNP; fewer patients (of 28) with a rs518147(C) allele had a body mass index increase of >=10% (p=0.0006), whereas (G;G) homozygotes did. This effect may also involve nearby SNP rs3813929. The association between HTR2C polymorphisms and obesity in psychiatric patients using antipsychotics: a cross-sectional study. The association between HTR2C gene polymorphisms and the metabolic syndrome in patients with schizophrenia. Multivariate permutation analysis associates multiple polymorphisms with subphenotypes of major depression. HTR2C gene ...
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Vitiligo http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000523 OR = 1.18, 95% CI = 1.06–1.32
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A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease. Caspase 7 influences susceptibility to rheumatoid arthritis. Genetic polymorphisms, their allele combinations and IFN-beta treatment response in Irish multiple sclerosis patients. Polymorphisms in the caspase genes and the risk of lung cancer.
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[PharmGKB:Curated Risk or phenotype-associated allele: A. Phenotype: This SNP was associated with acute cardiotoxicity in response to doxorubicin. Study size: 1697. Study population/ethnicity: Participants of the German non-Hodgkin lymphoma study. Significance metric(s): OR = 2.6; 95% CI, 1.3 to 5.1. Type of association: PD; ADR; TOX.]
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PPARG by dietary fat interaction influences bone mass in mice and humans. Joint effect of peroxisome proliferator-activated receptor gamma genetic polymorphisms and estrogen-related risk factors on breast cancer risk: results from a case-control study in Taiwan. Variants of the human PPARG locus and the susceptibility to chronic periodontitis. Association of peroxisome proliferator-activated receptor gamma polymorphisms with inflammatory bowel disease in a Hungarian cohort.
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[PharmGKB:Curated A sudy of 760 adult patients with moderate-to-severe depression, treated with escitalopram found that individuals carrying two minor alleles of rs9316233 variant in the HTR2A gene achieved an improvement that was on average 3.1 MADRS points more than individuals carrying two common alleles during escitalopram treatment. This explains 1.1% of variance (P=0.0016) of the response to escitalopram.]
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23andMe blog blood pressure [GWAS:Systolic blood pressure]
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Cholinergic nicotinic receptor genes implicated in a nicotine dependence association study targeting 348 candidate genes with 3713 SNPs. No evidence for association between 19 cholinergic genes and bipolar disorder. The CHRNA5/A3/B4 gene cluster variability as an important determinant of early alcohol and tobacco initiation in young adults. Identification of pharmacogenetic markers in smoking cessation therapy. Variants in nicotinic receptors and risk for nicotine dependence. Genetic variability in nicotinic acetylcholine receptors and nicotine addiction: converging evidence from human and animal research. Nicotinic receptor gene variants influence susceptibility to heavy smoking. Risk for nicotine dependence and lung cancer is conferred by mRNA expression levels and amino acid change in C...
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rs1884613 associated with type-2 diabetes in a Scandinavian population
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[PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: The SULT1C2: rs1402467 G variant was associated with positive clincial response (partial or complete response) to treatment. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.0083 Type of association: PD; CO]
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rs3803304 is an intronic SNP in the AKT1 gene. rs3803304 was significantly associated with longevity in a meta-analysis across three cohorts (odds ratio 0.78, CI: 0.68-0.89, adjusted p=0.043).
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X-inactivation in female human embryonic stem cells is in a nonrandom pattern and prone to epigenetic alterations. [PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: The ATP7A:rs2227291 G variant was associated with toxicity in response to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.006 Type of association: CO; TOX]
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[PharmGKB:Curated Risk or phenotype-associated allele: rs1801132 CC genotype. Phenotype: Increased prevalence of breast cancer in individuals with the combined genotypes of ESR1 rs1801132 CC and ERBB2 665 Ile/Val (rs1136201 A/C). Study size: 100 breast cancer patients (98 females) and 90 controls (84 females). Study population/ethnicity: Sudanese patients diagnosed between June 2004 and July 2005 in Khartoum. Significance metric(s): adjusted OR = 4.9; p = 0.05. Type of association: GN; CO.]
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Impact of genetic polymorphisms in CYP2C8 and rosiglitazone intake on the urinary excretion of dihydroxyeicosatrienoic acids. Role of cytochrome P450 2C8 and 2J2 genotypes in calcineurin inhibitor-induced chronic kidney disease. Cytochrome P450 2C8 pharmacogenetics: a review of clinical studies. [PharmGKB:Curated Risk or phenotype-associated allele: C. Phenotype: This variant was associated with reduced risk for neurotoxicity with paclitaxel treatment. Study size: 132. Study population/ethnicity: Patients with Neoplasms receiving paclitaxel; Spain. Significance metric(s): HR = 0.59 (0.36-0.94); p = 0.026. Type of association: PK; TOX.]
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23andMe blog blood pressure High Blood Pressure (Hypertension) [GWAS:Diastolic Blood Pressure]
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rs17435 is one of several SNPs in the methyl CpG binding protein 2 (MECP2) that have been associated with risk for systemic lupus erythromatosis (SLE). The MECP2 gene is located on the X chromosome, which may be instructive since lupus is a predominantly female disease. An initial survey of 600 Korean patients, followed by 1,000 Caucasian patients, ultimately led to a meta-analysis indicating an odds ratio for the rs17435(T) risk allele of 1.39 (CI: 1.24–1.56, p = 1.2×10e-08). Variants within MECP2, a key transcription regulator, are associated with increased susceptibility to lupus and differential gene expression in patients with systemic lupus erythematosus. Replication of recently identified systemic lupus erythematosus genetic associations: a case-contro...
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Pleiotropic effects of GIP on islet function involve osteopontin. Genetic variation in the glucose-dependent insulinotropic polypeptide receptor modifies the association between carbohydrate and fat intake and risk of type 2 diabetes in the Malmo Diet and Cancer cohort. [PharmGKB:Curated Risk or phenotype-associated allele: A . Phenotype 1: In a meta-analysis of nine genome-wide association studies (n = 15,234 nondiabetic individuals) and a follow-up of 29 independent loci (n = 6,958-30,620), this SNP was found to be associated with 2-h glucose level (a clinical measure of glucose tolerance). Effect (s.e.m.) = 0.09(0.01) mmol/l per A allele. Study size/population/ethnicity: 15,234 plus 6,958-30,620 nondiabetic individuals of European descent. Significance metric(s): p = 1.98 x 10(-15). Ph...
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rs1414334(C) associated with the metabolic syndrome in patients using *clozapine (OR, 9.20; 95% CI, 1.95-43.45) *risperidone (OR, 5.35; 95% CI, 1.26-22.83) [PharmGKB:Curated Risk or phenotype-associated allele: C. Phenotype: In a replication study, the C allele of HTR2C rs1414334 polymorphism is associated with development of the metabolic syndrome during treatment with antipsychotics. Study size: 186. Study population/ethnicity: 93% Caucasian; European; Dutch; The Netherlands. Significance metric(s): OR = 3.73; 95% CI= 1.29-10.79; P = 0.015. Type of association: CO.]
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[PharmGKB:Curated Risk or phenotype-associated allele: C allele. Phenotype: The C allele of rs2848716 shows strong association with carbamazepine (CBZ)-induced Stevens-Johnson syndrome (SJS)/Toxic Epidermal Necrolysis (TEN, Lyell's syndrome). Study size: 204. Study population/ethnicity: 60 CBZ-induced SJS/TEN cases and 144 CBZ-tolerant controls of Chinese descent. Significance metric(s): p = 7.58x10(-17), Pc = 2.10x10(-14), OR = 6.86. Type of association: GN; PD; TOX; ADR.]
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rs5128 (C3238G/3238C>G) is a SNP within the 3' UTR of APOC3 (Apolipoprotein C3). subjects with GC/GG genotypes and diabetes exhibited sig. higher triglyceride (p=0.004), total cholesterol (p=0.003) and glucose (p=0.016) compared to CC subjects [PharmGKB:Curated This 3' UTR variant is associated with hyperlipidemia (elevated triglyceride levels) for HIV-infected individuals treated with ritonavir.]
if diabetic, better response to rosiglitazone
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A total of 262 Korean type-2 diabetes patients were treated with 12 weeks of rosiglitazone at 4mg/day and genotyped to reveal that rs10192566(G) allele carriers responded better than (C) carriers. Patients with rs10192566(G) alleles had a larger decrease in fasting plasma glucose, 2-h postprandial glucose, and HbA1c than rs10192566(C;C) homozygotes. None of the other LPIN1 gene SNPs tested were associated with response. Note: rs11693809, rs10192566, and rs2278513 are in nearly complete linkage disequilibrium (D'>0.958, r(2) >0.882). [PharmGKB:Curated A study in patients with type 2 diabetes treated with rosiglitazone showed that this SNP in the LPIN1 gene was significantly associated with rosiglitazone treatment response. rs11693809 and rs2278513 are in nearly complete linkage diseq...
Shorter QT interval
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rs10918594, a SNP near the NOS1AP gene encoding the nitric oxide synthase I protein, accounts for some of the variation seen in abnormal heart rhythms, in particular, the QT interval. Based on studies totaling ~4,000 individuals of Caucasian ancestry, homozygotes for one allele have shorter QT intervals, while homozygotes for the other allele have a longer QT interval. A follow-up study determined that one rs10918594(G) allele was associated with a 3.6-ms (CI: 2.7 - 4.4ms, p=6.9x10(-17)) increase in QT interval duration, and two (G) alleles had twice that increase. No increase in risk for sudden death due to a cardiac problem was associated with this SNP, though. rs10494366 minor homozygotes had a 9.3 msec longer QT interval compared to major homozygotes (p=5.7x10(-5)); rs10918594 minor ho...
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rs1800471 encodes a change at codon 25 of the TGFB1 gene. It is reported to predispose several organs to fibrosis, and in relation to Crohn's disease, it was associated with stricturing Crohn's disease (odds ratio 2.63, CI: 1.16-5.88, p=0.01) and a shorter time to intestinal resection (p = 0.06) in a study of several hundred Australian patients. [PharmGKB:Curated In conjunction with polymorphism at codon 10, this SNP defines high-, medium- or low-producer haplotype. The Arg allele is associated with higher blood pressure. The C allele is associated with susceptibility to EBV-associated post-transplant lymphoproliferative disorder. The C allele is associated with susceptibility to chronic periodontitis; The G allele may be associated with brucellosis susceptibility. This SNP may play a rol...
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Vascular endothelial growth factor gene polymorphisms in Behcet's disease. A functional variant of vascular endothelial growth factor is associated with severe ischemic complications in giant cell arteritis. Analysis of vascular endothelial growth factor (VEGF) functional variants in rheumatoid arthritis. Association between functional haplotypes of vascular endothelial growth factor and renal complications in Henoch-Schonlein purpura. Polymorphisms in the vascular endothelial growth factor gene and breast cancer in the Cancer Prevention Study II cohort. Vascular endothelial growth factor gene haplotypes in Kawasaki disease. Functional variation in VEGF is not associated with type 2 diabetes in a United Kingdom Caucasian population. VEGF, FGF1, FGF2 and EGF gene polymorphisms and psoriatic...
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[PharmGKB:Curated Phenotype: Sequencing of the IL28B gene in 96 individuals found this SNP to be highly associated with rs12979860 (r - squared > 0.85), which, in a GWAS done in patients of European ancestry, African-Americans and Hispanics was significantly associated with rate of SVR (sustained virological response) to treatment of chronic Hepatitis C genotype I infection with peginterferon-alpha-2a or -2b combined with ribavirin.]
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Common genetic variation in IGF1, IGFBP-1, and IGFBP-3 in relation to mammographic density: a cross-sectional study. Genetic determinants of circulating insulin-like growth factor (IGF)-I, IGF binding protein (BP)-1, and IGFBP-3 levels in a multiethnic population. Polymorphisms in the insulin like growth factor 1 and IGF binding protein 3 genes and risk of colorectal cancer. Transcription factor 7-like 2 polymorphism and colon cancer. IGF-1, IGFBP-1, and IGFBP-3 polymorphisms predict circulating IGF levels but not breast cancer risk: findings from the Breast and Prostate Cancer Cohort Consortium (BPC3). Colon tumor mutations and epigenetic changes associated with genetic polymorphism: insight into disease pathways. Altered transmission of HOX and apoptotic SNPs identify a potential common ...
complex; possible association with anxiety related behaviours
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In mice, the genetic locus best correlated to anxiety-related behaviour contains the 'regulator of G protein signaling 2' gene . In humans, SNPs in the equivalent RGS2 gene have now been studied to see if they are correlated to anxiety related disorders. In the first part of one study, 119 families including children underwent standard lab-based behavioural assessments of behavioural inhibition, defined as a heritable temperamental profile characterized by a tendency to be shy, avoident, and behaviourally restrained in situations that are novel or unfamiliar. Along with some other RGS2 SNPs, carriers of a rs4606(G) allele were 3 fold more likely to exhibit behavioural inhibition (CI: 1.31-6.84, p = 0.0026). In the second part of this study, 744 college undergraduates (228 men, 516 women) w...
complex; generally normal risk
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This SNP in the tumor necrosis factor-alpha gene, rs1800629, is also known as the TNF-308 SNP. Occasionally the rs1800629(A) allele is referred to as 308.2 or TNF2, with the more common (G) allele being 308.1 or TNF1. The (A) allele is associated with higher levels of TNF expression. This SNP has been linked to a wide variety of conditions: * Allograft rejection ** Among 72 Polish patients receiving a kidney transplant, the risk of acute kidney allograft rejection was 2.5x higher among rs1800629(A) carriers compared to (G;G) homozygotes (CI: 1.19- 5.37, p<.05). * Asthma ** A meta-analysis of ~2,500 patients combined indicated that the rs1800629(A) allele was associated with a 1.46x increased risk for asthma. ** In a study of ~600 Mexican families and their asthmatic children, rs1800629(...
normal; no change in warfarin metabolism
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rs1799853 is a SNP in the CYP2C9 gene and is linked to poor warfarin metabolism. Advanced knowledge of this may influence initial warfarin dosing by physicians. Warfarin is monitored through INR (international normalized ratio) and proper dosing is influenced by a variety of factors including warfarin metabolism and diet. rs1799853 is a SNP in the CYP2C9 gene. The rs1799853(T) allele encodes a variant amino acid, cysteine, which has been linked to poor metabolism of warfarin and thus sensitivity . The common nomenclature for this polymorphism is CYP2C9*2 (Cys amino acid, T allele; the SNP is also known as C430T or Cys144Arg). The CYP2C9*2 allele is also associated with higher sensitivity to the anti-epileptic drug phenytoin. The effect of CYP2C9 variants on drug metabolism should not be pr...
normal; no effect on warfarin metabolism
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SNP rs1057910(A), located in the cytochrome p450 CYP2C9 gene, most commonly encodes the amino acid isoleucine at position 359, and the resulting allele is also known as CYP2C9*1. rs1057910(C) encodes a leucine at this same position, and the resulting allele is called CYP2C9*3. This SNP is also known as Ile359Leu or A1075C. The effect of CYP2C9 variants on drug metabolism should not be predicted without also considering CYP2C9*2, defined as the common loss of function variant rs1799853(T) (NM_000771:c.430C>T, NP_000762:p.144R>C) Studies of the effects of these alleles include: * rs1057910(C;C)] genotypes may clear drugs like celecoxib (trade name Celebrex) twice as slowly as rs1057910(A;A) genotypes; the rs1057910(A;C) genotypes are in-between clearance rates. Lower clearance rates wi...
a common variant
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The wild type (normal) allele at this SNP is (G). The (A) variant indicates the presence of a non-wild type CYP2D6 variant, but it appears in many different variants so it can not be used to determine the presence of any particular variant. Inheriting a normal number of copies of this allele results in CYP2D6 function that is indistinguishable from wild-type (normal) activity. However, this variant has been seen present in higher copy numbers, and in these cases, can result in the ultrafast metabolizer phenotype . [PharmGKB:In-Depth Risk or phenotype-associated allele: T. Phenotype: The CYP2D6*2A haplotype was associated with lower incidence of breast cancer on tamoxifen compared to placebo in a prevention study. The CYP2D6*2A allele may be associated with increased efficacy of tamoxifen....
common
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rs1080983 is a SNP near the 5' end of the CYP2D6 gene. Little is known of the significance of either allele.
normal fat metabolism; common in clinvar
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rs1801282, also known as Pro12Ala, is a common SNP in the peroxisome proliferator-activated receptor PPARG gene. The more common (C) allele (in dbSNP orientation) encodes the 'Pro' amino acid at this SNP position. rs1801282 has been reported to be associated with metabolic syndrome, but other studies have not been able to replicate any strong or significant effect. The association between type-2 diabetes and SNP rs1801282 is mentioned as being replicated in rs1801282 and risk of cognitive decline in elders? Maybe with diabetes. A ten-year study of 679 male patients with symptomatic coronary artery disease found that rs1801282(G) carriers had a much lower (10 year) cardiovascular risk, with the hazard ratio estimated to be 0.10 (CI: 0.01-0.70, p = 0.02) for ischemic heart disease and 0.24 f...
normal
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rs1799732 is a SNP in the D2 dopamine receptor gene DRD2 gene. Although dbSNP indicates the alleles as (C) or (-) (i.e. a deletion), investigators report the alleles as (C) or (T). In a study of individuals in the Polyp Prevention Trial with any, multiple (>/=2) or advanced colorectal adenoma recurrence after 4 years, compared to those without adenoma recurrence, rs1799732(C;T) individuals were significantly associated with all adenoma recurrence (odds ratio 1.30, CI: 1.01-1.69). The authors speculate this increased risk of adenoma recurrence (and an association with colorectal cancer) may be related to SNP-associated differences in alcohol and fat intake. 23andMe blog Alcoholism related *rs1799971(A;A) severe alcoholism 2x *rs1799732(I;I) severe alcoholism 1.85x [PharmGKB:Curated Risk...
normal
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This SNP, located in an intron of the GRIA3 gene (also known as AMPA3), has been linked in one study to increased thoughts of suicide in patients taking the anti-depressant drug citalopram. The increased risk is calculated to be 1.9x. If the individual is also carrying two rs2518224(C) alleles, i.e. is a rs2518224(C;C) homozygote, the odds ratio for having suicidal thoughts is increased to ~15x (CI: 3.7 - 60.6). [PharmGKB:Curated This SNP in the GRIA3 gene was associated with treatment-emergent suicidal ideation during citalopram therapy in a clinically representative cohort of outpatients with major depressive disorder. DNA samples from 1,915 participants were genotyped.]
normal
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rs3761847, a SNP located between two genes associated with chronic inflammation (TRAF1 and C5), is associated with increased risk of anti CCP-positive rheumatoid arthritis. The risk allele is (G); the odds ratio reported is 1.32 (95% confidence interval, 1.23 to 1.42; P=4x10-14) . rs3761847(G;G) associated with an increased risk of death (hazard ratio 3.96 [95% confidence interval 1.24-12.6], P = 0.020) as compared with (A;A) homozygote status. The excess mortality was attributed to deaths due to malignancies and sepsis but not cardiovascular disease (CVD). [PharmGKB:Non-Curated GWAS Results: TRAF1-C5 as a risk locus for rheumatoid arthritis--a genomewide study (Initial Sample Size: 1,493 cases, 1,831 controls; Replication Sample Size: 1,053 cases, 1,858 controls; Risk Allele: rs3761847-G...
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Based on a study of ~2500 female patients of European ancestry with sporadic postmenopausal breast cancer, this SNP in the FGFR2 showed the greatest risk. The risk allele is rs1219648(G), with a pooled odds ratio of 1.64 (CI:1.42-1.90) for rs1219648(G;G) homozygotes, and an odds ratio of 1.20 (CI: 1.07-1.42) for rs1219648(A;G) heterozygotes, compared with rs1219648(A;A) homozygotes. rs1219648 represents the SNP in the FGFR2 gene with the strongest association with breast cancer. However, nearby SNPs are almost as predictive. In particular, the following SNP alleles all have linkage values of 0.96 or greater with the rs1219648(G) allele in European populations: *rs2981579(A) *rs2420946(T) *rs11200014(A) An experimental rationale is presented indicating that this SNP is part of a haplotype t...
normal
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rs1801394, also known as A66G or Ile22Met, is a SNP in the methionine synthase MTRR gene. This gene encodes one of the two enzymes involved in the production of methionine (the other is MTR). The protein encoded by an rs1801394 allele has a lower affinity for MTR () and is inconsistently associated with homocysteine level, although it is a risk factor for neural tube defects () and Down syndrome () in conditions of higher homocysteine. Based on a study of British patients with primary brain tumors, (1,005 glioma cases and 631 meningioma cases), rs1801394(G;G) individuals were at higher risk for meningioma (odds ratio 1.41, CI: 1.02-1.94). In general, genotypes associated with increased 5,10-methylenetetrahydrofolate levels are associated with elevated risk for these types of brain cancer. ...
normal risk
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RNA made containing the rs688(T) SNP, a variant near exon 12 of the low-density lipoprotein receptor (LDLR) that is a receptor for ApoE proteins, is spliced at lower efficiency in males. Presumably due to this, the rs688(T;T) genotype was associated with increased risk for Alzheimer's disease odds in males (odds ratio 1.49, CI: 1.13-1.97, uncorrected p=0.005), but not in females. The presence of the rs688(T) allele associates with increased total and LDL-cholesterol in female members of the Framingham Offspring Study; rs688 was not associated with significant differences in HDL-cholesterol. The largest rs688-associated cholesterol differences were observed in pre-menopausal women. Taken together, rs688, a SNP present in approximately 60% of Caucasians, is associated with significant 10% in...
normal
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news rs2511989 not associated with AMD rs2511989(A;A) had a protective effect against age related macular degeneration. Comparison of the rs2511989(A;G) genotype and the wild type (G;G) genotype yielded an odds ratio of 0.63 (CI: 0.47 to 0.84) for age-related macular degeneration. Comparison of rs2511989(A;A) homozygotes with (G;G) homozygotes resulted in an odds ratio of 0.44 (CI: 0.31 to 0.64). [PharmGKB:Curated A case-control study in a UK sample of 479 patients with age-related macular degeneration and 479 controls identified a highly significant association of this variant in intron six of the SERPING1 gene with age-related macular degeneration.]
Magnitude: 0
Frequency: 38.9%
References:103
Frequency: 38.9%
References:103
normal
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Associated with smoking phenotype (p=0.007) based on association study of 2,000+ individuals, and functional studies demonstrated that the risk allele decreased response to a nicotine agonist, therefore the rs16969968(A) allele is likely to be involved in nicotine dependence. In a study 500+ individuals with cocaine dependence, the same rs16969968(A) allele was associated with a 0.67x decreased risk (p = 0.0045). A study of 200 individuals replicated the association between this SNP and nicotine dependence, and also concluded that the rs16969968(A) allele was significantly associated with 'enhanced pleasurable responses' to a person's first cigarette. 23andMe blog 23andMe considers rs1051730 equivalent The association between rs16969968 and lung cancer may, in part, be confounded by chroni...
normal risk
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rs5051 is a SNP in the promoter of the angiotensin AGT gene, and presumably due to it's tight linkage with rs699, the rs5051(T) allele - as oriented to the dbSNP entry, not as published - has been associated with increased risk for hypertension and complications thereof. rs699(T) is associated with higher plasma angiotensinogen levels, and therefore the increased risk of essential hypertension. The frequency of the rs699(T) allele is also generally higher in African populations compared to Caucasian populations, correlating to the higher incidence of hypertension in African population. rs5051 is also known as 'A-6G'. For more details, see rs699. rs5051(T;T) homozygotes have been reported to be at increased risk for Crohn's disease, as based on one cohort of ~350 Australian patients. The od...
normal
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Several SNPs in the VKORC1 gene have been linked to warfarin sensitivity, with perhaps the most common being this SNP rs9923231. Note that the orientation as published in scientific articles is often on the opposite strand compared to the orientation in dbSNP, so you will sometimes see it as a G>T snp. It is also known as *-1639G>A with the minus indicating that this is in an upstream promoter *3673 based on its position in GenBank accession number AY587020. *VKORC1*2. The main findings related to the treatment of venous thromboembolism (aka VTE; from hypercoagulability) with the blood thinner warfarin for this SNP are that carriers of the rs9923231(T) allele require significantly reduced doses of warfarin, and are (otherwise) at a higher risk of serious bleeding. Clinical studies de...
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risk of aortic calcification was calculated, adjusted for potential confounders. The T allele frequency of the VKORC1 1173C>T polymorphism was 38.8%. 1185 (37.2%) persons were homozygous CC, 1529 (48,0%) were heterozygous CT and 473 (14.8%) were homozygous TT. Persons with at least one T-allele had a statistically significant 19% (95% CI 2 to 40%) risk increase of calcification of the aortic far wall compared to CC homozygous persons [PharmGKB:Curated Double homozygous VKORC1 1173T/T, CYP4F2 433Val/Val (n = 5) showed the highest INR (3.1; 2.0-4.7) and required the lowest acenocoumarol dose (11 ± 3 mg/week) The addition of the V433M genotype to the VKORC1 genotype raised the R2 from 8% to 14% for INR, and from 12% to 19% for acenocoumarol dose requirements.] [OMIM:VITAMIN K EPOXIDE...
normal
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rs351855, a SNP in the fibroblast growth factor receptor 4 (FGFR4) gene, is also known as the Gly388Arg variant. The rs351855(T) allele encodes the risk (Arg) allele. The Arg form of this SNP is likely to cause a harder to treat version of node-positive breast cancer, including reducing the efficacy of Herceptin, based on a study of 372 patients. A study of ~500 Japanese prostate cancer patients found that individuals with a rs351855(T;T) genotype had a 2.2- and 1.9-fold increased risk of prostate cancer and benign prostate hyperplasia (BPH), and a 1.8-fold increased risk of metastatic prostate cancer compared to the (C;C) genotype. A meta-analysis published in 2011, surveying a total of 2,618 cases of prostate cancer, concluded that the odds ratio per rs351855(T) allele was 1.17 (CI: 1.07...
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T allele is associated with 3.47mg/dl increase in HDL cholesterol (good cholesterol). [PharmGKB:Non-Curated Phenotype: In a GWAS, this SNP was significantly associated with plasma concentrations of HDL-C and apolipoprotein A1. Study size: 6382. Study population/ethnicity: Caucasian women. Significance metric(s): HDL-C: p = 1.0 x 10 (-41);ApoA1: p = 1.1 x 10(-34). Type of association: CO; GN] [OMIM:?] [GWAS:HDL cholesterol]
normal
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rs1056836, also known as 4326C/G, Val432Leu or L432V, is a SNP in the cytochrome P450 1B1 (CYP1B1) gene. This gene is a member of the CYP1 gene family and one of the major enzymes involved in the hydroxylation of estrogens, a reaction likely to be relevant in hormonal carcinogenesis. [In dbSNP orientation, the (C) allele encodes the Leu; the (G) the Val.] In a study of 153 Hispanic Caucasians with prostate cancer the rs1056836(G;G) genotype showed decreased risk compared to the more common (C;C) genotype (odds ratio = 0.31, p = 0.04, CI: 0.10-0.96). This report cites another study as indicating that rs1056836(C;C) high-risk stage III and IV breast cancer patients receiving dose-intense paclitaxel in combination with doxorubicin and cyclophosphamide experience a longer progression-free surv...
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23andMe blog rs1006737 or (rs2159100) Each T at this SNP increased the odds of bipolar disorder by 1.18 times compared to having two CC copies [PharmGKB:Curated A genome-wide association analysis study in 4,387 cases and 6,209 controls identified a strong association of this variant in the CACNA1C gene with bipolar disorder.] [OMIM:MAJOR AFFECTIVE DISORDER 9; MAFD9] [GWAS:Bipolar disorder]
normal
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rs6280, also known as '''Ser9Gly''', is a SNP in the dopamine receptor D3 DRD3 gene. The rs6280(C) allele encodes a glycine, and the (T) allele encodes a serine (in dbSNP orientation). In a study of 88 patients being treated for schizophrenia with olanzapine, those who were rs6280(C;C) homozygotes had greater positive symptom remission (endpoint rating of minimal or none on all PANSS clinical response positive items, 39.1%), as compared with (C;T) or (T;T) genotypes (13.8%; p = 0.033). Ser9Gly has been implicated in executive function in some studies, but the results are conflicting. * Gly/Gly carriers showed significantly (p = 0.002) poorer performance than Ser/Ser carriers on executive functioning tasks in a somewhat small Caucasian sample (84 patients with first-episode psychosis and 85...
common in complete genomics
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Although somewhat lacking in statistical power, several reports have linked rs1205, a UTR mutation known as CRP4 in the C-reactive protein CRP to the autoimmune disorder SLE, systemic lupus erythematosus. The risk allele in dbSNP orientation is (T). C-reactive protein (CRP) levels obesity rs1205(G) allele had significantly higher CRP levels than noncarriers in a dose-dependent manner suggesting a possible association with fat localization 23andMe blog each rs1205(T) lowered CRP by 20% but no association with heart disease. Analysis of polymorphisms in 16 genes in type 1 diabetes that have been associated with other immune-mediated diseases. A prospective assessment of the Y402H variant in complement factor H, genetic variants in C-reactive protein, and risk of age-related macular degenerat...
normal
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Xenobiotic metabolizing gene variants, dietary heterocyclic amine intake, and risk of prostate cancer. Serum bilirubin levels on ICU admission are associated with ARDS development and mortality in sepsis. [OMIM:UDP-GLYCOSYLTRANSFERASE 1 FAMILY, POLYPEPTIDE A1; UGT1A1] [GWAS:Serum bilirubin levels]
common
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rs887829 is a SNP in the UGT1A1 gene. The minor allele of this SNP has been reported to be associated with higher levels of serum bilirubin, which has an inverse correlation with coronary artery disease. . This study of 2,000+ patients reports a recessive protective effect against coronary artery disease for the minor allele, with an age-adjusted odds ratio of 0.24 (CI: 0.10-0.60, p=0.0014). [PharmGKB:Curated This variant is in the promoter region of UGT1A1 and associated with serum bilirubin levels and hyperbilirubinemia in a genome wide association scan from 4300 Sardinian individuals.] [GWAS:Bilirubin levels]
Common genotype: normal homocysteine levels
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rs1801133 is a SNP that is relatively common and has been studied for (relatively) a long time. Also known as C677T, Ala222Val, and A222V, it encodes a variant in the MTHFR gene, which encodes an enzyme involved in folate metabolism. Homozygous rs1801133(T;T) individuals have ~30% of the expected MTHFR enzyme activity, and rs1801133(C;T) heterozygotes have ~65% activity, compared to the most common genotype, rs1801133(C;C). This reduced activity (i.e. this SNP) has been linked at least once to each of the following disorders (though not necessarily reproducibly): * autism * cancer, including ** gastric cancer ** lung cancer ** head and neck cancer ** renal cancer * cleft lip and cleft palate * coronary artery disease * dementia * depression * hyperhomocysteinemia * migraine * neural tube d...
normal
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rs4673, also known as C242T or H72Y, is a SNP in the NAD(P)H oxidase p22(phox) subunit CYBA gene. A study of German patients with ischemic stroke or transient ischemic attack under the age of 50 (n = 161) concluded that rs4673(T;T) individuals were almost 4 times more likely to experience cerebral ischemia (odds ratio 3.85, CI: 1.39-10.64) compared to rs4673(C;T) or (C;C) individuals after adjusting for classical risk factors. A meta-analysis concluded that the T allele effect may vary between ethnicities in both direction of effect and significance; Asian populations may have reduced coronary artery disease risk associated with the T allele. Genetic polymorphisms and susceptibility to lung disease. Genetic association of glutathione peroxidase-1 with coronary artery calcification in type ...
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news The effectiveness of 17 alpha-hydroxyprogesterone caproate for prevention of recurrent preterm birth is influenced by SNPs. Black women *rs471767 homozygous for the major allele treatment significantly reduced the rate of preterm birth. *rs578029 who had a least one copy of the major allele, treatment significantly reduced in preterm birth non-black women *a least one copy of the minor allele of rs503362 had a significant reduction with treatment *with at least one copy of the minor allele of rs666553 had a significant reduction in very preterm birth
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rs1041983, also known as C282T, is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The allele associated with slow NAT2 metabolization for this SNP is rs1041983(T). Genosets gs154 and gs156 evaluate predicated NAT2 metabolizer phenotype based on rs1041983 and rs1801280. [PharmGKB:Curated in vitro study; PK: 22-fold reduction in Vmax vs wild type]
Magnitude: 0
Frequency: 51.3%
Repute:Good
References:11
Frequency: 51.3%
Repute:Good
References:11
normal
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rs11805303 has been reported in a large study to be associated with Crohn's disease. The risk allele (oriented to the dbSNP entry) is (T); the odds ratio associated with heterozygotes is 1.39 (CI 1.22-1.58), and for homozygotes, 1.86 (CI 1.54-2.24). [OMIM:INTERLEUKIN 23 RECEPTOR; IL23R]
normal
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rs2297480 is a SNP in the FDPS gene, which encodes an enzyme in the mevalonate pathway and therefore might alter the response to amino-bisphonate (drug) treatment of postmenopausal osteoporosis. A study of 234 Danish postmenopausal women treated for at least 2 years with amino-bisphonates concluded that rs2297480(C;C) homozygotes do not respond as successfully as (A;A) or (A;C) genotypes. [PharmGKB:Curated This variant impacted the response to long-term N-bisphosphonates treatment in a study of 234 Danish postmenopausal women. Patients with the homozygous CC genotype showed a decreased response of bone turnover markers to amino-bisphosphonate therapy.]
normal risk
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rs7997012, located in an intron of the HTR2A gene, was found to be associated with a somewhat increased rate of successful response to treatment of depression with the drug citalopram. From this article : 'HTR2A encodes the serotonin 2A receptor, which is downregulated by citalopram. Participants who were homozygous for the A allele had an 18% reduction in absolute risk of having no response to treatment, compared with those homozygous for the other allele.' * See also Anxiety Blog posting [PharmGKB:Curated Risk or phenotype-associated allele: A. Phenotype: Patients with the 5-HTR2A intron 2 (rs7997012) AA genotype suffered from more pronounced side effects compared to carriers of the GA or GG genotype. Study size: 124. Study population/ethnicity: Caucasian; Patients with psychiatric diso...
normal
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In Caucasian non-Hispanics, the rs1360780(T) allele is associated with increased risk for depression, with an odds ratio of 1.39 (CI: 1.14-1.70, p=0.046). This same SNP, which is in the FKBP5 gene, may influence how patients respond to antidepressants including citalopram. rs1360780(T;T) homozgyotes tend to report more depressive episodes, but they also respond better to treatment with antidepressants. rs9296158 rs3800373 rs1360780 rs9470080 linked with the severity of child abuse to predict level of adult PTSD symptoms after correcting for multiple testing. [PharmGKB:Curated This variant is associated with higher chance of response to anti-depressant drugs.] [OMIM:FK506-BINDING PROTEIN 5; FKBP5]
common in complete genomics Predicted to be a NAT2 slow metabolizer.
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With 99% sensitivity and 95% specificity, at least in Caucasian populations, rs1495741 is reported to classify the NAT2 phenotype of an individual; it therefore is a candidate to replace the 7-SNP panel used in genosets such as gs138, gs139, and gs140. The rs1495741(A;A), (A;G) and (G;G) genotypes predicted slow, intermediate, and rapid NAT2 acetylation phenotypes, respectively. [GWAS:None]
Normal common for Caucasians on the 23andme platform
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rs1799930 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. Also known as G590A. The risk allele for this SNP is rs1799930(A). [PharmGKB:Curated in vitro study; PK: 22-fold reduction in Vmax vs wild type] [OMIM:?]
common on affy axiom data
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rs2472297 is a SNP located between the CYP1A1 and CYP1A2 genes on ch 15q24. A meta-analysis of four GWAS studies of coffee consumption among a total of ~8,000 coffee drinkers of European ancestry found that the rs2472297(T) was strongly associated with increased consumption (p = 5.4 x 10e-14). The estimated effect was an increase of 0.2 cups a day per allele for both this SNP and one other (rs6968865).
common in complete genomics
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rs1800588, also known as the -514C/T polymorphism of the LIPC gene, may influence the levels of the 'good' cholestorols, the high density lipoprotein (HDL) cholesterols. Generally, the (T) allele (as published) is considered to lead to higher HDL levels. However, high HDL cholesterol, at least when combined with another HDL raising SNP (rs708272), doesn't appear to actually protect individuals from coronary artery disease, at least based on one study of ~800 Caucasian male patients. Associations between HDL-cholesterol and polymorphisms in hepatic lipase and lipoprotein lipase genes are modified by dietary fat intake in African American and White adults. A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study. Low-density lipoprotein and high-density lipopr...
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Gene-smoking interaction associations for the ERCC1 polymorphisms in the risk of lung cancer. Bladder cancer predisposition: a multigenic approach to DNA-repair and cell-cycle-control genes. Genetic polymorphisms in the nucleotide excision repair pathway and lung cancer risk: a meta-analysis. A distinct ERCC1 haplotype is associated with mRNA expression levels in prostate cancer patients. Genetic susceptibility to cancer: the role of polymorphisms in candidate genes. Genotypes and haplotypes of ERCC1 and ERCC2/XPD genes predict levels of benzo[a]pyrene diol epoxide-induced DNA adducts in cultured primary lymphocytes from healthy individuals: a genotype-phenotype correlation analysis. Case-control analysis of nucleotide excision repair pathway and the risk of renal cell carcinoma. Genetic v...
Magnitude: 0
Frequency: 57.5%
Repute:Good
References:5
Frequency: 57.5%
Repute:Good
References:5
1.7x risk for RA; 1.6X for T1D; also MS?
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rs2104286 has also been reported in a large study to be associated with type-1 diabetes. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.30 (CI 1.02-1.65), and for homozygotes, 1.57 (CI 1.25-1.99). The same (A) allele of rs2104286, which is located in the first intron of the IL2RA gene, was calculated to confer a slight increase (19%) in the risk of developing multiple sclerosis. [PMID tbd; NEJM 357, 29 July 2007, DA Hafler et al.] Note that the (A) allele is the most common at this position in all known populations. blog post giving perspective on the significance of this SNP with respect to multiple sclerosis news announcement rs2104286 was significantly associated with UK cases of juvenile idiopathic arthritis (JIA)(allelic odds ra...
Magnitude: 0
Frequency: 60.2%
Repute:Good
References:106
Frequency: 60.2%
Repute:Good
References:106
normal
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rs12255372, also known as IVS4G>T and c.483+9017G>T, is a well-studied SNP in the TCF7L2 gene on chromosome 10. In some studies, it has been linked to slight increases in risk for type-2 diabetes, breast cancer and aggressive prostate cancer. '''* Type-2 Diabetes Risk Overview:''' numerous papers report an increase in risk, on the order of 1.5 - 2x for the risk genotypes compared to the non-risk genotype. Key papers include: ** reports the association of rs12255372 and rs7903146 with Type-2 diabetes in a Finnish sample. **rs12255372 Common variants (rs12255372 and rs7903146) in TCF7L2 seem to be associated with an increased risk of diabetes among persons with impaired glucose tolerance ** Considered for type-2 diabetes with rs7903146 rs12255372 rs10885406. ** Associated in a study of...
Magnitude: 0
Frequency: 61.1%
Repute:Good
References:58
Frequency: 61.1%
Repute:Good
References:58
normal
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rs10490924 was identified as a risk factor from chromosome 10 related to age related macular degeneration. The risk allele is (T). Odds ratios for heterozygotes and homozygotes are, respectively, 2.69 (CI: 2.22-3.27) and 8.21 (CI: 5.79-11.65). Disease risk in combination with the rs1061170 SNP in the CFH gene is dramatically increased. Homozygotes for both the rare/risk alleles at both loci are estimated to be at 57 fold higher risk for age related macular degeneration than individuals homozygous for the common alleles at both loci. A subsequent study indicated that the risk based on solely the ARMS2 SNP rs10490924 is significantly higher in smokers than in non-smokers. Based on a study of ~750 patients, rs10490924 is significantly higher in participants with choroidal neovascularization t...
common in clinvar
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[PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: The ABCC6 rs2238472 G variant was associated with toxicity in response to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.006 Type of association: CO; TOX] [OMIM:PSEUDOXANTHOMA ELASTICUM]
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[PharmGKB:Curated This variant is found to be a risk marker for statin induced myalgia]
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Associated with baseline cholesterol levels in a study of 9,000+ individuals in Washington County, Maryland. [PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: The PPAR delta SNP rs2016520 A>G was associated with positive clincial response (partial or complete response) to treatment. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.0056 Type of association: PD; CO]
normal
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rs2814707 is one of 2 SNPs from the ch 9p21.2 region associated in a large GWAS study with ALS risk, the other SNP being rs3849942. In this study, the reported odds ratio for rs2814707(A) was 1.22 (CI: 1.15 - 1.30, p = 4.72 x 10e-10). The odds ratio for the minor rs2814707(A) allele was 1.16 (p=7.45x10e-9). 23andMe blog rs2814707(T) 1.16x odds of ALS rs12608932(C) 1.2x odds of ALS [PharmGKB:Curated This variant is significantly associated with the efficacy of anti-TNF treatment in rheumatoid arthritis (Adjusted P-value: 0.000002; OR: 5.2 (1.8, 16.7)). The study is a genome-wide association study using the Illumina HapMap300 SNP chip on 89 RA patients prospectively followed after beginning of anti-TNF therapy.] [OMIM:?]
normal
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rs3849942 is one of 2 SNPs from the ch 9p21.2 region associated in a large GWAS study with ALS risk, the other SNP being rs2814707. In this study, the reported odds ratio for rs3849942(A) was 1.22 (CI: 1.15 - 1.30, p = 4.64 x 10e-10). The odds ratio for the minor rs3849942(A) allele was 1.15 (p=1.01x10e-8). From a study of 405 Finnish patients with ALS, rs3849942 was found within a 42 SNP haplotype associated with highly increased (p = 7 x 10e-33) risk when patients with familial ALS were compared to controls (odds ratio of 21.0, CI: 11.2-39.1). This haplotype overlapped with a region reported (by others) to associate with risk for frontotemporal dementia. In terms of population attributable risk, for the 93 patients with familial ALS, this 9p21 locus accounts for 38% and that of rs1304801...
common in clinvar
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Polymorphisms in the NMDA subunit 2B are not associated with alcohol dependence and alcohol withdrawal-induced seizures and delirium tremens. Association analysis of GRIN2B, encoding N-methyl-D-aspartate receptor 2B subunit, and Alzheimer's disease. Association between NMDA receptor subunit 2b gene polymorphism and Alzheimer's disease in Chinese Han population in Shanghai. Variations in the GRIN2B gene are associated with risky decision-making. Variation in the NMDA receptor 2B subunit gene GRIN2B is associated with differential language lateralization.
normal
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rs324420 is a SNP, also known as Pro129Thr, in the fatty acid amide hydrolase FAAH gene, which has shown associations with some substance use disorders. rs324420(C) encodes the more common Pro, while the (A) allele encodes the Thr. Among 80 individuals with drug abuse or alcoholism and over 1,000 controls, the odds ratio for risk of problem drug or alcohol use among rs324420(A;A) individuals was 4.5 (CI: 2.2 - 8.4); the odds ratio for risk of street drug use was 2.2 (CI: 1.3–3.7); and the odds ratio for risk of combined street drug use and problem drug/alcohol use was 4.9 (CI: 2.5–9.7) When this study was pooled with the results of another study of 249 subjects with documented multiple different drug addictions compared to drug free individuals of the same ethnic backgrounds, t...
common
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rs5370, also known as Lys198Asn or K198N, is a SNP in the endothelin-1 EDN1 gene on chromosome 6. The generally more common rs5370(G) allele encodes the Lys (K), and the rarer rs5370(T) allele encodes the Asn (N). Among the French-Canadian founder population of the Saguenay Lac St-Jean region of Quebec, rs5370(T) was associated with lower HDL cholesterol values in women (p = 1.3 x 10e-5), but not in men. In a study of 1,000+ Western Australians, no association was seen between HDL levels and rs5370. A study of ~400 rheumatoid arthritis patients found a 3x increase in the adjusted odds of being hypertensive for rs5370(T;T) homozygotes compared to (G;G) homozygotes (odds ratio 2.89, CI: 1.02 - 8.19, p=0.011). After adjustment for multiple potential confounders, haplotype analysis revealed an...
common in clinvar
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rs2234922, also known as His139Arg, is a SNP in the microsomal epoxide hydrolase EPHX1 gene. The genetics of chronic obstructive pulmonary disease. Orofacial cleft risk is increased with maternal smoking and specific detoxification-gene variants. Associations between smoking, polymorphisms in polycyclic aromatic hydrocarbon (PAH) metabolism and conjugation genes and PAH-DNA adducts in prostate tumors differ by race. Xenobiotic metabolizing enzyme gene polymorphisms predict response to lung volume reduction surgery. Genetic polymorphisms and benzene metabolism in humans exposed to a wide range of air concentrations. Correlating observed odds ratios from lung cancer case-control studies to SNP functional scores predicted by bioinformatic tools. Do genetic factors protect for early onset lung...
common/normal Val/val (normal) variant of the Val66Met snp in the BDNF gene that codes for brain-derived neurotrophic factor. Met/met is associated with susceptibility to neuropsychiatric disorders.
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rs6265, also known as Val66Met, is a SNP in brain-derived neurotrophic factor BDNF gene. The more common G allele encodes the Val, while the A allele encodes Met. Met/A allele associated with introversion The A allele may also be protective against depression when subjected to repeated defeat g2b2mh blog On a driving-based motor learning task subjects with this genotype showed greater error during short-term learning and poorer retention over 4 days, relative to subjects without the polymorphism. The presence of this BDNF polymorphism is associated with differences in brain motor system function, altered short-term plasticity, and greater error in short-term motor learning. Wired discusses the research as does 23andMe blog. Alzheimer's disease risk for non ApoE4 carriers is affected by the...
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A genome-wide association study of acenocoumarol maintenance dosage. [PharmGKB:Curated In a GWAS study, this SNP was modestly associated with warfarin dose, accounting for ~9% of the variance in dose. This SNP was in perfect linkage disequilibrium with rs4917639.] [GWAS:Warfarin maintenance dose]
common in clinvar
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rs1805124, also known as His558Arg or H558R, is a SNP in the cardiac sodium channel SCN5A gene. This SNP is quite common, a variants go, with an allele frequency of 10 - 25% in many populations. It seems to be considered to be a benign change. [PharmGKB:In-Depth Has been studied in association with long QT.] [OMIM:SODIUM CHANNEL, VOLTAGE-GATED, TYPE V, ALPHA SUBUNIT; SCN5A]
common in clinvar
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rs1800566 (C609T, Pro187Ser) is a snp within NQO1 (NAD(P)H dehydrogenase (quinone 1)). A Ser (T) at this location denotes the NQO1*2 allele. influences the risk of breast cancer according to the 23andMe blog rs1800566 increases susceptibility to Lung cancer 0.48 times for heterozygotes (CT) [PharmGKB:Curated Risk or phenotype-associated allele: C/T. Phenotype: There was no association between the NQO1*2 polymorphism and the risk of anthracycline-related CHF. Study size: 145. Study population/ethnicity: Nested case-control study was conducted within a cohort of 1979 patients enrolled in the Childhood Cancer Survivor Study who received treatment with anthracyclines and had available DNA. Significance metric(s): OR = 1.04; p = 0.97. Type of association: CO; TOX; ADR.] [OMIM:NAD(P)H DEHYDROGE...
common on affy axiom data
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rs10935838, rs2046934, rs5853517, and rs6809699 venous thromboembolism lower risk of incident DVT/PE as compared to the reference haplotype H1 (odds ratio=0.50, 95% CI=0.27-0.93, p=0.028)
Magnitude: 0
Frequency: 66.2%
References:28
Frequency: 66.2%
References:28
normal
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rs10499194 associated with rheumatoid arthritis In a concurrent study, the Wellcome Trust Case Control Consortium (WTCCC) has reported strong association of rheumatoid arthritis susceptibility to a different SNP located 3.8 kb from rs10499194 (rs6920220; P = 5 x 10(-6) in WTCCC). We show that these two SNP associations are statistically independent, are each reproducible in the comparison of our data and WTCCC data, and define risk and protective haplotypes for rheumatoid arthritis at 6q23. rheumatoid arthritis *rs6920220 [P= 2.6 x 10(-6), OR 1.22 (1.13-1.33)]. *rs5029937 *rs13207033 protective [P= 0.0001, OR 0.86 (0.8-0.93)] perfectly correlated with rs10499194 The combination of the carriage of both risk alleles of rs6920220 and rs5029937 together with the absence of the protective allel...
7x less likely to respond to certain antidepressants
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rs7787082 is a SNP in the ABCB1 gene (also known as the MDR1 gene), which encodes a protein that transports certain molecules across the blood-brain barrier. SNPs in ABCB1 may thus influence the intracerebral concentrations of certain drugs and thus their efficacy or potential for adverse side effects. rs7787082 is one of 9 SNPs found within a tight linkage block (r<sup>2</sup> >= 0.8 ) such that the minor allele at any one of them predicts (with ~80%+ accuracy) that the other SNPs will also be the minor allele. The list of the 9 SNPs is shown below. When treated for depression with substrates of the protein encoded by ABCB1, carriers of one or two minor alleles at these ABCB1 SNPs have been reported to respond better than non-carriers. The antidepressant drugs that are know...
common in complete genomics
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[PharmGKB:Curated This variant in the P2RY1 gene was found to have a significant association with platelet response to ADP.]
common on affy axiom data
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[PharmGKB:Non-Curated GWAS results: Does parental expressed emotion moderate genetic effects in ADHD? An exploration using a genome wide association scan. (Initial Sample Size: 909 trios; Replication Sample Size: NR); (Region: 4q23; Reported Gene(s): ADH1C; Risk Allele: rs1789891-A); (p-value= 0.000003).This variant is associated with Conduct disorder (interaction).] [GWAS:Conduct disorder (interaction)]
common in complete genomics
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No association of single nucleotide polymorphisms in one-carbon metabolism genes with prostate cancer risk. Lack of association of polymorphisms in homocysteine metabolism genes with pseudoexfoliation syndrome and glaucoma.
normal
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rs4363657 is a SNP in the SLCO1B1 gene, a gene which encodes a protein involved in the liver's uptake of certain drugs, including the statins used to lower cholesterol levels. rs4363657 in nearly complete linkage disequilibrium with rs4149056 SNP (r<sup>2</sup>=0.97), which has been linked to statin metabolism. rs4149056(C) odds ratio for myopathy among 20,000 individuals taking either 40 or 80mg of simvastatin daily was 4.5 (CI: 2.6-7.7) per copy of the C allele, and 16.9 (CI: 4.7-61.1) in (C;C) as compared with (T;T) homozygotes. See also rs4149056 for a more detailed description of the effect of SLCO1B1 gene SNPs on the metabolism of many drugs. SLCO1B1 genetic variant associated with statin-induced myopathy: a proof-of-concept study using the clinical practice research data...
common in complete genomics
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23andMe blog blood pressure [GWAS:Diastolic Blood Pressure]
normal
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rs1800630 is a SNP upstream of the tumor necrosis alpha (TNF) gene; this SNP is also typically called the -863 variant. In a study of 154 Thai patients with systemic lupus erythematosus (SLE), rs1800630(A) allele frequency was significantly increased, with an odds ratio of 1.85 (CI: 1.21-2.83, p(corr) = 0.009). This allele was also found to be significantly increased in the SLE group with Raynaud's phenomenon compared to SLE without Raynaud's phenomenon ( odds ratio of 2.23, CI: 1.21-4.10, p(corr) = 0.048). Separately, a meta-analysis of 10 case-control studies, including over 2,200 Graves' disease cases, concluded that rs1800630(A) carriers were associated with the disease.
common in complete genomics
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pancreatic cancer 702 cases and 785 controls *rs162049 P = .0018; OR, 1.33; 95% CI: 1.11-1.60 *rs10380 (His595Tyr) P = .0063; OR, 1.45; 95% CI: 1.11-1.88
Magnitude: 0
Frequency: 70.8%
References:10
Frequency: 70.8%
References:10
normal
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rs17234657 has been reported in a large study to be associated with Crohn's disease. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.54 (CI 1.34-1.76), and for homozygotes, 2.32 (CI 1.59-3.39). [OMIM:INFLAMMATORY BOWEL DISEASE 18; IBD18]
normal
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The rs1799971(G) allele in exon 1 of the mu opioid receptor OPRM1 gene causes the normal amino acid at residue 40, asparagine (Asn), to be replaced by aspartic acid (Asp). In the literature this SNP is also known as A118G, N40D, or Asn40Asp. Carriers of at least one rs1799971(G) allele appear to have stronger cravings for alcohol than carriers of two rs1799971(A) alleles, and are thus hypothesized to be more at higher risk for alcoholism. However, subsequent research results are mixed, and there are other studies both agreeing or disagreeing with this finding Among 200+ alcoholics treated with naltrexone, rs1799971(G) carriers receiving the drug (even without behavioral intervention) had an increased percentage of days abstinent (p = .07) and a decreased percentage of heavy drinking days (...
normal
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influences statin response *rs72559745 (SLCO1B1*1) AA AA *rs56061388 (SLCO1B1*3) TT TT *rs4149056 (SLCO1B1*5) TT TT *rs55901008 (SLCO1B1*6) TT TT rs4149056, also known as 37041T>C or V174A, is a SNP in the SLCO1B1 gene, which encodes the 'organic anion transporting polypeptide 1B1' (OATP1B1) protein. This protein, found primarily in the liver, regulates the uptake of numerous drugs and natural compounds. The rs4149056(C) SNP defines the SLCO1B1*5 allele. The rs4149056(C) allele gives rise to an amino acid change (from valine to alanine at residue 174) which has reduced uptake/transport activity. Therefore, drugs metabolized by OATP1B1 tend to build up to higher circulating concentrations than they would otherwise.. The drugs known (or in some cases, thought) to be transported less well ...
common in clinvar
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Technology to accelerate pangenomic scanning for unknown point mutations in exonic sequences: cycling temperature capillary electrophoresis (CTCE). Genetic variation in the one-carbon transfer pathway and ovarian cancer risk. Strong association of a common dihydropyrimidine dehydrogenase gene polymorphism with fluoropyrimidine-related toxicity in cancer patients. Genetic variation in TYMS in the one-carbon transfer pathway is associated with ovarian carcinoma types in the Ovarian Cancer Association Consortium. [PharmGKB:Curated Patients heterozygous for the C allele of this SNP exhibited increased incidence of medium-severe nausea and vomiting (as defined by WHO criteria) relative to those carrying only the T allele. The patient population consisted of individuals with gastric or colon ca...
common in complete genomics
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[PharmGKB:Curated Phenotype: This SNP, along with a second one in tight LD (rs71760050) was significantly associated, in a cohort of estrogen-receptor-positive patients with primary breast cancer larger than 3 cm, with change in aromatase activity before and after aromatase inhibitor neoadjuvant treatment . It was also associated, but not significantly so after adjustment for multiple testing, with change in estrone level and with pretreatment aromatase level. Study size: 45. Study population/ethnicity: Edinburgh female ER-positive patients, primary breast cancer larger than 3 cm. Significance metric(s): nominal p = 0.0063, p = 0.039 after adjustment for multiple testing. Type of association: PD; GN;FA. Second Phenotype: In a group of 200 women with early-stage breast cancer, who were trea...
normal
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This SNP, located in an intron of the GRIK2 gene, has been linked in one study to increased thoughts of suicide in patients using the anti-depressant drug citalopram. The risk is only seen for individuals carrying two rs2518224(C) alleles, i.e. the rs2518224(C;C) homozygotes. The odds ratio for these individuals is 8.2. If the individual also has at least one rs4825476(G) allele, the odds ratio for having suicidal thoughts is increased to ~15x (CI: 3.7 - 60.6). [PharmGKB:Curated This SNP in the GRIK2 gene was associated with treatment-emergent suicidal ideation during citalopram therapy in a clinically representative cohort of outpatients with major depressive disorder. DNA samples from 1,915 participants were genotyped.]
common in complete genomics
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[PharmGKB:Curated Risk or phenotype-associated allele: T Phenotype: The CYP4B1:rs4646487 T variant was associated with toxicity in response to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s):p = 0.008 Type of association: CO; TOX]
common
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23andMe blog rs8099917(C) less likely to respond to Hepatitis C treatment. rs12979860(C;C) better able to become naturally Hepatitis C virus-free. rs12980275(A) usually corresponds to the rs12979860(C) [PharmGKB:Curated Risk or phenotype-associated allele: G. Phenotype: This variant is associated with null virological response (NVR) and sustained virologic response (SVR) in Janapese patients with hepatitis C virus infection treated with PEG-INF-alpha plus ribavirin. Study size: Initial sample:154; Replication Sample: 172. Study population/ethnicity: Japanese. Significance metric(s): P=3.11 x 10(-15) (NVR); P = 1.11 x 10(-27)(SVR). Type of association: GN; CO] [OMIM:INTERLEUKIN 28B; IL28B] [GWAS:Response to Hepatitis C treatment]
Magnitude: 0
Frequency: 73.5%
Repute:Good
References:3
Frequency: 73.5%
Repute:Good
References:3
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JAMA rs12777823 and rs4244285 implicated in platelet response to clopidogrel [PharmGKB:Curated A GWAS found this variant (rs12777823) was the most significantly associated SNP with clopidogrel response. This SNP was in strong linkage disequilibrium with 12 further SNPs within the CYP2C18-CYP2C19-CYP2C9-CYP2C8 cluster (rs12777823; rs10109204; rs2025445; rs1326837; rs717238; rs2860838; rs2860903; rs9332105; rs9332113; rs12572351; rs10509679; rs1934951; rs1934680) and also with the loss-of-function variant CYP2C19*2 (rs4244285). Further findings in this study showed that the CYP2C19*2 genotype accounted for most of all the initially found association with diminished platelet response to clopidogrel.]
normal
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rs7158782 is one of 4 SNPs found on chromosome 14 near a gene known as T-cell leukemia/lymphoma 1A (TCL1A). This gene appears to be estrogen dependent. In a study of ~300 patients with early-stage estrogen receptor–positive (ER+) breast cancer who were treated with the aromatase inhibitor (AI) anastrozole or exemestane and who developed musculoskeletal toxicity severe enough to prompt discontinuation, rs7158782(G) allele carriers were at ~2x higher risk for toxicity (CI: 1.5 - 2.9, p < 10e-6). The population attributable risk (i.e., the fraction of such adverse events that could be due to this allele) was estimated to be 11%. An editorial accompanying this article downplays the clinical utility of this finding, since testing for this allele, given its frequency and (mere) doubling...
normal
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rs3736228 is a SNP in the LRP5 gene that is also known as Ala1330Val or A1330V; the more common (C) allele encodes the Ala (alanine), while the rarer (T) allele encodes the Val (valine), which is the risk allele. rs3736228(T) is associated with vertebral fractures and reduced bone mineral density (BMD), with an overall odds ratio for fractures of 1.06 per allele (CI: 1.01-1.12; 7802 fractures among 31,199 individuals studied). More specifically, the rs3736228(T) allele was associated with reduced lumbar spine BMD (p = 2.6 x 10<sup>-9</sup>), and femoral neck BMD (p = 5.0 x 10<sup>-6</sup>). Note that rs4988321, another LRP5 SNP (also known as Val667Met), was independently associated with BMD in this same study. news rs3736228 was associated with a 30% increase in th...
common in clinvar
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rs1805008, known as Arg160Trp or R160W, is one of several SNPs in the MC1R gene associated with red hair color (redheads), in this case in an Irish population although this has also been reported in Icelandic and Dutch populations . The risk allele is rs1805008(T), compared with the wild-type rs1805008(C) allele. blog about designing melanocortin analogs specific to these genotypes. See also OMIM 155555.0005 Melanoma Parkinson's disease [OMIM:SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 2; SHEP2]
normal
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rs2243250 is a SNP in the IL4 gene that is also known as the -589C>T SNP. In 300 patients younger than 50 years the rs2243250(T) allele was associated with a reduced risk of myocardial infarction (odds ratio 0.57, CI: 0.34-0.95). This result was replicated in another study, where carriers of one or two -589T alleles also had a reduced risk (odds ratio 0.67, CI: 0.47-0.95), with a strong protective effect of the -598T allele in homozygous -589T (odds ratio 0.33, CI: 0.10-1.05).
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[OMIM:?] [GWAS:Chronic Hepatitis C infection]
Magnitude: 0
Frequency: 75.2%
Repute:Good
References:16
Frequency: 75.2%
Repute:Good
References:16
common on affy axiom data
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CYP2C8 SNP, defining the CYP2C8*3 allele (along with rs11572080). Individuals carrying this SNP may show increased risk of developing acute gastrointestinal bleeding during the use of NSAIDs that are CYP2C8 or CYP2C9 substrates, such as aceclofenac, celecoxib, diclofenac, ibuprofen, indomethazine, lornoxicam, meloxicam, naproxen, piroxicam, tenoxicam and valdecoxib. [PharmGKB:Curated Risk or phenotype-associated allele: G. Phenotype: In woman, the risk of acute myocardial infarction (AMI) tended to be higher for subjects carrying the CYP2C8*3*3 genotype versus *1*1 (OR = 1.9). The CYP2C8*3 variants are 416G>A (rs10509681) and 1196A>G (rs11572080). Tested in all subjects, the risk of AMI was also higher in individuals carrying the CYP2C8*3 allele (*3*3; *1*3 versus*1*1) [1.2 (1.0-1.5...
normal
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rs1734787 is one of several SNPs in the methyl CpG binding protein 2 (MECP2) that have been associated with risk for systemic lupus erythromatosis (SLE). The MECP2 gene is located on the X chromosome, which may be instructive since lupus is a predominantly female disease. An initial survey of 600 Korean patients, followed by 1,000 Caucasian patients, ultimately led to a meta-analysis indicating an odds ratio for the rs1734787(C) risk allele of 1.42 (CI: 1.26–1.60, p = 1.6×10e-08).
normal
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rs4648317, a SNP in the dopamine D2 receptor DRD2 gene, has been linked to higher rates of smoking and higher nicotine dependence scores, based on a study of ~220 adolescents. The risk allele rs4648317(T).
normal
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rs1076560 is located in intron 6 of the dopamine receptor D2 gene. In one study of Japanese males, rs1076560(A) alleles were 1.3 fold more associated with Alcoholism than the rs1076560(C) alleles. The DRD2 risk allele A was more prevalent in the alcoholic patients than in the healthy controls. These data identify rs1076560 as a potentially important variable in the development of alcoholism. rs1076560 and the DAT 3'-VNTR variant influences memory Genetic variants altering dopamine D2 receptor expression or function modulate the risk of opiate addiction and the dosage requirements of methadone substitution [PharmGKB:Curated This variant is a potential marker for alcoholism. A allele was more prevalent in the alcoholic patients than in the healthy controls in a study consists of 248 alcohol...
Magnitude: 0
Frequency: 76.1%
Repute:Good
References:8
Frequency: 76.1%
Repute:Good
References:8
normal
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This position is odd. Under the older reference genome build36, it was on the plus strand; in build37 it is on the minus strand. This makes it very prone to some ambiguous flip confusion in the literature, plus, 23andMe users have self-reported the flipped form. IN addition, instead of the usual SNP listed as having 2 alleles, all 4 alleles are reported in dbSNP, even if this is probably due to the strand changes. dbSNP currently says the normal allele is C, and T is the rare geno which causes a premature stop, early in the gene. We at SNPedia suspect that the A & G alleles are not common enough to have ever been genuinely reported, but for de-novo mutations each allele would be non-synonymous and result in a different amino acid. http://snpedia.blogspot.com/2012/12/snpedias-nightmare-befo...
common on affy axiom data
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[PharmGKB:Curated Risk or phenotype-associated allele: T Phenotype: The SPG7:rs2292954 T variant was associated with toxicity in response to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.0004 Type of association: CO; TOX]
normal
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rs4244285 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*2 variant. This variant is the most common reason for poor metabolism of compounds like mephenytoin (an anti-convulsant), some antidepressants, the anti-platelet drug Plavix, and some drugs used for ulcer conditions of various types. The risk allele is rs4244285(A). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (trade name Prevacid). In Caucasians, SNPs in CYP2C19 are relatively rare (in contrast to SNPs in CYP2D6), but SNPs in this gene are common in Asians. Ulcer treatment with omeprazole to reduce Helicobacter pyl...
Magnitude: 0
Frequency: 76.8%
Repute:Good
References:3
Frequency: 76.8%
Repute:Good
References:3
normal risk
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rs1805007, known as Arg151Cys or R151C, one of several SNPs in the MC1R gene associated with red hair color (redheads), and in redheaded females, linked to being more responsive to the anesthetics pentazocine, nalbuphine, and butorphanol, often used by dentists The risk allele is rs1805007(T), compared with the wild-type rs1805007(C) allele. The risk allele has also been reported in several studies to be associated with increased risk for melanoma. For example, an odds ratio of 2.94 (CI: 1.04-8.31) has been reported for an Italian population , and similarly an odds ratio of 2.9 has been reported for a Polish population . Blog entry about designing melanocortin analogs specific to these genotypes. See also OMIM 155555.0004 Freckling [OMIM:SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 2; SHEP2]...
Magnitude: 0
Frequency: 77.0%
Repute:Good
References:2
Frequency: 77.0%
Repute:Good
References:2
Magnitude: 0
Frequency: 77.1%
Repute:Good
References:17
Frequency: 77.1%
Repute:Good
References:17
common on affy axiom data
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CYP2C8 SNP, defining the CYP2C8*3 allele (along with rs10509681). Individuals carrying this SNP may show increased risk of developing acute gastrointestinal bleeding during the use of NSAIDs that are CYP2C8 or CYP2C9 substrates, such as aceclofenac, celecoxib, diclofenac, ibuprofen, indomethazine, lornoxicam, meloxicam, naproxen, piroxicam, tenoxicam and valdecoxib. [PharmGKB:Curated Risk or phenotype-associated allele: A. Phenotype: This variant was associated with increased risk for neurotoxicity with paclitaxel treatment. Study size: 132. Study population/ethnicity: Patients with Neoplasms receiving paclitaxel; Spain. Significance metric(s): HR = 1.54 (0.96-2.47); p = 0.072. Type of association: PK; TOX.]
Normal risk for autoimmune disorders
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This SNP, located in the PTPN22 gene and also known as R620W, or 1858C>T, may influence Rheumatoid Arthritis and other autoimmune diseases, including but not limited to, multiple sclerosis, Crohn's disease, celiac disease and type-1 diabetes. In an expanded follow-up study of >6,000 controls and 6,000 patients, the heterozygote odds ratio for type-1 diabetes for this SNP was recalculated to be 1.98 (CI 1.82-2.15). rs2476601 was confirmed in another 2007 study to be a risk factor for RA . * confirms the association of rs2476601 rheumatoid arthritis * two copies of the PTPN22 R620W allele more than doubles the risk for RF positive RA * see rs2476601(A;G) * * * * * rs2476601 shows a 0.75 (r squared) correlation with rs6679677, a SNP in the RSBN1 gene associated with rheumatoid arthritis...
Magnitude: 0
Frequency: 77.6%
Repute:Good
References:3
Frequency: 77.6%
Repute:Good
References:3
common on affy axiom data
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Epigenetic regulation of human gamma-glutamyl hydrolase activity in acute lymphoblastic leukemia cells. [PharmGKB:Curated Patients (n= 66) with acute lymphoblastic leukemia showed large individual differences in cellular accumulation of long-chain MTXPG after high-dose methotrexate treatment. The frequency of the rs11545078 (452C>T, Thr127Ile) in GGH was significantly different among patients with low (17.6%), intermediate (9.4%) and high (0%) GGH activity (P = 0.025). Caucasians had a significantly higher frequency of the Ile127 allele (10.0%) than African-Americans (4.4%) (P = 0.033). Rs11545078 was detected in 2 of 4 patients with low GGH activity and none of the five patients with high GGH activity. This missense variant significantly increased Km for long chain polyglutamated meth...
normal
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rs6679677 has been reported in a large study to be associated with rheumatoid arthritis. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.98 (CI 1.72-2.27), and for homozygotes, 3.32 (CI 1.93-5.69). rs6679677 was also reported in the same study to be associated with type-1 diabetes. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.82 (CI 1.59-2.09), and for homozygotes, 5.19 (CI 3.15-8.55). Recently (Feb 2008), it has been asserted that the association between rs6679677 and type-1 diabetes is actually completely due to a closely linked, potentially causal variant identified as rs2476601, which is also known as Arg620Trp. In this study, apparently the largest to date, the odds ratio...
common on affy axiom data
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[PharmGKB:Curated Drug efflux and cell surface expression (by MRK-16 and C219 probes) of P-gp was not different between wild-type and variant forms (single mutants: N21D, F103L, S400N, A893S, A998T, and double mutants: 21D-S400N, N21D-A893S, and S400N-A893S) in an in vitro vaccinia virus-based transient expression system. Fluroescent substrates included calcein AM, bodipy-FL-forskolin, bodipy-FL-verapamil, bodipy-FL-vinblastine, bodipy-FL-prazosin, bisantrene, and bodipy-FL-paclitaxel. There was a slight increase in wild-type P-gp efflux of bodipy-FL-paclitaxel over mutants.]
common in clinvar you have the common genotype, but rare genotype has a beneficial effect on blood pressure and risk of myocardial infarction.
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[OMIM:MYOCARDIAL INFARCTION, DECREASED SUSCEPTIBILITY TO]
common in complete genomics
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rs2066844 is a SNP in the NOD2 gene; the SNP is also known as R702W or Arg702Trp, with the (C) allele encoding the Arg (R) and the (T) allele encoding the Trp (W). The two initial reports linking the minor(T) allele as strongly associated with Crohn's disease are and . rs2066844 is mentioned in as being strongly associated with Crohn's disease No association was found for NOD2/CARD15 SNPs (R702W, G908R) in Chinese patients with inflammatory bowel disease. [OMIM:CROHN DISEASE, SUSCEPTIBILITY TO]
normal
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rs2231142, also known as Q141K and C421A, is a SNP in the ABCG2 gene, indicating a missense variant. 'Our data indicate that at least 10% of all gout cases in whites are attributable to this causal variant.' A is the risk allele. A large study totaling 7,699 participants in the Framingham cohort and 4,148 participants in the Rotterdam cohort was conducted, with genome-wide significant SNPs then replicated in 11,000+ Caucasian and ~4,000 African-American individuals who took part in the study of Atherosclerosis Risk in Communities (ARIC). This study calculated an odds ratio of 1.74 for rs2231142 (CI: 1.51-1.99, p = 3.3x10e-15). A genetic score comprised of this SNP plus 2 others may stratify risk for gout. Among non-small cell lung cancer patients treated with gefitinib, there's a 4-5x high...
normal
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rs4553808, also known as A/G-1661, is a SNP in the upstream activator sequence of the cytotoxic T lymphocyte associated antigen-4 CTLA4 gene. This gene encodes the CD152 antigen. A study of 165 Swedish myasthenia gravis patients concluded that the rs4553808(G;G) homozygotes had an odds ratio of 0.05 (CI: 0.00286-0.874, p=0.0023) for the disease compared to healthy individuals, while the rs4553808(G) allele showed a less dramatic reduction in risk, with an odds ratio of 0.578 (CI: 0.373-0.897, p=0.015).
common on affy axiom data
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[PharmGKB:Curated Risk or phenotype-associated allele: None. Phenotype: Variants identified in a screen of 13 genes involved in the gemcitabine drug metabolic pathway. For the non-synonymous POLA2:2089G>A (G583R) SNP, the A (583Arg) allele was at frequency 0.18 in both Europeans and Africans. The frequency of GG, GA, AA genotypes were 0.65, 0.34, 0.01 in Europeans, and 0.71, 0.22, 0.07 in Africans, respectively. There was a significant difference between ethnic groups in genotype frequency distribution (p < 0.05). Study size: 184. Study population/ethnicity: Healthy, unrelated blood donors of European (n = 95) and African (n = 89) descent. Significance metric(s): p < 0.05. Type of association: GN.]
common in clinvar
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Variations in the peroxisome proliferator-activated receptor-gamma gene and melanoma risk. PPAR-gamma gene polymorphisms and psoriatic arthritis. The Genetics of PPARG and the Skeleton. The association of Pro12Ala polymorphism of peroxisome proliferator-activated receptor-gamma gene with serum osteoprotegerin levels in healthy Korean women. Association of stearoyl-CoA desaturase 1 activity with familial combined hyperlipidemia. Polymorphism of genes related to insulin sensitivity and the risk of biliary tract cancer and biliary stone: a population-based case-control study in Shanghai, China. PPAR Genomics and Pharmacogenomics: Implications for Cardiovascular Disease. Association of FTO with obesity-related traits in the Cebu Longitudinal Health and Nutrition Survey (CLHNS) Cohort. Differen...
Magnitude: 0
Frequency: 79.6%
Repute:Good
References:5
Frequency: 79.6%
Repute:Good
References:5
normal
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rs2542151 has been reported in a large study to be associated with Crohn's disease. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.3 (CI 1.14-1.48), and for homozygotes, 2.01 (CI 1.46-2.76). rs2542151 has been reported in the same study to be associated with type-1 diabetes. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.30 (CI 1.15-1.47), and for homozygotes, 1.62 (CI 1.17-2.24). In an expanded follow-up study of >6,000 controls and 6,000 patients, the heterozygote odds ratio for this SNP was recalculated to be 1.30 (CI 1.22–1.40). [PharmGKB:Non-Curated GWAS results: Meta-analysis of genome-wide association study data identifies additional type 1 diabete...
normal risk
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rs4762, a SNP in the angiotensin II AGT gene, has been reported to be associated with increased risk for developing pre-eclampsia, based on a study of ~180 French-Canadian women. The odds ratio associated with the rs4762(T) allele (encoding methionine) was 1.9 (CI:1.2–2.9, p=0.0033). Note that rs4762 is commonly referred to in the literature as 'T174M' or 'Thr174Met'; however, databases now indicate that the amino acid that varies is #207 (not 174), as the protein is currently numbered. rs4762 was also reported to play the major role in the 2.1 fold increased risk (CI: 1.4-3.4, p=0.0008) for pre-eclampsia of the rs3889728(A)-rs4762(T)-rs699(C) haplotype. Correction of population stratification in large multi-ethnic association studies. Ten renin-angiotensin system-relate...
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rs2066853 has been associated with increased risk for colorectal polyps depending on the amount of meat eaten or overall exposure to heterocyclic amines. lung cancer in a Chinese population heterozygous rs2158041 OR=1.53 for GA vs compared with the (G;G) and rs7811989 OR=1.48 for (G;A) compared with the GG genotype) *rs2066853 (p.Arg554Lys) and cumulative cigarette smoking and the Lys/Lys genotype conferred an increased risk of lung cancer in the heavy smokers OR=3.36 [PharmGKB:In-Depth Very common variant with controversial associations.]
common in complete genomics
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[PharmGKB:Non-Curated Increased metformin uptake in transfected cells] [GWAS:Blood metabolite levels]
common in complete genomics
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[PharmGKB:Non-Curated Phenotype: In a GWAS, this SNP was significantly associated with plasma concentrations of LDL-C and apolipoprotein B. Study size: 6382. Study population/ethnicity: Caucasian women. Significance metric(s): LDL-C: p = 5.2 x 10 (-15);ApoB: p = 7.0 x 10(-18). Type of association: CO; GN] [OMIM:?] [GWAS:LDL cholesterol]
normal risk of ADHD
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T allele may be associated with Attention deficit hyperactivity disorder.
common in complete genomics
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Sex-dependent genetic markers of CYP3A4 expression and activity in human liver microsomes. Prediction of CYP3A4 enzyme activity using haplotype tag SNPs in African Americans. CYP3A7, CYP3A5, CYP3A4, and ABCB1 genetic polymorphisms, cyclosporine concentration, and dose requirement in transplant recipients.
normal
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rs4994, also known as Trp64Arg or as the Arg64 variant, is a SNP in the ADRB3 gene. The rs4994(C) allele encodes the variant arginine. In a study of 600+ women initially referred for coronary angiography and then followed for 6 years, during which time 115 experienced a heart problem, rs4994(C) individuals were calculated to be at higher risk (adjusted hazard ratio 2.10, CI: 1.05-4.24). This risk was due to subtle increases in risk for all of the individual endpoints, and was only seen in women without obstructive coronary artery disease. Response to Diet and Exercise [PharmGKB:Curated Arg in position 64 associated with olanzapine-induced weight gain] [OMIM:OBESITY, SUSCEPTIBILITY TO]
Magnitude: 0
Frequency: 84.1%
Repute:Good
References:8
Frequency: 84.1%
Repute:Good
References:8
common in complete genomics
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[PharmGKB:Curated This promoter variant affects total DRD2 mRNA expression. The C allele is associated with enhanced total DRD2 mRNA expression and is associated with working memory activity in prefrontal cortex and striatum of schizophrenia patients.]
common in complete genomics
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[PharmGKB:Curated No association with coronary artery disease, myocardial infarction, diabetes, hypertension, or weight loss.]
common in complete genomics
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Genetic variation in the serotonin 2A receptor and suicidal ideation in a sample of 270 Irish high-density schizophrenia families.
Magnitude: 0
Frequency: 84.8%
Repute:Good
References:2
Frequency: 84.8%
Repute:Good
References:2
common in complete genomics
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[PharmGKB:Curated One study at 115 subjects with pancreatitis and 66 controls found that the CASR R990G variant is a significant risk factor for chronic pancreatitis.]
Magnitude: 0
Frequency: 85.0%
Repute:Good
References:1
Frequency: 85.0%
Repute:Good
References:1
Magnitude: 0
Frequency: 85.0%
Repute:Good
References:1
Frequency: 85.0%
Repute:Good
References:1
lower risk for skin cancer
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rs1799782, a SNP also known as Arg194Trp located in the DNA-repair gene XRCC1, is associated with a reduced risk for certain types of cancer. The (T) allele encodes the Trp amino acid. A study of ~200 Korean cases of skin cancer indicated that the rs1799782(T;T) genotype was inversely associated with squamous cell cancer risk (adjusted odds ratio 0.06, CI: 0.006-0.63). A meta-analysis of 8 case-control studies concluded that significant association was found between the rs1799782 polymorphism and oral cancer risk among Asians, showing an odds ratio of 1.347 (CI: 1.0 - 1.81) for allele comparison, 1.378 (CI: 1.070 - 1.775) for (T;T) homozygotes vs (C;C) homozygotes, and 1.420 (CI: 1.041 - 1.936) for comparison under a dominant model. 18067C>T possibly related to non-Hodgkin lymphoma rs20...
common in complete genomics
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23andMe blog rs2237892(C) is associated with an increased risk for developing type-2 diabetes. each C at rs2237892 increased the odds of type 2 diabetes by 1.4 times, compared to the TT genotype. It’s important to note, however, that the C version is actually pretty common. In Asian populations, the C version of rs2237892 increased a person’s odds of type 2 diabetes by 1.42 times compared to people with TT. But because about 50% of the Asian population is actually CT at this SNP, it could be viewed that CC has 1.3 times the odds compared to typical, while TT has 0.61 times the typical odds. In European populations, about 85% of people are CC. This means that the results of Yasuda et al really show that compared to most Europeans, people with CT at rs22...
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Association of chromosome 12 locus with antihypertensive response to hydrochlorothiazide may involve differential YEATS4 expression. [PharmGKB:Non-Curated GWAS results: Genomic association analysis suggests chromosome 12 locus influencing antihypertensive response to thiazide diuretic (Initial Sample Size: 194 blacks, 195 whites; Replication Sample Size: NR). This variant is associated with Response to diuretic therapy.] [GWAS:Response to diuretic therapy]
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This SNP is a variant in the ABO gene, and is therefore potentially useful in determining ABO blood group, such as through the use of genosets. 23andMe reports this as a G/T while decodeme reports it as a an A/C. [PharmGKB:Curated Risk or phenotype-associated allele: A Phenotype: Angiotensin converting enzyme activity was increased per copy of the rs8176746 A allele. Carriage of the A allele is associated with the B blood group antigen. Study size: 623 Study population/ethnicity: Academia Sinica Multi-Centered Young-Onset Hypertension (AS-YOH) Genetic Study; Han Chinese individuals with Hypertension. Significance metric(s): p = 9.3 × 10−5 Type of association: PD] [OMIM:?] [GWAS:Hematological and biochemical traits]
common on affy axiom data
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[PharmGKB:Curated The DPYD:496A>G variant was associated with toxicity of fluoropyrimidine-based chemotherapy in patients with gastroesophageal and breast cancer, but did not reach significance in patients with colorectal malignancies.]
Magnitude: 0
Frequency: 85.8%
References:14
Frequency: 85.8%
References:14
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23andMe blog blood pressure [GWAS:Systolic blood pressure]
common in clinvar
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rs1736557, also known as Val257Met, is a SNP in the FMO3 gene. It has been linked to trimethylaminuria; see variant .0002, OMIM 136132. [OMIM:?]
Magnitude: 0
Frequency: 85.9%
Repute:Good
References:3
Frequency: 85.9%
Repute:Good
References:3
common in clinvar
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age related macular degeneration [OMIM:COMPLEMENT FACTOR B; CFB] [GWAS:Age-related macular degeneration]
normal
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http://www.scientificblogging.com/news_releases/comorbidity_ghrelin_hunger_hormone_implicated_in_alcohol_dependence Jörgen Engel, professor of pharmacology at the Sahlgrenska Academy, University of Gothenburg For this research, scientists recruited 417 Spanish individuals from the general population (n=279) as well as heavy drinkers (n=138) admitted to a hospital for treatment. The study sample – comprised of abstainers, moderate and heavy alcohol drinkers – was then examined for single nucleotide polymorphisms (SNPs) in the pro-ghrelin and growth hormone secretagogue receptors (GHS-R1A) (GHSR) gene. Findings showed that SNP rs2232165 of the GHS-R1A gene was associated with heavy alcohol consumption (and therefore presumably alcohol dependence). SNP rs2948694 of the same g...
Magnitude: 0
Frequency: 86.6%
Repute:Good
References:3
Frequency: 86.6%
Repute:Good
References:3
Magnitude: 0
Frequency: 86.7%
Repute:Good
References:3
Frequency: 86.7%
Repute:Good
References:3
common in complete genomics
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[PharmGKB:Non-Curated Genome-wide association study of response to methylphenidate in 187 children with attention-deficit/hyperactivity disorder. (Initial Sample Size: 187 children; Replication Sample Size: NR); (Region: 5p15.31; Reported Gene: Intergenic; Risk Allele: rs11134178-T) This variant is associated with Attention-deficit/hyperactivity disorder.] [GWAS:Attention-deficit/hyperactivity disorder]
common on affy axiom data
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Distinct genetic loci control plasma HIV-RNA and cellular HIV-DNA levels in HIV-1 infection: the ANRS Genome Wide Association 01 study.
common in clinvar common for Caucasians on the 23andme platform
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rs2228479, known as Val92Met or V92M, is one of several SNPs in the MC1R gene commonly associated with red (or blond) hair and poor tanning, but note its high presence in one Asian population The risk allele is rs2228479(A), compared with the wild-type rs2228479(G) allele. See also OMIM 155555.0002 [OMIM:?]
normal
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rs2031920 is a SNP in the CYP2E1 gene. The rs2031920(T) allele defines the CYP2E1_-1055C>T variant. [OMIM:CYTOCHROME P450, SUBFAMILY IIE; CYP2E1]
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[PharmGKB:Curated SNP influences the efficacy of methotrexate in patients with psoriasis.]
higher risk for RA
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rs6314, also known as C1354T or His452Tyr/H452Y, is a SNP in the serotonin 2A receptor HTR2A gene. Based on a study of 166 Caucasian patients being treated for depression with paroxetine, rs6314 heterozygotes were associated with better response. There was a significantly higher frequency of heterozygotes in the remitter and response groups in comparison to the non-remitter (odds ratio 7.50, p=0.002) and non-response groups (odds ratio 5.25, p=0.01). * rs6314 is part of a 4-SNP haplotype in the serotonin 2A receptor gene HTR2A that has been associated with rheumatoid arthritis in a study of 1800 European patients. The risk allele is rs6314(C). The overall risk for the haplotype CTCC of SNPs rs6311-rs1328674-rs6313-rs6314 is 1.68 (CI: 1.20 - 2.34, p = 0.02). Note: the orientation of rs13286...
common The rs2395029(T;T) genotype is the common genotype for this SNP, against which the rs2395029(T;G) and rs2395029(G;G) genotypes that are associated with reduced HIV viral load in HIV carriers are compared. See also rs9264942 and HIV.
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rs2395029 is a SNP in the major histocompatibility complex (MHC) region, and several studies have shown that the rs2395029(G) allele is 99.9% predictive of the presence of an HLA-B*5701 allele. This HLA allele, in turn, has been associated with several conditions. A study of 51 cases of flucloxacillin drug-induced liver injury (DILI), an important cause of serious liver disease, along with a replication study of another 23 cases, found that the rs2395029(G) carriers were at highly increased risk (odds ratio 80, p=8.7x10(-33)). * see also: 23andMe blog rs2395029(G;G) increases the odds of drug-induced liver injury in response to flucloxacillin by 45x This SNP is thought to be involved in determining the HIV viral load set point during the asymptomatic period of infection. This SNP is estima...
common
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rs6427528 is a SNP in the chromosome 1q23 region apparently located near enough to the CD84 locus to affect it's expression. A GWAS study of 2,700+ rheumatoid arthritis (RA) patients treated with one of three anti-TNF drugs found that rs6427528(A) carriers had higher CD84 expression and responded better to etanercept treatment. The effect was statistically significant but not that large in magnitude, totaling 2.6% of the variance in response to etanercept treatment. The result was seen in European (Caucasian) patients, but perhaps due to small patient numbers, was not statistically supported in Japanese patients. [GWAS:Response to anti-TNF treatment in rheumatoid arthritis]
Not a C282Y hemochromatosis carrier.
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rs1800562 represents a SNP that accounts for ~85% of all cases of hemochromatosis, a disorder whose symptoms include cirrhosis of the liver, diabetes, hypermelanotic pigmentation of the skin, and heart failure. OMIM indicates that liver cancer is responsible for about one-third of deaths of rs1800562(A;A) homozygotes, and since hemochromatosis is a relatively easily treated disorder if diagnosed, this is a form of preventable cancer. The rs1800562(A) allele is known as the C282Y or Cys282Tyr mutation, and it is found at a frequency of around 5-10% in many Caucasian populations, leading to an incidence of (A;A) homozygotes around 1 in 200. Early identification of rs1800562(A;A) homozygotes can prevent complications of hemochromatosis; however, the percentage of all (A;A) homozygotes who act...
common in complete genomics
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[PharmGKB:Curated Risk or phenotype-associated allele: C. Phenotype: An in vitro PFA-100 analysis was performed within 4 h of phlebotomy (blood drawn from healthy volunteers), using CADP and CEPI cartridges. GP1BA: -5T>C significantly effected platelet responses to collagen plus ADP (CADP). After accounting for multiple testing (Bonferroni adjustment), a statistically significant inverse correlation remained between CADP CT and GP1BA -5C (adjusted P = 0.011).] [GWAS:Hematological and biochemical traits]
common on affy axiom data
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[PharmGKB:Curated Risk or phenotype-associated allele: A. Phenotype: This SNP was part of a haplotype associated with acute cardiotoxicity in response to doxorubicin. Study size: 1697. Study population/ethnicity: Participants of the German non-Hodgkin lymphoma study. Significance metric(s): OR = 2.3; 95% CI, 1.0 to 5.4. Type of association: PD; ADR; TOX.]
common in complete genomics
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An IL-6 haplotype on human chromosome 7p21 confers risk for impaired renal function in type 2 diabetic patients. C-reactive protein, interleukin-6, and prostate cancer risk in men aged 65 years and older. Association of genetic variation in serum amyloid-A with cardiovascular disease and interactions with IL6, IL1RN, IL1beta and TNF genes in the Cardiovascular Health Study.
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Association between ADORA2A and DRD2 polymorphisms and caffeine-induced anxiety. Physiogenomic analysis of localized FMRI brain activity in schizophrenia. Evaluation of genetic variability in the dopamine receptor D2 in relation to behavioral inhibition and impulsivity/sensation seeking: an exploratory study with d-amphetamine in healthy participants. Pharmacogenetics and antipsychotics: therapeutic efficacy and side effects prediction. [PharmGKB:Curated Risk or phenotype-associated allele: A. Phenotype: Having the AA genotype of this variant was associated with a protective effect from increased prolactin concentration. Study size: 90. Study population/ethnicity: 7-17-year-old patients chronically treated with risperidone; non-Hispanic Caucasians. Significance metric(s): p = 0.002. Type ...
common in complete genomics
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rs2066992 coronary artery disease 190 affected Asian Indian sibling pairs
common in complete genomics
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[PharmGKB:Curated In an 80-patient study, this variant was not associated with plasma concentrations of montelukast or with response to treatment with montelukast.]
normal
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rs1000113 has been reported in a large study to be associated with Crohn's disease. The risk allele (oriented to the dbSNP entry) is (T); the odds ratio associated with heterozygotes is 1.54 (CI 1.31-1.82), and for homozygotes, 1.92 (CI 0.92-4.00). [PharmGKB:Non-Curated GWAS Results: Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls (Initial Sample Size: 1,748 cases, 2,938 controls; Replication Sample Size: (see Parkes 2007); Risk Allele: rs1000113-T). This variant is associated with crohn's disease.] [GWAS:Crohn's disease]
normal risk
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rs25489, a SNP also known as Arg280His located in the DNA-repair gene XRCC1, is associated with an increased risk for breast cancer based on a study of 1,100 Cypriot women. The odds ratio for the rs25489(A;A) homozygote is 4.68, CI: 1.01-21.7, p=0.03. rs25489(A;G) prostate cancer patients being treated by radiation therapy are more likely (67% compared to 24%, p=0.048) to develop erectile dysfunction after irradiation than (G;G) patients, based on a study of 135 patients. A meta-analysis concludes that this SNP is not associated with risk of gastric cancer. Kin-cohort estimates for familial breast cancer risk in relation to variants in DNA base excision repair, BRCA1 interacting and growth factor genes. Multiplex pyrosequencing of two polymorphisms in DNA repair gene XRCC1. DNA repair gene...
normal
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[PharmGKB:Curated Risk or phenotype-associated allele: allele 4. Phenotype: Tagging SNP for HLA-B*5701 (0.011 allele frequency). Study size: 45. Study population/ethnicity: Unrelated Han Chinese from Beijing, China. Significance metric(s): Type of association: GN]
common in complete genomics
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[PharmGKB:Curated Risk or phenotype-associated allele: T. Phenotype: CYP2B6*2 genotype in the transplant recipient was associated with hemorrhagic cystitis. Study size:107 . Study population/ethnicity: Donors and patients with leukemia after HLA-identical hematopoietic stem cell transplantation, France. Significance metric(s): p = 0.03. Type of association: TOX]
Magnitude: 0
Frequency: 92.9%
Repute:Good
References:3
Frequency: 92.9%
Repute:Good
References:3
common in complete genomics
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[PharmGKB:Curated Risk or phenotype-associated allele: UGT1A8*3 (defining allele: 830A, 277Tyr). Phenotype: In vitro catalytic activity and protein expression. Genetic analysis of UGT1A8 (exclusively expressed in extrahepatic tissue) in 69 individuals identified four alleles, of which UGT1A8*3 was defined as having tyrosine at amino acid 277. In vitro studies in HEK293 cells show UGT1A8*3 (830A, 277Y) has a dramatic reduction in catalytic activity compared to wildtype, but no loss in protein expression. Study size: 69. Study population/ethnicity: Lung cancer patients and family members and other volunteers who served as controls. Type of association: GN; FA]
normal
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rs2070672 is a SNP in the CYP2E1 gene. The rs2070672(G) allele defines the CYP2E1*7_-352A>G variant.
common in complete genomics
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ADH single nucleotide polymorphism associations with alcohol metabolism in vivo.
common in complete genomics
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[PharmGKB:Non-Curated GWAS Results: Whole genome association study identifies polymorphisms associated with QT prolongation during iloperidone treatment of schizophrenia (Initial Sample Size: 183 individuals; Replication Sample Size: NR; Risk Allele: rs4933824-T). This variant is associated with Response to iloperidone treatment (QT prolongation).] [GWAS:Response to iloperidone treatment (QT prolongation)]
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Also known as Ile462Val A4889G CYP1A1*2C Genome amplification of single sperm using multiple displacement amplification. Decision forest analysis of 61 single nucleotide polymorphisms in a case-control study of esophageal cancer; a novel method. Multilocus analysis of SNP and metabolic data within a given pathway. CYP1A1 and CYP1B1 polymorphisms and their association with estradiol and estrogen metabolites in women who are premenopausal and perimenopausal. Dietary phytoestrogen intake is associated with reduced colorectal cancer risk. Associations between smoking, polymorphisms in polycyclic aromatic hydrocarbon (PAH) metabolism and conjugation genes and PAH-DNA adducts in prostate tumors differ by race. Cytochrome P450 1A1 (CYP1A1) polymorphisms and breast cancer risk in Korean women. Cor...
common in complete genomics
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rs1256049 is a SNP in the estrogen receptor 2 gene ESR2. rs1256049(A) allele carriers have higher mean carotid artery intima-media thickness (CIMT) as well as maximal CIMT, but this result may be limited to the population studied, in this case individuals from the Cardiovascular Risk in Young Finns study. [Association between single-nucleotide polymorphisms in estrogen receptor beta gene and risk of prostate cancer]. Polymorphisms in the estrogen receptor beta (ESR2) gene are associated with bone mineral density in Caucasian men and women. Allelic estrogen receptor 1 (ESR1) gene variants predict the outcome of ovarian stimulation in in vitro fertilization. CA repeat and RsaI polymorphisms in ERbeta gene are not associated with infertility in Indian men. Haplotypes of the estrogen receptor ...
common on affy axiom data
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nortriptyline response [PharmGKB:Curated Risk or phenotype-associated allele: A Phenotype: The SNP within an intron of the uronyl 2-sulphotransferase gene was associated with outcome at a genome-wide level of significance and with a very small posterior probability of being a false positive. Carriers of the minor A allele experienced less improvement of depression symptoms than carriers of the GG homozygote from week 4 onward. Study size: 312 Study population/ethnicity: Individuals with unipolar depression of at least moderate severity treated with nortriptyline. Type of association: GN] [GWAS:Response to antidepressants]
common in complete genomics
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[PharmGKB:Curated This variant is in exon 1b of ABCB1 and may be associated with tacrolimus pharmacokinetics in renal transplant recipients. It was also associated with lower ABCB1 mRNA expression and possibly being an useful invasive marker predicting poorly-differentiated colorectal adenocarcinomas and thereby the poor prognosis of the Japanese patients in the study.]
normal
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rs4986790, a SNP also known as Asp299Gly (and also 896A/G) in the TLR4 gene, is often studied along with a cosegregating SNP known as Thr399Ile, rs4986791. (TLR4 encodes a receptor involved in the innate immune response.) Together, these SNPs have been reported to be associated with a wide variety of both infectious and non-infectious diseases, although there are conflicting or even contradictory results also reported in some cases. The risk allele for rs4986790 is (G). Reported associations include : * Diabetic neuropathy ** These SNPs may be protective * Heart disease ** Men with the risk alleles for both SNPs are at increased risk for myocardial infarction in this study of over 2000 individuals. ** rs4986790(G) carriers are not at increased risk for myocardial infartions, at least in th...
normal
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rs4986791, a SNP also known as Thr399Ile (and also 1196C/T) in the TLR4 gene, is often studied along with a cosegregating SNP known as Asp299Gly, rs4986790. (TLR4 encodes a receptor involved in the innate immune response.) Together, these SNPs have been reported to be associated with a wide variety of both infectious and non-infectious diseases, although there are conflicting or even contradictory results also reported in some cases. The risk allele for rs4986791 is (T). Reported associations include : * Diabetic neuropathy ** These SNPs may be protective * Heart disease ** Men with the risk alleles for both SNPs are at increased risk for myocardial infarction in this study of over 2000 individuals. ** rs4986790(G) carriers are not at increased risk for myocardial infartions, at least in t...
common in complete genomics
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[PharmGKB:Curated This variant is the defining SNP for CYP19A1*4. It is associated with significant decreases in levels of activity compared with the wild-type (WT) enzyme after transient expression in COS-1 cells.]
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[PharmGKB:Curated Drug efflux and cell surface expression (by MRK-16 and C219 probes) of P-gp was not different between wild-type and variant forms (single mutants: N21D, F103L, S400N, A893S, A998T, and double mutants: 21D-S400N, N21D-A893S, and S400N-A893S) in an in vitro vaccinia virus-based transient expression system. Fluroescent substrates included calcein AM, bodipy-FL-forskolin, bodipy-FL-verapamil, bodipy-FL-vinblastine, bodipy-FL-prazosin, bisantrene, and bodipy-FL-paclitaxel. There was a slight increase in wild-type P-gp efflux of bodipy-FL-paclitaxel over mutants.]
common in clinvar
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rs1142345 is a SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The risk allele for this SNP is rs1142345(G), and when it is the only variant in the TPMT gene, it encodes the TPMT*3C allele. While still rare, it is more common in African-Americans (2.4% of all alleles) than in Caucasians. Note that if the same allele also carries the rs1800460(A) SNP, the allele is actually a TPMT*3A allele (OMIM). The medicine 6-Mercaptopurine is metabolized by TPMT. Individual differences in TPMT activity associated with this SNP are now used to determine appropriate dosage range and interval for treatment. 23an...
common in complete genomics
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[PharmGKB:Curated system: membrane vessicles from HEK cells transfected with WT or variant; FA: variant had approx 50% decrease in transport of tritium labelled 17[beta]-estradiol-17[beta]-D-glucuronide and tritium labelled methotrexate]
common in complete genomics
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23andMe blog Influences QT interval [PharmGKB:Curated Associated with noise-induced hearing loss.] [OMIM:POTASSIUM CHANNEL, VOLTAGE-GATED, ISK-RELATED SUBFAMILY, MEMBER 1;]
normal
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http://www.scientificblogging.com/news_releases/comorbidity_ghrelin_hunger_hormone_implicated_in_alcohol_dependence Jörgen Engel, professor of pharmacology at the Sahlgrenska Academy, University of Gothenburg For this research, scientists recruited 417 Spanish individuals from the general population (n=279) as well as heavy drinkers (n=138) admitted to a hospital for treatment. The study sample – comprised of abstainers, moderate and heavy alcohol drinkers – was then examined for single nucleotide polymorphisms (SNPs) in the pro-ghrelin and growth hormone secretagogue receptors (GHS-R1A) (GHSR) gene. Findings showed that SNP rs2232165 of the GHS-R1A gene was associated with heavy alcohol consumption (and therefore presumably alcohol dependence). SNP rs2948694 of the same g...
Magnitude: 0
Frequency: 95.6%
Repute:Good
References:2
Frequency: 95.6%
Repute:Good
References:2
common in complete genomics
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[PharmGKB:Curated Risk or phenotype-associated allele: None. Phenotype: Variants identified in a screen of 13 genes involved in the gemcitabine drug metabolic pathway. For the non-synonymous SLC28A1:1543G>A (R510C) SNP, the A (510Cys) allele was at frequency was 0.02 and 0.09 in Europeans and Africans, respectively. There was a significant difference between ethnic groups in genotype frequency distribution (p < 0.05). Study size: 186. Study population/ethnicity: Healthy, unrelated blood donors of European (n = 93) and African (n = 93) descent. Significance metric(s): p < 0.05. Type of association: GN.]
normal/common
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rs6025 represents a SNP in the Factor V F5 gene, encoding a change in the protein from an arginine at position 506 to a glutamine. The resulting rs6025(A) allele encodes a mutation known as the Leiden mutation, R506Q, found in perhaps 3 to 5% of the individuals in most populations. About 1 in 10 individuals harboring the R506Q will experience clinically significant venous thromboembolism in their lifetimes (according to OMIM). Overall, the rs6025(A) allele appears to be necessary but not sufficient for the development of venous thromboembolism. Patients who are rs6025(A;G) heterozygotes but lack other risk-enhancing SNPs have a risk of recurrent deep venous thrombosis equal to patients with no such SNPs. In contrast, patients who are heterozygotes for both rs6025 and the prothrombin rs1799...
common in complete genomics
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[PharmGKB:Curated This variant is associated with end-of-induction minimal risidual disease (MRD) in childhood acute lymphoblastic leukemia (ALL) from 2 independent cohorts (GWAS result). Risk Allele: G, MAF= 0.05, combined P value= 1.12E-04. It is also associated with greater methotrexate clearance.]
common in complete genomics
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[PharmGKB:Curated Risk or phenotype-associated allele: T. Phenotype: In a study of bacterial expressed and purified human CBR3 proteins, the 93Ile variant had significantly reduced maximal reaction velocity (V(max)) for both anthracyclines compared with the wild-type enzyme. Type of association: FA.]
normal
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rs662799 is a SNP in the APOA5 gene. The rarer rs662799(C) allele has been associated in multiple reports (cited below) to be associated with higher triglyceride levels. Independently of triglyceride levels, perhaps, a study based on 1,864 Italian patients <45 years old at the time of their first heart attack (myocardial infarction) concluded that this SNP is associated with higher risk for an early heart attack, with a per C allele odds ratio of 1.44 (CI: 1.23-1.69, p = 6.7 × 10(-5)). This SNP has also been reported to help prevent weight gain from high fat diets. 1,073 men and 1,207 women participating in the Framingham Offspring Study rs662799 -1131T>C in modulates the effect of fat intake on BMI and obesity risk in both men and women. Individuals with at least one C allele g...
common in complete genomics
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rs2304016 (IVS7-32A>G) is a SNP within the SCN2A (sodium channel, voltage-gated, type II, alpha subunit). among 471 Chinese epilepsy patients (of which 272 were drug responsive and 199 drug resistant), A-allele carriers associated with resistance to anti-epileptic drugs (OR 2.1, 95% CI 1.2-3.7, p=0.007), haplotypes containing A-alleles were also associated w/ drug resistance [PharmGKB:Curated The A allele of this SNP was associated with resistance to sodium channel-blocking anti-epileptic drugs in a Chinese patient population.]
common in complete genomics
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[PharmGKB:Curated Human lymphocyte cell lines homozygous for the A allele of this variant, common in Japanese populations, exhibit reduced surface membrane levels of ABCC4 protein and increased sensitivity to 6-mercaptopurine toxicity relative to cell lines homozygous for the G allele. The A-allele and G-allele cell lines have similar overall protein expression levels.]
common
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[PharmGKB:Curated This study showed a highly significant association between a COMT haplotype of two functional SNPs (Ala72Ser and Val158Met) and aggressive behavior in schizophrenia.] [OMIM:SCHIZOPHRENIA, SUSCEPTIBILITY TO]
Magnitude: 0
Frequency: 98.2%
Repute:Bad
References:19
Frequency: 98.2%
Repute:Bad
References:19
normal Since the rare geno is good, this can be considered slightly bad
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rs11591147, also known as R46L, is a SNP in the PCSK9 gene. As early as 2006, the minor rs11591147(T) allele was reported to be associated with lower LDL cholesterol levels, and most studies since have found that this also correlates to a two to three fold reduced risk for both early- and late-onset cardiovascular events and disease. As part of a 9 SNP set studied in a meta-analysis totaling over 300,000 patients, rs11591147 was the SNP with the greatest effect on LDL-C and therefore cardiovascular risk reduction. The set of SNPs was as follows, ordered from strongest to least effect on coronary risk, and the allele shown is the one associated with reduced LDL-C levels along with the associated (or nearby) lipid metabolism gene: * rs11591147(T), PCSK9 * rs4420638(A), APOE * rs6511720(T), L...
common in clinvar
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rs1799931 is a SNP in the NAT2 gene, potentially encoding a variant detoxifying protein known as an N-acetyltransferase, but which NAT2 variant depends on which other NAT2 SNPs were also inherited. See the discussion of the NAT2 gene for a more complete explanation. The risk allele for this SNP is rs1799931(A). [PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: The NAT2:rs1799931 G variant was associated with toxicity in response to docetaxel and thalidomide. Study size: 47 Study population/ethnicity: Patients diagnosed with castration-resistant prostate cancer enrolled in a randomized phase II clinical trial comparing docetaxel to docetaxel with thalidomide. Significance metric(s): p = 0.003 Type of association: CO; TOX] [OMIM:?]
common in complete genomics
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[PharmGKB:Curated Based on an study on 284 Mexican Americans, this variant in the 5' UTR of PSMB4 is significantly associated with major depressive disorder (MDD). The results implicate that the specific UTR variation increases the risks for a T-cell dysfunction in MDD in the studied population.]
normal risk
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rs1800750, a SNP located at position -376 of the TNF gene, has been linked to increased risk for recurrent acute otitis in a study of 348 children. The (adjusted) odds ratio is 3.06 for (G;G) genotypes (p=0.07).
common in complete genomics
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[PharmGKB:Curated Risk or phenotype-associated allele: A Phenotype: Kinetic studies using purified, histidine-tagged, recombinant enzymes demonstrated that the V88I mutation leads to a significantly reduced maximal rate of activity for doxorubicin and daunorubicin compared to wild type protein. Type of association: FA]
Magnitude: 0
Frequency: 99.1%
Repute:Good
References:0
Frequency: 99.1%
Repute:Good
References:0
Typical BuChE
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rs1799807, also known as D70G, is a SNP in the BCHE gene. This SNP affects the structure, activity, and substrate specificity of the BuChE (butyrylcholinesterase) enzyme. [Cholinesterases and cholinesterase inhibitors, p. 48] The variant form, rs1799807(G), replaces aspartate with glycine at the secondary substrate/inhibitor binding site. This single base substitution yields the 'atypical' version of BChE. This version has a lower affinity for many substrates, including many Cholinesterase Inhibitors (CIs). A different cholinesterase (acetylcholinesterase, AChE) is an important component of neurotransmission by acetylcholine (ACh), terminating the action of ACh after it has been released during neurotransmission. BChE is found widely in the plasma and normally binds to CIs, protecting AChE...
Magnitude: 0
Frequency: 99.1%
Repute:Good
References:1
Frequency: 99.1%
Repute:Good
References:1
common in complete genomics
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CYP2B6 (c.516G-->T) and CYP2A6 (*9B and/or *17) polymorphisms are independent predictors of efavirenz plasma concentrations in HIV-infected patients. [PharmGKB:In-Depth This variant decreases enzyme activity and affects metabolism of coumarin and nicotine; part of the CYP2A6*17 haplotype.]
common in complete genomics
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23andMe reports that the A allele of rs3918290 is associated with the rare recessive disorder dihydropyrimidine dehydrogenase deficiency (DPD), also known as hereditary thymine-uraciluria or familial pyrimidinemia. Note that the terms used in the literature for this gene can be confusing, since the gene is in reverse orientation to the chromosome strand on the reference genome. pharmgkb - defines *2A allele, which has a significantly higher chance of 5-fluorouracil toxicity Fluorouracil Toxicity [PharmGKB:In-Depth Heterozygosity for the A allele of this SNP is associated with mucositis and leukopenia drug toxicity in cancer patients treated with fluorouracil. Heterozygous males were more likely than heterozygous females to develop severe toxicity. In this study, no A/A homozygotes were ob...
normal
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rs4986909, also known as 1247C>T, 22026C>T or P416L, is a SNP in the CYP3A4 gene. The rs4986909(T) allele defines the CYP3A4*13 variant. [PharmGKB:In-Depth Defining variant for CYP3A4*13; in vitro, this allele did not result in detectable P450 holoprotein.]
common in clinvar
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rs7626962, also known as Ser1103Tyr or S1103Y, is a SNP in the cardiac sodium channel SCN5A gene. Although relatively common (for a rare allele; 10 - 20% of individuals) in those of African ancestry, in all populations the rs7626962(T) allele has been reported to increase the risk for cardiac issues such as long QT syndrome but also arrhythmias and even sudden infant death syndrome. The odds ratio for displaying signs of arrhythmia for anyone carrying a rs7626962(T) allele is reported as 8.7 (CI 3.2 - 23.9) ; as for sudden infant death syndrome, at least in African-ancestry populations, the odds ratio for the same allele is reported as 4.9, leading to an odds ratio of 24 for rs7626962(T;T) homozygotes. This variant meets the criteria published in 2013 by the ACMG regarding incidental findi...
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:9
Frequency: 100.0%
Repute:Good
References:9
normal
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rs10264272, also known as 14690G>A, is a SNP in the CYP3A5 gene. indicates that this corresponds with CYP3A5*6, however, this seems doubtful. CYP3A5 allele nomenclature found at http://www.cypalleles.ki.se/cyp3a5.htm indicates that CYP3A5*6 (also known as 14690G>A) is a splicing defect resulting in essentially no activity in the gene. This does not correspond with dbSNP, which indicates that is a nucleotide substition (624G-A) which only results in a 'silent' substitution of AAG (Lysine) to AAA (Lysine). [PharmGKB:In-Depth Nonfunctional allele present predominantly in the African American population.]
common in clinvar The rs1050828 G allele is located within the G6PD gene and is associated with 'normal' levels of glucose-6-phosphate dehydrogenase enzyme production.
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rs1050828 is a SNP residing in the G6PD gene and is located the X chromosome. G6PD codes for the enzyme glucose-6-phosphate dehydrogenase, which helps protect the cell from oxidative damage. Depending on genotype, an individual may possess one of two primary versions of the G6PD gene; type A and type B. Type A is predominantly found in people who have African ancestry. Mutations of G6PD can cause varying degrees of G6PD deficiency, which is a disease affecting red blood cells. For example, an G to A substitution mutation at the rs1050828 (also referred to as G202A) is associated with a reduction of G6PD. The G6PD deficient genotype A- (~8-20% reduction of G6PD) is typically defined by the possession of the rs1050828 A allele (rs1050828(A;A)). In addition, individuals who are type A- almost...
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:1
Frequency: 100.0%
Repute:Good
References:1
common in complete genomics
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The human multidrug resistance protein 4 (MRP4, ABCC4): functional analysis of a highly polymorphic gene. Analysis of 17,576 potentially functional SNPs in three case-control studies of myocardial infarction. [PharmGKB:Non-Curated Increased intracellular azidothymidine and PMEA levels (decreased function) in transfected cells]
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:1
Frequency: 100.0%
Repute:Good
References:1
common in complete genomics
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[PharmGKB:Curated Greatly reduced the efficiency of metabolism of carvedilol.]
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:2
Frequency: 100.0%
Repute:Good
References:2
normal
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rs12720461 is a SNP in the CYP1A2 gene. The rs12720461(T) allele defines the CYP1A2*1K_-729C>T variant. [PharmGKB:Curated Likely disrupts transcription factor binding, leading to reduced function.]
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:2
Frequency: 100.0%
Repute:Good
References:2
common in complete genomics
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[PharmGKB:Curated study of 54 livers; variant not associated with altered midazolam clearance]
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:1
Frequency: 100.0%
Repute:Good
References:1
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[GWAS:Response to irinotecan and platinum-based chemotherapy in non-small-cell lung cancer]
common in complete genomics
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PharmGKB indicates that this SNP is relevant to Warfarin dosing. rs339097(G) is associated with 14.5% higher therapeutic warfarin dose in African Americans. This variant is also more common in African Americans with minor allele frequencies of 11–14% , but only 0.2% in Caucasians. Genetic and nongenetic factors associated with warfarin dose requirements in Egyptian patients. [PharmGKB:Curated Risk or phenotype-associated allele: G allele was associated with higher required warfarin dose. Phenotype: The G allele of this SNP was associated with a 14.5% (SD +/- 7%) higher therapeutic warfarin dose in African Americans. Study size/population/ethnicity: Discovery cohort was 108 outliers(53 patients in the low dose group and 55 in the high dose group) selected from patients who attended a...
normal
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rs3798220, also known as I4399M or Ile4399Met, is a SNP in the apolipoprotein(A) LPA gene that has been reported to be associated with elevated plasma lipoprotein(a) [Lp(a)] and increased cardiovascular risk, and in particular, coronary artery disease. In one study, 25,131 initially healthy Caucasian participants in the Women's Health Study were followed for ~10 years. rs3798220(C) allele carriers (3.7%) in the placebo (i.e. not receiving aspirin) group had a 2x higher risk of major cardiovascular events than non-carriers (age-adjusted hazard ratio (HR) of 2.21, CI: 1.39-3.52). Among rs3798220(C) carriers, the risk was reduced more than twofold by aspirin: for aspirin compared with placebo the age-adjusted HR was 0.44 (CI: 0.20-0.94). The risk was not significantly reduced among non-carrie...
normal
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Something seems wrong between dbSNP and the results from 23andMe and FTDNA. See Talk:Rs4148323 for more information. rs4148323, a SNP also known as 211G>A or G71R, occurs in the UGT1A1 gene, and defines the UGT1A1*6 allele. This allele is associated with Gilbert's syndrome among Asians, Crigler-Najjar syndrome type II (CN-II), and transient familial neonatal hyperbilirubinemia. rs4148323(A) in exon 1 of the UGT1A1 gene is associated with hyperbilirubinemia. rs4148323 and several other nearby SNPs help predict serum total bilirubin levels, based on a study of 750 Japanese. [PharmGKB:Curated *6 is the most common UGT1A1 coding variant found in Asians. It may result in reduced capacity to metabolize irinotecan and hence irinotecan toxicity.] [OMIM:UDP-GLYCOSYLTRANSFERASE 1 FAMILY, POLYPEP...
common in complete genomics
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[PharmGKB:Curated The C allele of this variant was associated with increased risk of toxicity in African American Rheumatoid Arthritis patients receiving methotrexate.]
normal
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rs4986907, also known as 485G>A, 14269G>A or R162Q, is a SNP in the CYP3A4 gene. The rs4986907(A) allele defines the CYP3A4*15A variant. [PharmGKB:In-Depth Defining variant for CYP3A4*15A.]
normal
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rs4986913, also known as 1399C>T, 23237C>T or P467S, is a SNP in the CYP3A4 gene. The rs4986913(T) allele defines the CYP3A4*19 variant. [PharmGKB:In-Depth Part of CYP3A4*19.]
normal
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rs4987161, also known as 566T>C, 15615T>C or F189S, is a SNP in the CYP3A4 gene. The rs4987161(C) allele defines the CYP3A4*17 variant. [PharmGKB:In-Depth Defining variant for CYP3A4*17, defective in metabolizing the hypertensive drug nifedipine in vitro; exhibited lower turnover numbers than wild-type for testosterone and chlorpyrifos in vitro.]
common in complete genomics
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[PharmGKB:In-Depth Has been studied in association with long QT.]
common in complete genomics
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[PharmGKB:Non-Curated Increased sensitivity to inhibition by TBA in oocytes]
common in clinvar
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[PharmGKB:Curated In a family linkage study, rs846664 was shown to be significantly associated with risk for alcohol dependence. The risk allele appears at a much higher frequency in African Americans than in European Americans.] [OMIM:TASTE RECEPTOR, TYPE 2, MEMBER 16; TAS2R16]
normal
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rs9332239, also known as 1465C>T, 50338C>T or P489S, is a SNP in the CYP2C9 gene. The rs9332239(T) allele defines the CYP2C9*12 variant. According to a 23andMe discussion This is one of the SNPs which were re-analyzed April 2009. Customers with older data may wish to redownload. SNPs effected rs4420638, rs34276300, rs3091244, rs34601266, rs2033003, rs7900194, rs9332239, rs28371685, rs1229984, and rs28399504.
common in complete genomics
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[PharmGKB:In-Depth Risk or phenotype-associated allele: C. Phenotype: An in vitro PFA-100 analysis was performed within 4 h of phlebotomy (blood drawn from healthy volunteers), using CADP and CEPI cartridges. P2RY1: 893C>T significantly effected platelet responses to collagen plus ADP (CADP). After accounting for multiple testing (Bonferroni adjustment), a statistically significant inverse correlation remained between CADP CT and P2RY1 893C (adjusted P = 0.032).]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in complete genomics
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[PharmGKB:Non-Curated Reduced uptake of estrone sulfate and methotrexate in oocytes] [GWAS:None]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in complete genomics
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[PharmGKB:Non-Curated Increased intracellular azidothymidine and PMEA levels (decreased function) in transfected cells]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
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[PharmGKB:Curated Patients (n= 66) with acute lymphoblastic leukemia showed large individual differences in cellular accumulation of long-chain MTXPG after high-dose methotrexate. The synonymous SNP in exon 2 of GGH (174G>A, A34A) was detected in only one of four patients with low GGH activity who were sequenced for the gene.]
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Pharmacogenetics of asthma. 5-lipoxygenase pharmacogenetics in asthma: overlap with Cys-leukotriene receptor antagonist loci. Genetics and pharmacogenetics of the leukotriene pathway. Pharmacogenomic approaches to asthma treatment. [PharmGKB:Curated Associations were found between genotypes of SNPs in the ALOX5 (rs2115819) and MRP1 (rs119774) genes and changes in FEV(1) (p < 0.05) in asthma patients treated with montelukast.]
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
common in complete genomics
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[PharmGKB:Curated Reduced metformin and MPP+ uptake in transfected cells]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
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rs12721634, also known as 44 T>C or L15P, is a SNP in the CYP3A4 gene. The rs12721634(C) allele defines the CYP3A4*14 variant. [PharmGKB:In-Depth Defining variant for CYP3A4*14.]
Magnitude: 0
Repute:Good
References:5
Repute:Good
References:5
common
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rs17238540, also known as SNP 29, is located in the HMG-CoA reductase HMGCR gene. The protein encoded by this gene is the target for drugs designed to inhibit its action, in order to lower cholesterol levels. SNPs in the HMGCR gene may affect how well such drugs (typically statins) work. In a study of ~1,500 patients treated with 40mg/d of pravastatin, rs17238540(G;T) heterozgyotes had a mean decrease in total cholesterol of 32.5 mg/dL (0.85 mmol/L), while the mean change for rs17238540(T;T) homozygotes was 41.8 mg/dL (1.09 mmol/L), a reduction in overall efficacy of 22.3% (absolute difference, 9.3 mg/dL, CI: 3.8-14.7 mg/dL, p<.001). The drop in total cholesterol was almost completely due to the decrease in LDL cholesterol, as there was no significant difference in the change in HDL cho...
normal
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rs1800460 is a SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The risk allele for this SNP is rs1800460(A), and when it is the only variation in the TPMT gene, it encodes the TPMT*3B allele. While still rare, it is more common in Caucasians (4.5% of all alleles) than in African-Americans (0.8%). Note that if the same allele also carries the rs1142345(G) SNP, the allele is actually a TPMT*3A allele (OMIM). The medicine 6-Mercaptopurine is metabolized by TPMT. Individual differences in TPMT activity associated with this SNP are now used to determine appropriate dosage range and interval for treatm...
normal
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A study of 733 breast cancer cases for 10 SNPs concluded that the rs2241766(G;T) genotype, in combination with certain genotypes at rs1501299, was at reduced risk (odds ratio 0.61, CI: 0.46-0.80). After categorizing individuals by adiponectin signaling status, this study found that compared with high signalers, intermediate signalers had a 4.16-fold increase in breast cancer risk (CI: 0.49-35.19), and low signalers had a 6.56x higher breast cancer risk (CI: 0.78-54.89, p(trend) = 0.001). Adiponectin signaling status was assigned as follows: rs1501299(G,G) + rs2241766(T,T) = low signaler<br> rs1501299(G,T) + rs2241766(T,T) = low signaler<br> rs1501299(G,G) + rs2241766(G,T) = low signaler<br> rs1501299(T,T) + rs2241766(T,T) = intermediate signaler<br> rs1501299(G,T) +...
common in complete genomics
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[PharmGKB:Curated This variant was present at a frequency of 0.126 in African American DNA samples from the Coriell Repository (HD100AA) and when expressed in COS-1 cells had the same level of immunoreactive protein as wild type.]
better response to inhaled corticosteroid in patients with COPD
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rs242941 is a SNP in the corticotrophin-releasing hormone receptor 1 CRHR1 gene. (G;G) better response to inhaled corticosteroids fluticasone propionate and salmeterol in patients with COPD in a Korean study with 84 subjects. [PharmGKB:Curated Haplotype tagging SNP.]
normal
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The rs2740574(G) allele encodes a variant form of CYP3A4 known as CYP3A4*1B. rs2740574(G) alleles are associated with an ~10 fold higher risk of aggressive prostate cancer in African American males. [PMID 16414488, OMIM A pooled study (1,400+ samples) along with a replication study conducted by members of the Ovarian Cancer Association Consortium found a 2.5-2.8x increased risk for ovarian cancer] for rs2740574(G;G) individuals (CI: 1.2-6.5, p=0.017). The authors note that CYP3A4 encodes a key enzyme in estrogen metabolism and which may be linked to ovarian carcinogenesis. [PharmGKB:Curated Risk or phenotype-associated allele: CYP3A4*1B, rs2740574 G allele. Phenotype: CYP3A4*1B (rs2740574 G) allele carriers show a significantly increased risk for SCLC (OR = 2.25, p = 0.02), which showed a...
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
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[PharmGKB:Curated SNP influences the efficacy of methotrexate in patients with psoriasis.]
Magnitude: 0
Repute:Good
References:5
Repute:Good
References:5
normal
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rs28371685, also known as 1003C>T, 42542C>T or R335W is a SNP in the CYP2C9 gene. The rs28371685(T) allele defines the CYP2C9*11 variant, which has decreased activity. According to a 23andMe discussion This is one of the SNPs which were re-analyzed April 2009. Customers with older data may wish to redownload. SNPs effected rs4420638, rs34276300, rs3091244, rs34601266, rs2033003, rs7900194, rs9332239, rs28371685, rs1229984, and rs28399504. [PharmGKB:Curated Phenotype: In African Americans patients, weekly warfarin dose requirements were lower in those with the CYP2C9*8 allele (34 (30-47) mg; P = 0.023) and the CYP2C9 *2, *3, *5, *6, or *11 allele (33(28-40 mg); P < 0.001) as compared with those with the CYP2C9*1/*1 genotype (43 (35-56) mg). Adding the *5,*6,*8 and *11 alleles to a...
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
normal
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rs28371706, also known as 1023C>T or T107I, is a SNP in the CYP2D6 gene. The rs28371706(T) allele is found in several CYP2D6 variants: * CYP2D6*17 decreased activity variant * CYP2D6*40 non-functioning variant * CYP2D6*58 variant * CYP2D6*64 variant [PharmGKB:In-Depth Variant was identified as being part of the reduced function haplotype CYP2D6*17.]
Magnitude: 0
Repute:Good
References:5
Repute:Good
References:5
normal
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rs28371725, also known as 2988G>A, is a SNP in the CYP2D6 gene. The rs28371725(A) allele defines the CYP2D6*41 variant, which has decreased activity. 23andMe also has SNP i4001476 at the same position. [PharmGKB:In-Depth This variant is part of the CYP2D6*41 IM haplotype. Plasma concentrations of metoprolol were shown to be were 4.9-fold higher in the PMs, with greater reductions in heart rate, diastolic blood pressure, and mean arterial pressure in PMs than in non-PMs.]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
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rs28371759, also known as 878T>C, 20070T>C or L293P, is a SNP in the CYP3A4 gene. The rs28371759(C) allele defines the CYP3A4*18 variant. [PharmGKB:Curated In a study of 2,178 women of ages 40-79 years, this variant in the CYP3A4 gene was significantly associated with low bone mass. In vitro functional analyses indicate that CYP3A4*18 is a gain-of-function mutation in sex steroid metabolism, resulting in rapid oxidation of estrogens and testosterone.]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
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[PharmGKB:In-Depth This variant is part of the *10 haplotype and affects nicotine metabolism.]
Magnitude: 0
Repute:Good
References:11
Repute:Good
References:11
common in complete genomics
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[PharmGKB:In-Depth Risk or phenotype-associated allele: TC. Phenotype: This variant is statistically correlated with the mean of maximum transaminase values (ALT) in patients from Mozambique, with ALT mean value of 91.68 U/l for TT, and 221.45 U/l for TC genotypes (p < 0.001). Study size: 156. Study population/ethnicity: HIV infected patients from Mozambique. Significance metric(s): p< 0.001. Type of association: GN; CO]
Magnitude: 0
Repute:Good
References:7
Repute:Good
References:7
normal
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rs28399504 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*4 variant. This variant has been linked to poor metabolism of compounds like mephenytoin. It is also known as M1V or Met1Val. The risk allele is rs28399504(G). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (Prevacid). According to a 23andMe discussion This is one of the SNPs which were re-analyzed April 2009. Customers with older data may wish to redownload. SNPs effected rs4420638, rs34276300, rs3091244, rs34601266, rs2033003, rs7900194, rs9332239, rs28371685, rs1229984, and rs28399504. Clopidogrel Efficacy [Pharm...
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar common
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(T;T) has a moderate change in BCHE activity according to annerwright Pseudocholinesterase Deficiency [PharmGKB:Curated This variant is associated with prolonged apnea is response to succinyldicholine (also known as succinylcholine).] [OMIM:BCHE, FLUORIDE 1]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in clinvar
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(T;T) abolishes catalytic activity in BCHE according to annerwright Pseudocholinesterase Deficiency [PharmGKB:Curated This variant is associated with prolonged apnea is response to succinyldicholine (also known as succinylcholine).] [OMIM:BCHE, FLUORIDE 2]
normal
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rs3025039, also known as the +936C/T SNP in the VEGFA gene, has been associated with age-related macular degeneration (ARMD). A study of 190 Taiwanese patients with late wet age related macular degeneration found that the rs3025039(T) allele was associated with increased risk, with an odds ratio of 2.61 (CI: 1.68 to 4.07, p = 1.45 x 10e-5). Note that this association may be completely due to the tight linkage (D' = 0.99) between this SNP and rs1061170, which has been reported by numerous studies to be associated with ARMD. C->T was associated with increased risk for altitude sickness. Vascular endothelial growth factor gene polymorphisms in Behcet's disease. Polymorphisms in the vascular endothelial growth factor gene and breast cancer in the Cancer Prevention Study II cohort. Vascular ...
later onset of BP
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Although not associated with increased risk for developing bipolar disorder, amongst those with it, the (G) allele of this SNP has been reported to have a somewhat protective effect in that individuals who have a (G) allele develop bipolar disorder at a later age than those with the more common (A;A) genotypes. Also known as the -50T/C SNP from this GSK3-beta (GSK3B) gene. may effect lithium treatment response - C allele carriers showed considerably greater response with lithium treatment, with remissions of 56.25% after 4 weeks compared to 31% for T/T carriers [PharmGKB:Curated This variant is in the promoter region of GSK3B. T allele is associated with greater transcription activity compared with the A allele. This variant is associated with antidepressant treatment response in Chinese ...
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
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Suspect: Variation suspected to be false positive due to artifacts of the presence of a paralogous sequence in the genome (Musumeci et al. 2010) (Sudmant et al. 2010) or evidence suggested sequencing error or computation artifacts. [PharmGKB:Curated The CYP2B6:1132C>T variant results in a truncated protein and high plasma levels of efavirenz in patients.]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
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[PharmGKB:Non-Curated Reduced metformin and MPP+ uptake in transfected cells]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
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[PharmGKB:Curated Risk or phenotype-associated allele: C. Phenotype: CYP2B6 mRNA expression and bupropion hydroxylase activity were approximately 2-fold higher in livers genotyped -82TC as in those genotyped -82TT. Study size: 85 (expression); 77 (activity). Study population/ethnicity: Non-tumorous liver samples from White individuals, Germany. Significance metric(s): p = 0.007 (expression); p = 0.042 (activity). Type of association: FA; PD]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
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[OMIM:?]
Magnitude: 0
References:1
References:1
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[PharmGKB:Curated A study in 207 Caucasian participants receiving farglitazar plus insulin or glyburide combination therapies this polymorphism in the SCNN1B gene was significantly associated with oedema. This variant in the promoter region of the gene was predicted to modify transcriptional interactions and in a transfected COS cell luciferase reporter gene assay exhibited higher promoter activity. The identified association has low penetrance in the fluid retention/oedema case population reflecting that SCNN1B variation may be only one of the covariates that contribute to the development of PPAR[gamma]-induced fluid retention.]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
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[PharmGKB:Curated system: membrane vessicles from HEK cells transfected with WT or variant; FA: variant had approx 50% decrease in transport of tritium labelled 17[beta]-estradiol-17[beta]-D-glucuronide (17E2b-g) due to decrease in Km]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
normal
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Also known as the R125W variant, rs35859249 is a SNP in the TBC1D1 gene that has been associated with familiar - but not nonfamilial - obesity in several studies. The (C) allele encodes the (R), arginine, and the (T) allele encodes the (W), tryptophan. In the first study to be published about this SNP, an analysis of primarily Utah families with obesity implicated the rs35859249(T) allele as a predisposing factor. This allele segregated with affected females in a majority of the chromosome 4p15–14-linked obesity-prone pedigrees, was enriched on disease-associated haplotypes (P=0.000007), accounted for the majority of the linkage evidence at 4p15–14, and appeared to be the causal variant. This study also implied a gene-gene interaction including another...
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
common in complete genomics
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[PharmGKB:Curated The CYP2B6*27 allele shows an 85% decrease in enzyme activity leading to high plasma levels of efavirenz in patients.]
complex; generally normal risk
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rs361525 is also known as the TNF-238 SNP, and occasionally the rs361525(A) allele is referred to as 238.2 (with the more common (G) allele being 238.1). This SNP in the tumor necrosis factor-alpha gene has been linked to a wide variety of conditions: * Breast cancer ** A large study of over 5,000 Caucasian women found that rs361525(A) allele carriers were at somewhat elevated risk for breast cancer compared to the (G;G) genotype, with an odds ratio per allele of 1.18, CI: 1.04-1.35, p(trend)= 0.008. ** However, a 2009 European study of 30,000 breast cancer cases, compared to 30,000 controls, found no association, or as they put it, 'persuasive evidence against an overall association between invasive breast cancer risk and (this SNP)'. * Graft versus host disease (GVHD) ** A study of ~100 ...
Magnitude: 0
Repute:Good
References:10
Repute:Good
References:10
common in complete genomics
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[PharmGKB:Curated in vitro studies showed cisapride has same sensitivity for WT and this varian]
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G allele associated with schizophrenia among 120 (likely Japanese) first-episode neuroleptic-naive schizophrenics treated with risperidone genotyped for 30 variants in misc. dopamine and serotonin (receptors and otherwise) two SNPs in DRD2 (rs1799989 and rs1800497) and two SNPs in AKT1 (rs3803300 and rs2494732) were significant predictors of treatment response to risperidone The ancestral allele is G in the dbSNP database. [PharmGKB:Curated This SNP is significant predictor of treatment response to risperidone in first-episode schizophrenia.]
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Association of warfarin dose with genes involved in its action and metabolism. The largest prospective warfarin-treated cohort supports genetic forecasting.
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
normal
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Defines the CYP2C19 variant known as CYP2C19*8. Carriers of the rs41291556(C) allele may have decreased activity and poor metabolizer (PM) phenotype. This variant is associated with a dramatic (approximately 90% and 70%) reduction in the metabolism of S-mephenytoin and tolbutamide in vitro. Clopidogrel Efficacy [PharmGKB:Curated This variant is the defining SNP for CYP2C19*8 and leads to decreased activity and poor metabolizer (PM) phenotype.This variant is associated with a dramatic (approximately 90% and 70%) reduction in the metabolism of S-mephenytoin and tolbutamide in vitro.]
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
common in complete genomics
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[PharmGKB:In-Depth Subjects with the G variant showed higher plasma pravastatin AUC and Cmax relative to A variant]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in complete genomics
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[PharmGKB:Curated Risk or phenotype-associated allele: T Phenotype: Kinetic studies using purified, histidine-tagged, recombinant enzymes demonstrated that the P131S mutation leads to decreased catalytic efficiency (Kcat/Km) for doxorubicin and daunorubicin compared to wild type protein. Type of association: FA]
common on affy axiom data
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Genetic-epidemiological evidence on genes associated with HDL cholesterol levels: a systematic in-depth review. Scavenger receptor class B type I protein as an independent predictor of high-density lipoprotein cholesterol levels in subjects with hyperalphalipoproteinemia. [PharmGKB:Curated This variant was significantly associated with postfenofibrate change for triglycerides. Subjects bearing minor allele A tend to have higher responsiveness to fenofibrate in lowering TG. A total of 1,327 subjects (639 men and 688 women) from 148 families were genotyped. Of these 1,327 subjects, 861 subjects (427 men and 434 women) went through the fenofibrate trial and had complete lipid phenotype and genotype data.]
average
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rs4444903 is a SNP, also known as +61, located in the promoter region of the epidermal growth factor EGF gene that influences the amount of EGF produced. The rs4444903(G) allele appears to produce higher amounts of EGF than the (A) allele. A study of 2 Caucasian populations of patients with alcoholic cirrhosis indicates that, for these patients, the presence of the risk allele rs4444903(G) increases the chances of developing hepatocellular carcinoma (liver cancer). After adjusting for age, sex, race, etiology, and severity of cirrhosis the number of (G) copies led to an odds ratio for either (G;G) or (A;G) genotypes versus the (A;A) genotype of 3.49 (CI: 1.29-9.44, p=.01). In another study, analysis of 197 glioma patients showed that the rs4444903(G) allele conferred higher risks for gliom...
Magnitude: 0
Repute:Good
References:4
Repute:Good
References:4
common on affy axiom data
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The G671V variant of MRP1/ABCC1 links doxorubicin-induced acute cardiac toxicity to disposition of the glutathione conjugate of 4-hydroxy-2-trans-nonenal. [PharmGKB:Curated Risk or phenotype-associated allele: 2012GT (671Gly/Val) genotype. Phenotype: Carriers the heterozygous 2012GT (671Gly/Val) genotype had lower serum HDL cholesterol than the GG (671Gly/Gly) genotype carriers (p = 0.015). Study size: 136. Study population/ethnicity: Hypercholesterolemic individuals, treated with atorvastatin (10mg/day/4 weeks), evaluated for CAD risk factors at the Institute Dante Pazzanese of Cardiology and the Hospital of the Sao Paulo University in Sao Paulo City, Brazil. Significance metric(s): p = 0.015. Type of association: GN; PD; FA]
normal
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rs4986893 is a SNP in the CYP2C19 gene, potentially encoding the CYP2C19*3 variant. This variant has been linked to poor metabolism of compounds like mephenytoin as well as proguanil, and it therefore has implications for malaria prophylaxis. The risk allele is rs4986893(A). As a nonfunctioning CYP2C19, this variant would be expected to be a poor metabolizer of several commonly prescribed drugs, including anti-ulcer drugs like omeprazole (trade names Losec and Prilosec), esomeprazole (trade name Nexium), and lansoprazole (Prevacid). Clopidogrel Efficacy [PharmGKB:Curated In contrast to other PPIs, esomeprazole-induced healing of GERD appears to be unrelated to the CYP2C19*3 variant.] [OMIM:MEPHENYTOIN, POOR METABOLISM OF]
normal
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rs4986908 is a SNP in the CYP3A4 gene. The rs4986908(A) allele defines the CYP3A4*_14313G>A(E174H) variant. [PharmGKB:In-Depth Defining variant for CYP3A4*10.]
normal
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rs4986910, also known as 1334T>C, 23171T>C or M445T, is a SNP in the CYP3A4 gene. The rs4986910(C) allele defines the CYP3A4*3 variant. [PharmGKB:In-Depth Risk or phenotype-associated allele: CYP3A4*3 (rs4986910) 445Thr, 1334 C allele Phenotype: Two patients taking tacrolimus carried the CYP3A4*3 (445Thr) allele. The tacrolimus dose-adjusted C(0) in these 2 patients was higher than that in patients with the wild-type (455 Met/Met) genotype (n = 62), as follows: 134.9 (106.6-163.2) versus 83.83 (33.83-397.8) ng/mL per mg/kg, respectively. This difference was also observed at 12 months after transplantation, as follows: 147.3 (117.0-177.5) versus 88.79 (26.0-432.0) ng/mL per mg/kg. Study size: 64. Study population/ethnicity: Renal transplant recipients from the outpatient clinic of th...
common in clinvar
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rs5030868, also known as c.653C>T, p.Ser218Phe and S218F, is a SNP located on the X-Chromosome and associated with moderate to severe Glucose-6-Phosphate Dehydrogenase (G6PD) deficiency. Often referred to as the “Mediterranean variant”, the 563C->T mutation encodes a non-synonymous Serine to Phenylalanine substitution at Amino Acid position 188 (S188F) resulting in reduced catalytic efficiency and stability G6PD . In red blood cells, G6PD acts as the primary electron source for reactions that neutralize reactive oxygen species; thus the red blood cells of G6PD deficient individuals are especially susceptible to damage from oxidative stress . The Mediterranean variant of G6PD has been associated with acute hemolytic anemia induced by the ingestion of fava beans, glibenclam...
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[PharmGKB:Curated Risk or phenotype-associated allele: T. Phenotype: Carrying the T allele of SNP-63: rs5030952 was associated with increased risk of posttransplant diabetes in response to tacrolimus. Study size: 214. Study population/ethnicity: Patients who had undergone organ transplantation (kidney) and were treated with tacrolimus. Significance metric(s): OR = 2.45; p = 0.023. Type of association: CO.] [OMIM:CALPAIN 10; CAPN10]
common in complete genomics
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[PharmGKB:In-Depth This variant affects heat stability and affects nicotine metabolism; part of the CYP2A6*7 and CYP2A6*10 haplotypes.]
normal risk
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rs5186, a SNP known as +1166A/C or A1166C, is located in the 3' untranslated region of the angiotensin II receptor type 1 gene AGTR1, which is also known as AT2R1 or AT1R. It is among the most studied of over 50 SNPs in AGTR1. The rs5186(C) allele is associated with increased risk for essential hypertension in Caucasian populations with an odds ratio of 7.3 (homozygote (C;C) compared to (A;C) and (A;A), CI: 1.9-31.9,p=0.0015). There are likely to be ethnic differences in risk; while the rs5186(C) allele was associated with hypertension in a Chinese population , it was not been observed as a risk in a Japanese population. Age and gender may also influence risk, as discussed in a review of AGTR1 SNPs and their role in hypertension and related disorders. Pregnant women who are rs5186(C) allel...
Magnitude: 0
Repute:Good
References:0
Repute:Good
References:0
common/normal
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rs55886062, also known as c.1679 T>G, encodes the DPYD*13 allele of the DPYD gene on chromosome 1. Note that the terms used in the literature for this gene can be confusing, since the gene is in reverse orientation to the chromosome strand on the reference genome.
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
normal
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rs58597806 (Asp256Asn/D256N) is a SNP within UGT1A9 (UDP glucuronosyltransferase 1 family, polypeptide A9). reduced propofol glucuronidation - considerably lowered glucuronidation of mycophenolic acid, 1-naphthol, and naringenin. may be at risk adverse effects w/ propofol and other UGT1A9 substrate administration essentially non-functional with regard to SN-38 (7-ethyl-10-hydroxycamptothecin) glucuronidation, an active metabolite of irinotecan [PharmGKB:Curated A study in 100 healthy Japanese volunteers showed that carriers of D256N may be at risk of suffering adverse effects of propofol and other substrates that are primarily metabolized by UGT1A9. In in vitro analyses the K(m) of wild-type and D256N for propofol glucuronidation were 111.2 and 43.6 microM, respectively. The V(max) of D25...
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in clinvar
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rs59172778, also known as c.1013T>C or p.Met338Thr, is a mutation in the KCNJ1 gene. The rare rs59172778(G) allele is reported to a mutation leading to the recessively inherited type 2 Bartter syndrome. The (G) allele is rare, usually being found in just under 1% of allele counts, but Bartter syndrome may be rarer and the presentation is often heterogeneous. This implies that the (G) allele may not be fully causative or penetrant. [OMIM:?]
Magnitude: 0
Repute:Good
References:5
Repute:Good
References:5
common in complete genomics
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[PharmGKB:Curated Risk or phenotype-associated allele: None. Phenotype: Variants identified in a screen of 13 genes involved in the gemcitabine drug metabolic pathway. For the non-synonymous CDA:208G>A (A70T) SNP, the A allele (70Thr) was at frequency 0.00 and 0.13 in Europeans and Africans, respectively. There was a significant difference between ethnic groups in genotype frequency distribution (p < 0.001) Study size: 177. Study population/ethnicity: Healthy, unrelated blood donors of European (n = 93) and African (n = 84) descent. Significance metric(s): p < 0.001. Type of association: GN.] [OMIM:CYTIDINE DEAMINASE; CDA]
Magnitude: 0
Repute:Good
References:13
Repute:Good
References:13
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Contrary to the claims of a test being marketed, a large study (8,500+ patients and >10,000 controls) found no evidence for any association between rs61764370 and any form of ovarian cancer. This letter in the Lancet challenges the claims of an association with triple-negative breast cancer in
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
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rs62205366 ( 393T>C ) is a SNP within GNAS (GNAS complex locus - encoding the Gs alpha subunit). differential response to dobutamine (beta-1 / [mild] beta-2 receptor agonist) noted in a Chinese sample of unknown size, individuals homozygous for C displayed greater response as compared to those homozygous for T homozygous TT individuals associated with greater incidence of hyperthyroidism (as well as higher TRAb levels) relapse in a sample of 359 Graves' disease patients
Magnitude: 0
Repute:Good
References:8
Repute:Good
References:8
common in clinvar
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rs63749869, aka p.Arg4861His or p.R4861H, is a SNP in the RYR1 gene associated with central core disease as well as a congenital neuromuscular disease. [OMIM:?]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in complete genomics
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[PharmGKB:Curated Phenotype: This SNP, along with a second one in tight LD (rs6493497) was significantly associated, in a cohort of estrogen-receptor-positive patients with primary breast cancer larger than 3 cm, with change in aromatase activity before and after aromatase inhibitor neoadjuvant treatment . It was also associated, but not significantly so after adjustment for multiple testing, with change in estrone level and with pretreatment aromatase level. Study size: 45. Study population/ethnicity: Edinburgh female ER-positive patients, primary breast cancer larger than 3 cm. Significance metric(s): nominal p = 0.0063, p = 0.039 after adjustment for multiple testing. Type of association: PD; GN;FA. Second Phenotype: In a group of 200 women with early stage breast cancer, who were treat...
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
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rs72547517, also known as 5166G>A, 5347T>C or R456H, is a SNP in the CYP1A2 gene. The rs72547517(A) allele defines the CYP1A2*8 variant. [PharmGKB:Curated Risk or phenotype-associated allele: A Phenotype: In an in vitro system, this variant showed no activity for the drug substrates clozapine or phenacetin even at the highest substrate and double membrane concentrations, it also showed reduced expression of holoprotein in bacterial cells. Type of association: FA]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
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[PharmGKB:Curated cell based studies; enhanced basal activity of cyp3a4 transcription wrt WT]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
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[PharmGKB:Curated cell based studies; decreased basal activity on cyp3a4 transcription wrt WT; increased fold induction w/ rifampicin]
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in complete genomics
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rs72552713, also known as Gln126Ter, is a SNP in the ABCG2 gene. gout association, based on ; note that this publication refers to risk allele (T) based on the minus strand, whereas for dbSNP and SNPedia, rs72552713 is defined as on the plus strand, so therefore the risk allele is (A). The case-control analysis of 1993 patients with gout and 1334 controls concluded that rs72552713(A) was significantly associated with gout (odds ratio 2.86, CI:2.1-3.8,p=4.4x10e-12). The risk is independent of the risk posed by another ABCG2 gene SNP, rs2231142, since these two SNPs are on different haplotypes. Both ABCG2 SNPs are, however, associated with the ROL gout subtype, defined as when urinary urate excretion (UUE) is over 25.0 mg/h/1.73 m2 (600 mg/day/1.73 m2) and urate clearance (urate clearance/cr...
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
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[PharmGKB:Curated Drug efflux and cell surface expression (by MRK-16 and C219 probes) of P-gp was not different between wild-type and variant forms (single mutants: N21D, F103L, S400N, A893S, A998T, and double mutants: 21D-S400N, N21D-A893S, and S400N-A893S) in an in vitro vaccinia virus-based transient expression system. Fluroescent substrates included calcein AM, bodipy-FL-forskolin, bodipy-FL-verapamil, bodipy-FL-vinblastine, bodipy-FL-prazosin, bisantrene, and bodipy-FL-paclitaxel. There was a slight increase in wild-type P-gp efflux of bodipy-FL-paclitaxel over mutants.]
normal
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rs7900194, also known as 449G>A, 3627G>A or R150H, is a SNP in the CYP2C9 gene. The rs7900194(A) allele defines the CYP2C9*8 variant, which has decreased activity. According to a 23andMe discussion This is one of the SNPs which were re-analyzed April 2009. Customers with older data may wish to redownload. SNPs effected rs4420638, rs34276300, rs3091244, rs34601266, rs2033003, rs7900194, rs9332239, rs28371685, rs1229984, and rs28399504. [PharmGKB:Curated Phenotype: In African Americans patients, weekly warfarin dose requirements were lower in those with the CYP2C9*8 allele (34 (30-47) mg; P = 0.023) and the CYP2C9 *2, *3, *5, *6, or *11 allele (33(28-40 mg); P < 0.001) as compared with those with the CYP2C9*1/*1 genotype (43 (35-56) mg). Adding the *5,*6,*8 and *11 alleles to a mod...
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[PharmGKB:Non-Curated Increased resistance to daunorubicin, doxorubicin, valinomycin, or actinomycin D in transformed yeast]
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In 2009, a large, multi-sample replication study failed to find any significant association with Intelligence for this or other SNPs in CHRM2 . Earlier work had observed that this snp (and perhaps its neighbors) influenced intelligence and alcohol dependence CHRM2 gene predisposes to alcohol dependence, drug dependence and affective disorders: results from an extended case-control structured association study. And the earlier and or this pdf poster show association between the CHRM2 gene and intelligence . In this study of ~300 Caucasians, the (T;T) genotype appeared to typically have a 4 point higher IQ than the (A;T) genotype, which had a 4 point higher IQ (on average) than the (A;A) genotype. A nearby SNP, rs324640, showed similar results to rs324650, and was in linkage disequilibrium (...
common
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rs7566605 was initially reported as being associated in at least 4 independent populations as being associated with obesity however replications are inconsistent, and a recent (2009) large meta-analysis comprising 34 studies (and over 70,000 subjects) has concluded that there is no evidence for overall association of the rs7566605 polymorphism with obesity. See also: Poster At least one population has since been reported in which this association was not seen. Furthermore, a study of 18,000 Danish subjects also failed to find any direct role for this SNP in the development of obesity, except that among physically inactive subjects, (C)-allele carriers tended to have a higher body mass index (by O.5 kg/m2) than (G)-allele carriers. On the other hand, a report has also been published indicat...
Not a H63D hemochromatosis carrier.
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rs1799945, also known as H63D or His63Asp, represents a SNP that accounts for a mild form of hereditary hemochromatosis (HH), an iron overload condition in which mutations of certain genes involved in iron metabolism disrupt the body’s ability to regulate uptake of iron, causing increased intestinal iron absorption. The most common form is caused by mutations in the HFE gene, which are inherited recessively. The gene for HH is closely linked to the HLA-A3 locus on the short arm of chromosome 6 . In 1996, HFE, a gene for HH, was found to have two missense mutations . A mutation at amino acid 282 (C282Y) was found to be homozygous in 83 percent of patients with HH. This is a point mutation from guanine to adenine, resulting in a missense mutation from cysteine to tyrosine. Such mutatio...
common
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rs2230199, a SNP in the complement component C3 gene, has been reported by several investigators to be associated with ARMD. The common allele at this SNP is known as Arg102; the variant and risk allele is known as Gly102. The risk allele, in orientation to the dbSNP entry for this rs#, is (G). In one of the largest case-control studies, the odds ratio associated with heterozygotes is 1.61, and for homozygotes, 3.26 (p = 4.5 x 10e-12). NEJM reports significant associate with ARMD. blog post [PharmGKB:Curated rs2230199 was found to be associated with risk of age-related macular degeneration in English and Scottish case-control studies.] [OMIM:MACULAR DEGENERATION, AGE-RELATED, 9; ARMD9] [GWAS:Age-related macular degeneration]
common in clinvar
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[PharmGKB:Curated Phenotype: In a GWAS, this SNP was significantly associated with plasma concentrations of triglycerides. Study size:6382. Study population/ethnicity: Caucasian women. Significance metric(s): P = 4.7 x 10(-11). Type of association: CO; GN] [OMIM:LIPOPROTEIN LIPASE; LPL] [GWAS:HDL cholesterol]
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The rs964184(G;G) genotype is associated with hypertriglyceridemia. [PharmGKB:Non-Curated GWAS results: Common variants at 30 loci contribute to polygenic dyslipidemia. (Initial Sample Size: 19,840 individuals; Replication Sample Size: Up to 20,623 individuals); (Region: 11q23.3; Reported Gene(s): APOA1, APOC3, APOA4, APOA5; Risk Allele: rs964184-G); (p-value= 0.000000000001).This variant is associated with HDL cholesterol.] [GWAS:HDL cholesterol]
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rs11676382 was associated with a warfarin maintenance dose across all analysis methods. the effects of GGCX are potentially population/treatment-dependent and will not have broad utility for determining warfarin dosing.
normal risk for gallstones
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rs11887534, a SNP in the hepatic cholesterol transporter ABCG8 gene, has been implicated in gallstone disease, a process known formally as cholelithiasis. The common allele, rs11887534(G), encodes the aspartic acid (D), while the minor (C) allele encodes histidine (H). In a study of ~1,000 German patients, the overall odds ratio associated with rs11887534(C) carriers was 2.2 (CI: 1.8-2.6, p=1.4x10<sup>-14</sup>), and for (C;C) homozygotes, 7x. Up to 10% of the population attributable risk for gallstones may be accounted for by this SNP. [PharmGKB:Curated GWAS Results: A genome-wide association scan identifies the hepatic cholesterol transporter ABCG8 as a susceptibility factor for human gallstone disease (Initial Sample Size: 280 cases, 360 controls; Replication Sample Size: 2...
common in complete genomics
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[PharmGKB:Curated Alleles positive for this variant are designated CYP2C8*4. In in vitro experiments, the paclitaxel 6 alpha-hydroxylase acivity associated with CYP2C8*4 appeared lower than the wildtpe but the difference was not significant.]
common on affy axiom data
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[PharmGKB:Curated Risk or phenotype-associated allele: A. Phenotype: This SNP was part of a haplotype associated with acute cardiotoxicity in response to doxorubicin. Study size: 1697. Study population/ethnicity: Participants of the German non-Hodgkin lymphoma study. Significance metric(s): OR = 2.3; 95% CI, 1.0 to 5.4. Type of association: PD; ADR; TOX.]
common in complete genomics
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[PharmGKB:Curated This variant is the defining SNP for CYP3A7*2 which has increased catalytic acitivity compared to wild type.]
normal
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Also known as CYP2E1_-1295G>C, this SNP is reported to mark the c2 allele of CYP2E1. The rs3813867(C) allele defines the CYP2E1_-1295G>C variant allele. [OMIM:CYTOCHROME P450, SUBFAMILY IIE; CYP2E1]
common on affy axiom data appears to be common on the 23andMe platform
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Rs3135506 (also known as S19W) is associated with severe hypertriglyceridemia. 132 patients of European ancestry with severe HTG (fasting plasma TG>10 mmol/L), and 351 matched normolipidemic controls. It is discussed in ; however, the SNP that prevents weight gain from high fat diets is rs662799. [PharmGKB:Curated Phenotype: In a GWAS, this SNP was significantly associated with plasma concentrations of triglycerides and apolipoprotein B. Study size:6382. Study population/ethnicity: Caucasian women. Significance metric(s): triglycerides: p = 5.5 x 10(-12); ApoB: p = 8.4 x 10(-8). Type of association: CO; GN] [OMIM:?]
normal
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age related macular degeneration Genetic markers and biomarkers for age-related macular degeneration. C2 and CFB genes in age-related maculopathy and joint action with CFH and LOC387715 genes. Analysis of rare variants in the complement component 2 (C2) and factor B (BF) genes refine association for age-related macular degeneration (AMD). Variations in five genes and the severity of age-related macular degeneration: results from the Muenster aging and retina study. Multilocus analysis of age-related macular degeneration. Plasma complement components and activation fragments: associations with age-related macular degeneration genotypes and phenotypes. Complement component 3: an assessment of association with AMD and analysis of gene-gene and gene-environment interactions in a Northern Irish...
common in clinvar
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minor form is a slow metaboliser according to pharmgkb [PharmGKB:In-Depth This variant results in enzyme inactivity and is considered to be part of the %22slow metabolizer%22 group; part of the CYP2A6*2 haplotype.] [OMIM:?] [GWAS:Smoking behavior]
common in complete genomics appears to be common on the 23andMe platform
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rs1800796 IL-6 572G>C polymorphism (and h.211 haplotype) is associated with abdominal aortic aneurysm (AAA). The risk allele is C. Our results provide evidence that there is a clear genetic influence of IL6 -572C>G polymorphism on plasma levels of fibrinogen and CRP, but this polymorphism does not lead to elevated blood pressure. rs1800797, rs1800796 and rs1800795 have been shown to affect both the transcription and secretion of IL-6, to symptomatic distal interphalangeal osteoarthritis based on 535 women. the G alleles of two promoter single-nucleotide polymorphisms (SNP) G-597A and G-174C were more common among the subjects with symptomatic DIP OA than among those with no disease (p-values corrected for multiple testing 0.020 and 0.024). Also, the carriage of at least one G allele ...
common in complete genomics
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[PharmGKB:Non-Curated altered substrate specificity in transfected cells]
common in complete genomics
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[PharmGKB:Curated The variant is part of the CYP2C8*2 allele. In an in vitro study, the CYP2C8*2 allele exhibited a two-fold lower clearance for paclitaxel than the wildtype.]
common
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This SNP encodes a variation in the 33rd amino acid of the protein encoded by the TBX21 gene. Although 95% or so of all Caucasians carry two copies of the rs2240017(G) allele, as oriented in dbSNP orientation, and are thus rs2240017(G;G) homozygotes, a few individuals are rs2240017(C;G) heterozygotes. These heterozgotes are reported to improve better over time in response to corticosteroid treatment for asthma than the rs2240017(G;G) homozygotes. So far, studies have not linked, however, this SNP to any change in the overall risk of asthma itself. Although the effect observed was strong, in that treating rs2240017(C;G) heterozygotes ultimately (over 4 years) yields average airway responsiveness in the normal range (i.e. in the same range as for nonasthmatics), the authors point out that th...
common in complete genomics
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[PharmGKB:Curated Risk or phenotype-associated allele: T. Phenotype: In a study of bacterial expressed and purified human CBR3 proteins, the 235Leu variant had significantly reduced maximal reaction velocity (V(max)) for DOX compared with the wild-type enzyme. Type of association: FA.]
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located in 5' UTR of GRIN1 significant (p = .0000013) assoc. w/ schizophrenia in a sample of 2455 Han Chinese mentioned w/ possible schizophrenia association in a sample of 677 Germans (354 patients, 323 controls), but the initial association did not survive multiple correction [OMIM:GLUTAMATE RECEPTOR, IONOTROPIC, N-METHYL-D-ASPARTATE, SUBUNIT 1; GRIN1]
normal
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rs12721627, also known as 554C>G, 15603C>G or T185S, is a SNP in the CYP3A4 gene. The rs12721627(G) allele defines the CYP3A4*16 variant. [PharmGKB:Curated in vitro study; PK: variant shows substrate altered kinetics compared to wild type]
more responsive to statin treatment
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rs17244841, also known as SNP 12, is located in the HMG-CoA reductase HMGCR gene. The protein encoded by this gene is the target for drugs designed to inhibit its action, in order to lower cholesterol levels. SNPs in the HMGCR gene may affect how well such drugs (typically statins) work. In a study of ~1,500 patients treated with 40mg/d of pravastatin, rs17244841(A;T) heterozgyotes had a mean decrease in total cholesterol of –32.8 mg/dL (–0.85 mmol/L), while the mean change for rs17244841(A;A) homozygotes was –42.0 mg/dL (–1.09 mmol/L), a reduction in overall efficacy of 21.8% (absolute difference, 9.2 mg/dL, CI: 3.8-14.6 mg/dL, p=.001). The drop in total cholesterol was almost completely due to the decrease in LDL...
common in clinvar
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rs1799895, also known as c.691C>G, p.Arg231Gly and R231G, is a SNP in the SOD3 gene on chromosome 4. About 2-3% of the population carries a rs1799895(G) allele, which leads to ~10 fold higher concentrations of extracellular superoxide dismutase (EC-SOD). This in turn leads to a slightly higher (~1.5x) relative risk for ischemic heart disease. See also OMIM 185490.0001 [OMIM:?]
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rs1800544 (C-1291G) is a SNP located in the promoter region of ADRA2A (adrenergic receptor alpha 2A). GG genotype carriers had significantly higher consumption of sweet food products (Estonian Children Personality Behavior and Health Study subset, n = 419) GG genotype carriers had significantly higher scores on an assessment of depression, and significantly lower scores on morality and orderliness compared to CC carriers. girls with CC and CG genotypes scored higher than boys with the same genotypes on an assessment of extraversion. boys with GG genotypes, however, scored higher than girls with GG genotypes. GG genotype assoc. w/ higher scores of inattention Food Preference [OMIM:ALPHA-2A-ADRENERGIC RECEPTOR; ADRA2A]
normal risk
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rs1801028 is a SNP in the dopamine D2 receptor DRD2 gene. A meta-analysis comprising 27 samples and over 3,707 schizophrenia patients concluded that Cys/Ser heterozygotes, i.e. rs1801028(C;G) genotypes, were at elevated risk for schizophrenia when compared to either homozygote genotype (rs1801028(C;C) or rs1801028(G;G)). The odds ratio was 1.4 (p<0.005). An earlier meta-analysis comprising over 9,000 schizophrenia patients concluded pretty much the same thing: the Cys311 (rs1801028(G)) allele frequency led to an odds ratio of 1.43 (CI: 1.16-1.78, p<0.001) for this risk allele. A study of ~120 Chinese patients with schizophrenia concluded that Cys/Ser heterozygotes may not respond to risperidone treatment as well as Ser/Ser homozygotes. A paper has been published describing mistakes m...
normal common for Caucasians on the 23andme platform
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rs28371686, also known as 1080C>G, 42619C>G or D360E, is a SNP in the CYP2C9 gene. The rs28371686(G) allele defines the CYP2C9*5 variant, which appears to have decreased activity. [PharmGKB:Curated Phenotype: In African Americans patients, weekly warfarin dose requirements were lower in those with the CYP2C9*8 allele (34 (30-47) mg; P = 0.023) and the CYP2C9 *2, *3, *5, *6, or *11 allele (33(28-40 mg); P < 0.001) as compared with those with the CYP2C9*1/*1 genotype (43 (35-56) mg). Adding the *5,*6,*8 and *11 alleles to a model containing the *2 and *3 alleles plus the VKORC1 -1639 G>A allele (along with clinical variables) explained 36% vs. 30% of the variability in dose requirements. Study size: 226 . Study population/ethnicity: African-American . Type of association: PD;GN;...
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ITPKC functional polymorphism associated with Kawasaki disease susceptibility and formation of coronary artery aneurysms. Clinical Implication of the C Allele of the ITPKC Gene SNP rs28493229 in Kawasaki Disease: Association With Disease Susceptibility and BCG Scar Reactivation. ITPKC and CASP3 polymorphisms and risks for IVIG unresponsiveness and coronary artery lesion formation in Kawasaki disease. Single-nucleotide Polymorphism rs2290692 in the 3'UTR of ITPKC Associated With Susceptibility to Kawasaki Disease in a Han Chinese Population. Calcineurin Inhibitor Treatment of Intravenous Immunoglobulin-Resistant Kawasaki Disease. Genetic polymorphisms in the ITPKC gene and cervical squamous cell carcinoma risk. [OMIM:INOSITOL 1,4,5-TRISPHOSPHATE 3-KINASE C; ITPKC]
common/normal
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rs67376798, also known as c.2846 A>T, is a SNP in the DPYD gene on chromosome 1. Note that the 'A>T' term in the name used in the literature for this SNP can be confusing, since the gene is in reverse orientation to the chromosome strand on the reference genome.
normal
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rs72547516, also known as 2499A>T or I386F, is a SNP in the CYP1A2 gene. The rs72547516(T) allele defines the CYP1A2*4 variant. [PharmGKB:Curated Risk or phenotype-associated allele: T Phenotype: In an in vitro system, this variant showed no activity for the drug substrates clozapine or phenacetin even at the highest substrate and double membrane concentrations, it also showed reduced expression of holoprotein in bacterial cells. Type of association: FA]
1326 snps
(hide) Placebo
maybe: higher scores on anxiety-related personality traits; greater placebo response One study of (only) 25 people shows this genotype was a significant predictor of clinical placebo response, being associated with greater improvement in anxiety symptoms. A criticism of this study has also been published, and it has not been replicated since the original publication years ago. This SNP has been linked to several psychiatric and/or behavioral phenomena, including: *higher scores on anxiety-related personality traits *obsessive compulsive disorder *panic disorder with a possible gender-dependent effect
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rs4570625, also known as G-703T, is a SNP in the tryptophan hydroxylase 2 TPH2 gene. This SNP has been linked to several psychiatric and/or behavioural phenomena, including: * rs4570625 and rs4565946 linked to the pathogenesis of early-onset obsessive compulsive disorder * rs4570625 and rs11178997 in TPH2's regulatory region display preferential transmission * rs4570625(G;G) homozygosity was a significant predictor of clinical placebo response, being associated with greater improvement in anxiety symptoms. g2b2mh is rs4570625(G;G) is a significant predictor of clinical placebo response? maybe not panic disorder with a possible gender-dependent effect Transmission disequilibrium of polymorphic variants in the tryptophan hydroxylase-2 gene in attention-deficit/hyperactivity disorder. Associa...
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rs4570625 and rs4565946 linked to the pathogenesis of early-onset obsessive compulsive disorder Tourette's Syndrome
multiple associations, see details
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rs4680 (Val158Met) is a well studied SNP in the COMT gene. 23andMe blog summarizes them as *rs4680(A) = Worrier. Met, more exploratory, lower COMT enzymatic activity, therefore higher dopamine levels; lower pain threshold, enhanced vulnerability to stress, yet also more efficient at processing information under most conditions *rs4680(G) = Warrior. Val, less exploratory, higher COMT enzymatic activity, therefore lower dopamine levels; higher pain threshold, better stress resiliency, albeit with a modest reduction in executive cognition performance under most conditions Roughly speaking, the predominant wisdom (known colloquially as the warrior/worrier hypothesis; summary at ) posits that people with Val alleles have increased COMT activity and lower prefrontal extracellular dopamine compar...
common for Caucasians on the 23andme platform
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rs4570625 and rs11178997 in TPH2's regulatory region display preferential transmission paper Association with and bipolar disorder in a Northern Swedish, Isolated Population. 182 patients and 364 unrelated control individuals. P = .001 rs11178997 significantly reduced TPH2 transcriptional activity by 22% and 7% in cell lines might have implications for the development and function of the serotonergic system in the brain. paper Carriers of the A-Allele of rs11178997 showed a decreased cortisol and ACTH stimulation. might be crucial factors for major depression pdf paper associated with bipolar disorder Minor allele yielded odds ratio of 1.5 (CI:1.2-1.9) for increased risk for bipolar disorder in a study of 883 Russian patients. Transmission disequilibrium of polymorphic variants in the tryp...
4 snps
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Avg. fasting Plasma Glucose 5.18 mmol/L (93 mg/dl). Slightly higher blood glucose. Fasting Plasma Glucose is the amount of sugar in your blood when you wake up. It's required to power your body, but too much is very bad for you. Fasting plasma glucose between 5.6 mmol/L and 6.9 mmol/L (101 – 125 mg/dl) is considered pre-diabetes. Fasting plasma glucose higher than 7 mmol/L (126 mg/dl) is considered diabetes.
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rs560887, p = 4 x 10(-7)) *654 normoglycemic subjects, replicated in 9,353 subjects *fasting plasma glucose (FPG) (beta = -0.06 mmol/l per A-allele, combined p = 4 x 10(-23)) and with pancreatic beta-cell function (Homa-B model, combined p = 3 x 10(-13)) in three populations; however it was not associated with type 2 diabetes risk. (ageing) Blood Glucose [PharmGKB:Non-Curated Phenotype 1: In a meta-analysis of 21 GWAS cohorts followed by analysis in additional individuals, this SNP was found to be associated with fasting glucose level. Study size: 119,169. Significance metric(s): p = 8.7 x 10(-218). Phenotype 2: In the same study, this SNP was found to be associated with HOMA-B (homeostasis model assessment of beta-cell function). Study size: 94,839. Significance metric(s): p = 1.5 x 10(-...
some risk linked to a number of metabolic conditions including obesity, coronary artery disease, insulin resistance and therefore diabetes, left ventricular hypertrophy, and hypertension. It has also been linked to how well a patient responds to Viagra (sildenafil).
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rs5443, a SNP in the G-protein beta3 subunit (GNB3) gene that is more commonly known as the C825T variant, has been linked to a number of metabolic conditions including obesity, coronary artery disease, insulin resistance and therefore diabetes, left ventricular hypertrophy, and hypertension. It has also been linked to how well a patient responds to Viagra (sildenafil). Several studies have been unable to replicate one or more of the associations in at least some populations between this SNP and these conditions. The more notable studies include: *rs5443(T) allele carriers are 2-3 fold more likely to be obese in Caucasian, Chinese, and African American populations. *rs5443(T) carriers are clearly at higher risk for hypertension, but this review indicates that whether they are also at incre...
1.2x increased risk for type-2 diabetes
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rs4402960 replicated as significant for type-2 diabetes risk in 1,900 Japanese patients, with odds ratio of 1.23 (CI: 1.11-1.36, p = 8.1 x 10e-5) associated with type-2 diabetes significantly associated with type-2 diabetes p = 0.00009; in 1,630 Japanese subjects and in 1,064 controls 1,638 type-2 diabetes patients and 1,858 controls *rs4402960 borderline (OR 1.10, 95% CI: 0.99-1.22). Neither rs4402960 or rs1470579 were found to be associated with type-2 diabetes in a study of 3,000 French Caucasians. This SNP was confirmed to be associated with type-2 diabetes in a study of 500+ Japanese patients plus pooled meta-analysis with 6 previous association studies (also of Japanese). Note: rs4402960 is fairly tightly linked (r<sup>2</sup>=0.87) with another IGF2BP2 gene SNP also asso...
Normal (lower) risk of Type 2 Diabetes and Gestational Diabetes. Normal insulin secretion in the pancreas. This has been confirmed in most races.
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This SNP in TCF7L2 influences the risk of Type-2 diabetes (T2D). This SNP is also known as IVS3C>T. rs7903146(C;T) rs7903146(T;T) strongly predicted future type-2 diabetes. Considered in context with rs7903146 rs12255372 rs10885406. Note: this is one of two SNPs within the TCF7L2 gene that have been reported to be associated with type-2 diabetes, the other being rs4506565. They have approximately equal power to estimate risk for type-2 diabetes, and the results from one correlate 92% of the time with the other. Full text of the paper is available from from Plos Medicine. Or from NCBI as . TCF7L2 polymorphisms and progression to diabetes in the Diabetes Prevention Program. reconfirmed in a diverse population Associated in a study of ~1000 Hispanic-Americans with reduced insulin secretion...
Mothers have typical Birth-Weight babies. Slightly lower risk of Type 2 Diabetes.
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rs1799884, known also as the -30 SNP of the GCK gene, has been associated with type-2 diabetes. This SNP is one of 4 relatively common SNPs reported to represent risk for type-2 diabetes in the DESIR prospective study of 3,877 Caucasian participants. Under a recessive model, the odds ratio for rs1799884(A;A) homozygotes is 2.70 (CI: 1.51-4.83, p=0.0008); under an additive model, the odds ratio is 1.34 (CI: 1.07-1.69, p=0.01). For the 4 SNPs, each risk allele increased type-2 diabetes risk by 1.34x (p=2x10e-6), with an odds ratio of 2.48 (CI: 1.59-3.86) for carriers of 4 or more compared to those with one or none (risk alleles). A common haplotype of the glucokinase gene alters fasting glucose and birth weight: association in six studies and population-genetics analyses. Type 2 diabetes TCF...
1.3x increased risk for type-2 diabetes
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rs5219, also known as E23K, is a SNP in the KCNJ11 gene. The association between type-1 diabetes and rs5219 is mentioned as being replicated in ; there is also a 90% correlation between rs5219 and rs5215. This SNP is one of 4 relatively common SNPs reported to represent risk for type-2 diabetes in the DESIR prospective study of 3,877 Caucasian participants. Under an additive model, the odds ratio for the minor (risk) allele (T) is 1.15 (CI: 0.95-1.4, p=0.2, ie not significant). But for the 4 SNPs, each risk allele increased type-2 diabetes risk by 1.34x (p=2x10e-6), with an odds ratio of 2.48 (CI: 1.59-3.86) for carriers of 4 or more compared to those with one or none (risk alleles). Genotyping of ~4000 Chinese as well a meta-analysis concluded that rs5219 was associated with type-2 diabet...
preterm birth rs4696480 (T-16934A and Arg753Gln) and rs5743708) (Thr399Ile) earlier birth for infants carrying two (-16934TA/AA and 753ArgGln/GlnGln)
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preterm birth rs4696480 (T-16934A and Arg753Gln) and rs5743708) (Thr399Ile) earlier birth for infants carrying two (-16934TA/AA and 753ArgGln/GlnGln)
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[GWAS:Preeclampsia]
Frequency: 17.7%
References:1
References:1
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[GWAS:Preeclampsia]
Frequency: 20.4%
References:0
References:0
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A study of maternal and fetal DNA from 370 US Caucasian birth-events (172 cases and 198 controls) concluded that the single strongest effect in fetal DNA was associated with rs17121510 in the interleukin-10 receptor antagonist (IL-10RA) gene at both allelic (p = 0.01) and genotypic (p = 3.34x10e-4) levels. The odds ratio for preterm birth for the genotypic additive model was 1.92 (CI: 1.15-3.19, p = 2.00x10e-3). Role of polymorphic variants as genetic modulators of infection in neonatal sepsis.
normal risk of hypertension
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rs699 is a SNP in the angiotensin AGT gene that encodes a functional change. In most published literature, the name for this SNP is M235T, or perhaps Met235Thr, however its amino acid 268 (not 235) that varies based on the numbering in todays databases. rs699 is also occasionally known as C4072T. In any case, the rs699(C) allele encodes the threonine variant, which is associated with higher plasma angiotensin levels, and ultimately higher blood pressure leading to increased risk for hypertension associated disorders. This association was first reported in 1992 , and many studies, though not all, have replicated these findings. rs699 is also (generally) reported to be in tight linkage with rs5051, a neighboring SNP in the promoter of the AGT gene. rs699(C) has also been implicated as a risk...
Adverse reaction more likely to carbamazepine in epileptic patients
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rs2273697, also known as c1249G>A or p.V471I, is a nonsynonymous polymorphism in the ABCC2 gene. From an initial case-control study of 146 patients with epilepsy, followed by replication (p=0.001) in another 279 patients, the rs2273697(A) allele was associated with neurological adverse drug reactions from taking carbamazepine. Functional studies showed that this SNP selectively reduced carbamazepine transport across the cell membrane. [PharmGKB:Curated Risk or phenotype-associated allele: A. Phenotype: This SNP showed a strong association with the neurological adverse drug reaction caused (ADR) by carbamazepine (P=0.005). The study results indicate that the c.1249A variant is an independent risk factor of carbamazepine CNS ADR. Study size: 146 patients with epilepsy who had been prescr...
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A study of maternal and fetal DNA from 370 US Caucasian birth-events (172 cases and 198 controls) concluded that the single strongest effect observed in maternal DNA was for SNP rs879293, with a significant allelic (p = 2.30x10e-3) and genotypic association (p = 2.0x10e-6) with spontaneous preterm birth (PTB). The odds ratio for this SNP was 2.80 (CI:1.77-4.44) under a recessive model.
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[PharmGKB:Non-Curated GWAS results: A variant near MTNR1B is associated with increased fasting plasma glucose levels and type 2 diabetes risk. (Initial Sample Size: 2,151 individuals; Replication Sample Size: 6,332 cases, 9,132 controls); (Region: 11q21; Reported Gene(s): MTNR1B; Risk Allele: rs1387153-T); (p-value= 2E-36).This variant is associated with Fasting plasma glucose.] [OMIM:?] [GWAS:Fasting plasma glucose]
Frequency: 50.8%
Repute:Bad
References:60
Repute:Bad
References:60
increased type-2 diabetes risk; higher gestational diabetes risk
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rs10830963 was associated with an increased risk of type-2 diabetes in our Han Chinese cohort (OR 1.16, 95% CI 1.03-1.31, p = 0.015). As previously described, the risk variant was also associated with increased fasting plasma glucose, showing an increase of 0.068 mmol/l (95% CI 0.036-0.100, p = 4 x 10(-5)) per risk allele rs10830962, rs4753426, and rs10830963 were significantly associated with higher fasting plasma glucose concentrations and reduced OGTT- and IVGTT-induced insulin release. rs3781638 displayed significant association with lower fasting plasma glucose levels and increased OGTT-induced insulin release A study totaling 19,000+ Europeans concluded that rs10830963 had the most influence of any MTNR1B gene SNP on the risk for type-2 diabetes. Specifically, the (G) allele increase...
1.6x risk for ICP
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rs3740066, a SNP in the ABCC2 gene, is reported to be associated with a higher risk of developing intrahepatic cholestasis of pregnancy (ICP) based on a study of ~70 Argentinian patients. ICP is associated with increased fetal risks such as premature birth or intrauterine death. The risk allele is rs3740066(A), and the odds ratio for homozygous rs3740066(A;A) mothers is 4.44 (CI: 1.83 - 10.78), and for heterozygous mothers 1.65 (CI: 0.76 - 3.64), compared to rs3740066(G;G) mothers. [PharmGKB:Curated The AUCs of irinotecan, SN-38, SN-38 glucuronide, and APC are influenced by rs3740066, rs2306283, rs35605, rs10276036, and rs717620 .]
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[GWAS:Preeclampsia]
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[GWAS:Preeclampsia]
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[GWAS:Preeclampsia]
Frequency: 82.3%
References:1
References:1
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[GWAS:Preeclampsia]
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[GWAS:Preeclampsia]
Frequency: 85.0%
References:1
References:1
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[GWAS:Preeclampsia]
Frequency: 86.7%
References:1
References:1
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[GWAS:Preeclampsia]
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[GWAS:Preeclampsia]
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A variant upstream of the CDH13 adiponectin receptor gene and metabolic syndrome in Swedes. Dissecting complex traits: recent advances in hypertension genomics. [PharmGKB:Non-Curated GWAS results: Genome-wide scan identifies CDH13 as a novel susceptibility locus contributing to blood pressure determination in two European populations. (Initial Sample Size: 364 cases, 590 controls; Replication Sample Size: 1,043 cases, 1,769 controls); (Region: 16q23.3; Reported Gene(s): CDH13; Risk Allele: rs11646213-T); (p-value= 0.000008).This variant is associated with Hypertension.] [GWAS:Hypertension]
Magnitude: 0
Frequency: 55.8%
Repute:Good
References:2
Frequency: 55.8%
Repute:Good
References:2
common in clinvar
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rs10509305, also known as Glu608Asp or E608D, is a variant in the storkhead box 1 STOX1 gene. In and subsequent publications, it is reported that when fetuses are rs10509305(C;C), their mothers are likely to have pre-eclampsia and possibly also pregnancy-induced hypertension. [OMIM:?]
Magnitude: 0
Frequency: 60.2%
Repute:Good
References:106
Frequency: 60.2%
Repute:Good
References:106
normal
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rs12255372, also known as IVS4G>T and c.483+9017G>T, is a well-studied SNP in the TCF7L2 gene on chromosome 10. In some studies, it has been linked to slight increases in risk for type-2 diabetes, breast cancer and aggressive prostate cancer. '''* Type-2 Diabetes Risk Overview:''' numerous papers report an increase in risk, on the order of 1.5 - 2x for the risk genotypes compared to the non-risk genotype. Key papers include: ** reports the association of rs12255372 and rs7903146 with Type-2 diabetes in a Finnish sample. **rs12255372 Common variants (rs12255372 and rs7903146) in TCF7L2 seem to be associated with an increased risk of diabetes among persons with impaired glucose tolerance ** Considered for type-2 diabetes with rs7903146 rs12255372 rs10885406. ** Associated in a study of...
normal risk
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rs4762, a SNP in the angiotensin II AGT gene, has been reported to be associated with increased risk for developing pre-eclampsia, based on a study of ~180 French-Canadian women. The odds ratio associated with the rs4762(T) allele (encoding methionine) was 1.9 (CI:1.2–2.9, p=0.0033). Note that rs4762 is commonly referred to in the literature as 'T174M' or 'Thr174Met'; however, databases now indicate that the amino acid that varies is #207 (not 174), as the protein is currently numbered. rs4762 was also reported to play the major role in the 2.1 fold increased risk (CI: 1.4-3.4, p=0.0008) for pre-eclampsia of the rs3889728(A)-rs4762(T)-rs699(C) haplotype. Correction of population stratification in large multi-ethnic association studies. Ten renin-angiotensin system-relate...
normal
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The INSR A-603G promoter rs1864010 SNP, which is located within a known Sp1-binding site, was associated with the risk of colorectal cancer, with carriers of the G allele having a decreased risk (odds ratios (OR) 0.71, 95% confidence interval (CI) 0.54-0.93). Carrying the variant allele of the IRS1 Gly972Arg rs1801278 SNP further decreased the risk among the INSR-603G allele carriers (OR 0.28, 95% CI 0.11-0.70) multiple myeloma *rs1801278 [C/T versus C/C genotypes; OR, 4.3; 95% confidence interval (CI), 1.5-12.1] *rs6684439 (T/T versus C/C; OR, 2.9; 95% CI, 1.2-7.0) *rs7529229 (C/C versus T/T; OR, 2.5; 95% CI, 1.1-6.0) *rs8192284 (C/C versus A/A; OR, 2.5, 95% CI, 1.1-6.0)
common on affy axiom data
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[PharmGKB:Curated Risk or phenotype-associated allele: A. Phenotype: This SNP was part of a haplotype associated with acute cardiotoxicity in response to doxorubicin. Study size: 1697. Study population/ethnicity: Participants of the German non-Hodgkin lymphoma study. Significance metric(s): OR = 2.3; 95% CI, 1.0 to 5.4. Type of association: PD; ADR; TOX.]
Magnitude: 0
Frequency: 90.3%
Repute:Good
References:1
Frequency: 90.3%
Repute:Good
References:1
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[GWAS:Preeclampsia]
normal
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rs4986791, a SNP also known as Thr399Ile (and also 1196C/T) in the TLR4 gene, is often studied along with a cosegregating SNP known as Asp299Gly, rs4986790. (TLR4 encodes a receptor involved in the innate immune response.) Together, these SNPs have been reported to be associated with a wide variety of both infectious and non-infectious diseases, although there are conflicting or even contradictory results also reported in some cases. The risk allele for rs4986791 is (T). Reported associations include : * Diabetic neuropathy ** These SNPs may be protective * Heart disease ** Men with the risk alleles for both SNPs are at increased risk for myocardial infarction in this study of over 2000 individuals. ** rs4986790(G) carriers are not at increased risk for myocardial infartions, at least in t...
normal/common
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rs6025 represents a SNP in the Factor V F5 gene, encoding a change in the protein from an arginine at position 506 to a glutamine. The resulting rs6025(A) allele encodes a mutation known as the Leiden mutation, R506Q, found in perhaps 3 to 5% of the individuals in most populations. About 1 in 10 individuals harboring the R506Q will experience clinically significant venous thromboembolism in their lifetimes (according to OMIM). Overall, the rs6025(A) allele appears to be necessary but not sufficient for the development of venous thromboembolism. Patients who are rs6025(A;G) heterozygotes but lack other risk-enhancing SNPs have a risk of recurrent deep venous thrombosis equal to patients with no such SNPs. In contrast, patients who are heterozygotes for both rs6025 and the prothrombin rs1799...
normal risk
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rs5186, a SNP known as +1166A/C or A1166C, is located in the 3' untranslated region of the angiotensin II receptor type 1 gene AGTR1, which is also known as AT2R1 or AT1R. It is among the most studied of over 50 SNPs in AGTR1. The rs5186(C) allele is associated with increased risk for essential hypertension in Caucasian populations with an odds ratio of 7.3 (homozygote (C;C) compared to (A;C) and (A;A), CI: 1.9-31.9,p=0.0015). There are likely to be ethnic differences in risk; while the rs5186(C) allele was associated with hypertension in a Chinese population , it was not been observed as a risk in a Japanese population. Age and gender may also influence risk, as discussed in a review of AGTR1 SNPs and their role in hypertension and related disorders. Pregnant women who are rs5186(C) allel...
normal
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The accuracy of claims about this snp are called into question by table 1 of discusses the process of including this snp into Coriell and raises some doubt about the value of its inclusion. rs7754840 replicated as significant for type-2 diabetes risk in 1,900 Japanese patients, with odds ratio of 1.28 (CI: 1.17-1.41, p = 4.5 x 10e-7) type-2 diabetes Carriers of the (C;G) and (C;C) genotypes of rs7754840 had 11% and 24% lower first-phase insulin release in an IVGTT compared to that in carriers of the (G;G) genotype (P=0.002). The C allele was also associated with higher glucose area under the curve in an OGTT (P=0.016). rs7754840 type-2 diabetes Ashkenazi Jewish population shows an even stronger effect for rs7754840 than the general Caucasian population, based on 1,131 cases versus 1,147 co...
common on affy axiom data
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[PharmGKB:Curated Risk or phenotype-associated allele: A. Phenotype: This SNP was part of a haplotype associated with acute cardiotoxicity in response to doxorubicin. Study size: 1697. Study population/ethnicity: Participants of the German non-Hodgkin lymphoma study. Significance metric(s): OR = 2.3; 95% CI, 1.0 to 5.4. Type of association: PD; ADR; TOX.]
37 snps
(hide) QT interval
Magnitude: 2
Frequency: 40.7%
References:30
Frequency: 40.7%
References:30
Shorter QT interval
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rs10494366, a SNP in the NOS1AP gene encoding the nitric oxide synthase I adaptor protein, accounts for some of the variation seen in abnormal heart rhythms, in particular, the QT interval. Based on studies totaling ~4,000 individuals of Caucasian ancestry, homozygotes for one allele have shorter QT intervals, while homozygotes for the other allele have a longer QT interval. A follow-up study determined that one rs10494366(G) allele was associated with a 3.8-ms (CI: 3.0 - 4.6ms, p=7.8x10(-20)) increase in QT interval duration, and two (G) alleles had twice that increase. No increase in risk for sudden death due to a cardiac problem was associated with this SNP, though. rs10494366 minor homozygotes had a 9.3 msec longer QT interval compared to major homozygotes (p=5.7x10(-5)); rs10918594 mi...
Frequency: 9.7%
References:4
References:4
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23andMe blog Influences QT interval [PharmGKB:Non-Curated GWAS results: Common variants at ten loci influence QT interval duation in the QTGEN Study. (Initial Sample Size: 13,685 individuals; Replication Sample Size: 15,854 individuals); (Region: 3p22.2; Reported Gene(s): SCN5A; Risk Allele: rs12053903-C); (p-value= 0.00000000000001).This variant is associated with QT interval.] [GWAS:QT interval]
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23andMe blog Influences QT interval [PharmGKB:Non-Curated GWAS results: Common variants at ten loci influence QT interval duation in the QTGEN Study. (Initial Sample Size: 13,685 individuals; Replication Sample Size: 15,854 individuals); (Region: 16p13.13; Reported Gene(s): LITAF,CLEC16A, SNN, ZC3H7A, TNFRSF17; Risk Allele: rs8049607-T); (p-value= 0.000000000000005).This variant is associated with QT interval.] [GWAS:QT interval]
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[GWAS:QT interval]
Frequency: 27.7%
References:1
References:1
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[GWAS:QT interval]
Frequency: 28.1%
References:2
References:2
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23andMe blog Influences QT interval [PharmGKB:Non-Curated GWAS results: Common variants at ten loci influence QT interval duation in the QTGEN Study. (Initial Sample Size: 13,685 individuals; Replication Sample Size: 15,854 individuals); (Region: 6q22.31; Reported Gene(s): c6orf204,SLC35F1, PLN, ASF1A; Risk Allele: rs11756438-A); (p-value= 5E-22).This variant is associated with QT interval.] [GWAS:QT interval]
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[GWAS:QT interval]
Frequency: 31.9%
References:4
References:4
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[PharmGKB:Non-Curated GWAS results: Common variants at ten loci modulate the QT interval duration in the QTSCD Study. (Initial Sample Size: 15,842 individuals; Replication Sample Size: up to 13,602 individuals); (Region: 3p22.2; Reported Gene(s): SCN5A; Risk Allele: rs11129795-A); (p-value= 0.00000000000005).This variant is associated with QT interval.] [GWAS:QT interval]
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[GWAS:QT interval]
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23andMe blog Influences QT interval [PharmGKB:Non-Curated GWAS results: Common variants at ten loci influence QT interval duation in the QTGEN Study. (Initial Sample Size: 13,685 individuals; Replication Sample Size: 15,854 individuals); (Region: 16q21; Reported Gene(s): CNOT1,GINS3, NDRG4, SLC38A7, GOT2; Risk Allele: rs37062-G); (p-value= 3E-25).This variant is associated with QT interval.] [GWAS:QT interval]
Frequency: 35.4%
References:4
References:4
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[PharmGKB:Non-Curated GWAS results: Common variants at ten loci modulate the QT interval duration in the QTSCD Study. (Initial Sample Size: 15,842 individuals; Replication Sample Size: up to 13,602 individuals); (Region: 11p15.5; Reported Gene(s): KCNQ1; Risk Allele: rs12296050-T); (p-value= 0.00000000000000003).This variant is associated with QT interval.] [GWAS:QT interval]
Frequency: 35.4%
References:1
References:1
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[GWAS:QT interval]
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[GWAS:QT interval]
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23andMe blog Influences QT interval [PharmGKB:Curated Associated with altered myocardial repolarization.] [GWAS:Electrocardiographic traits]
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[GWAS:QT interval]
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[PharmGKB:Non-Curated GWAS results: Common variants at ten loci modulate the QT interval duration in the QTSCD Study. (Initial Sample Size: 15,842 individuals; Replication Sample Size: up to 13,602 individuals); (Region: 16q21; Reported Gene(s): NDRG4; Risk Allele: rs7188697-A); (p-value= 7E-25).This variant is associated with QT interval.] [GWAS:QT interval]
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[PharmGKB:Non-Curated GWAS results: Common variants at ten loci modulate the QT interval duration in the QTSCD Study. (Initial Sample Size: 15,842 individuals; Replication Sample Size: up to 13,602 individuals); (Region: 1q23.3; Reported Gene(s): NOS1AP; Risk Allele: rs4657178-T); (p-value= 7E-33).This variant is associated with QT interval.] [GWAS:QT interval]
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[GWAS:QT interval]
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New atypical antipsychotics for schizophrenia: iloperidone. [PharmGKB:Non-Curated GWAS Results: Whole genome association study identifies polymorphisms associated with QT prolongation during iloperidone treatment of schizophrenia (Initial Sample Size: 183 individuals; Replication Sample Size: NR; Risk Allele: rs993648-T). This variant is associated with Response to iloperidone treatment (QT prolongation).] [GWAS:Response to iloperidone treatment (QT prolongation)]
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[GWAS:QT interval]
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[PharmGKB:Non-Curated GWAS Results: Whole genome association study identifies polymorphisms associated with QT prolongation during iloperidone treatment of schizophrenia (Initial Sample Size: 183 individuals; Replication Sample Size: NR; Risk Allele: rs4799915-T). This variant is associated with Response to iloperidone treatment (QT prolongation).] [GWAS:Response to iloperidone treatment (QT prolongation)]
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[GWAS:QT interval]
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[PharmGKB:Non-Curated GWAS Results: Whole genome association study identifies polymorphisms associated with QT prolongation during iloperidone treatment of schizophrenia (Initial Sample Size: 183 individuals; Replication Sample Size: NR; Risk Allele: rs7142881-A). This variant is associated with Response to iloperidone treatment (QT prolongation).] [GWAS:Response to iloperidone treatment (QT prolongation)]
Frequency: 47.8%
References:3
References:3
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Common variants at ten loci influence QT interval duration in the QTGEN Study. [PharmGKB:Non-Curated GWAS results: Common variants at ten loci modulate the QT interval duration in the QTSCD Study. (Initial Sample Size: 15,842 individuals; Replication Sample Size: up to 13,602 individuals); (Region: 17q24.3; Reported Gene(s): KCNJ2; Risk Allele: rs17779747-T); (p-value= 0.000000000006).This variant is associated with QT interval.] [GWAS:QT interval]
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[GWAS:QT interval]
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QT interval rs3807375 rs2880058 [GWAS:QT interval]
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[GWAS:QT interval]
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QT interval rs3807375 rs2880058 [PharmGKB:Curated QT prolongation] [GWAS:Electrocardiographic traits]
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[GWAS:QT interval]
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[GWAS:QT interval]
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[GWAS:QT interval]
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[GWAS:QT interval]
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23andMe blog Influences QT interval [PharmGKB:Non-Curated GWAS results: Common variants at ten loci influence QT interval duation in the QTGEN Study. (Initial Sample Size: 13,685 individuals; Replication Sample Size: 15,854 individuals); (Region: 7q36.1; Reported Gene(s): KCNH2; Risk Allele: rs4725982-T); (p-value= 0.0000000000000005).This variant is associated with QT interval.] [GWAS:QT interval]
Frequency: 71.7%
References:3
References:3
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23andMe blog Influences QT interval [PharmGKB:Non-Curated GWAS results: Common variants at ten loci influence QT interval duation in the QTGEN Study. (Initial Sample Size: 13,685 individuals; Replication Sample Size: 15,854 individuals); (Region: 1q23.3; Reported Gene(s): NOS1AP; Risk Allele: rs12029454-A); (p-value= 3E-45).This variant is associated with QT interval.] [GWAS:QT interval]
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[GWAS:QT interval]
Frequency: 72.6%
References:3
References:3
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23andMe blog Influences QT interval [PharmGKB:Non-Curated GWAS results: Common variants at ten loci influence QT interval duation in the QTGEN Study. (Initial Sample Size: 13,685 individuals; Replication Sample Size: 15,854 individuals); (Region: 11p15.5; Reported Gene(s): KCNQ1; Risk Allele: rs12576239-T); (p-value= 0.000000000000001).This variant is associated with QT interval.] [GWAS:QT interval]
Frequency: 73.4%
References:4
References:4
normal
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rs16847548 and rs16856785 strongly associated with QT interval Based on a large study of 19,000+ adults, SNPs rs10494366, rs4657139 and rs16847548 were significantly associated with adjusted QT interval in whites but not in African-Americans. The relative hazard of sudden cardiac death (SCD) associated with each rs16847548(C) allele was 1.31 (CI: 1.10 - 1.56, p=0.002). rs12567209 was also independently associated with SCD in whites (relative hazard 0.57, CI: 0.39 - 0.83, p=0.003).
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[GWAS:QT interval]
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[GWAS:QT interval]
Frequency: 81.4%
References:1
References:1
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[GWAS:QT interval]
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[GWAS:QT interval]
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[GWAS:QT interval]
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[GWAS:QT interval]
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[GWAS:QT interval]
Frequency: 100.0%
References:1
References:1
(hide)
[GWAS:QT interval]
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[GWAS:QT interval]
References:1
(hide)
[GWAS:QT interval]
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[PharmGKB:Non-Curated GWAS results: Common variants at ten loci modulate the QT interval duration in the QTSCD Study. (Initial Sample Size: 15,842 individuals; Replication Sample Size: up to 13,602 individuals); (Region: 7q36.1; Reported Gene(s): KCNH2; Risk Allele: rs2968863-T); (p-value= 0.000000000000002).This variant is associated with QT interval.] [GWAS:QT interval]
Shorter QT interval
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rs10918594, a SNP near the NOS1AP gene encoding the nitric oxide synthase I protein, accounts for some of the variation seen in abnormal heart rhythms, in particular, the QT interval. Based on studies totaling ~4,000 individuals of Caucasian ancestry, homozygotes for one allele have shorter QT intervals, while homozygotes for the other allele have a longer QT interval. A follow-up study determined that one rs10918594(G) allele was associated with a 3.6-ms (CI: 2.7 - 4.4ms, p=6.9x10(-17)) increase in QT interval duration, and two (G) alleles had twice that increase. No increase in risk for sudden death due to a cardiac problem was associated with this SNP, though. rs10494366 minor homozygotes had a 9.3 msec longer QT interval compared to major homozygotes (p=5.7x10(-5)); rs10918594 minor ho...
Magnitude: 0
Frequency: 75.8%
Repute:Good
References:3
Frequency: 75.8%
Repute:Good
References:3
common on affy axiom data
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[PharmGKB:Non-Curated GWAS results: Common variants at ten loci modulate the QT interval duration in the QTSCD Study. (Initial Sample Size: 15,842 individuals; Replication Sample Size: up to 13,602 individuals); (Region: 1q24.2; Reported Gene(s): ATP1B1; Risk Allele: rs10919071-A); (p-value= 0.000000000000001).This variant is associated with QT interval.] [GWAS:QT interval]
Magnitude: 0
Frequency: 85.8%
Repute:Good
References:0
Frequency: 85.8%
Repute:Good
References:0
common in complete genomics
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rs10494366, rs4657139 and rs16847548 were significantly associated with adjusted QT interval in whites. relative hazard of SCD associated with each C allele at rs16847548 was 1.31. rs12567209 was also independently associated with SCD in whites (relative hazard 0.57, 95% confidence interval 0.39 to 0.83, P=0.003). No significant associations observed in blacks. Multiple independent genetic factors at NOS1AP modulate the QT interval in a multi-ethnic population. Genetic variation in NOS1AP is associated with sudden cardiac death: evidence from the Rotterdam Study.
Magnitude: 0
Frequency: 86.7%
Repute:Good
References:1
Frequency: 86.7%
Repute:Good
References:1
Magnitude: 0
Frequency: 88.3%
Repute:Good
References:1
Frequency: 88.3%
Repute:Good
References:1
common on affy axiom data
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23andMe blog Influences QT interval [PharmGKB:Non-Curated GWAS results: Common variants at ten loci influence QT interval duation in the QTGEN Study. (Initial Sample Size: 13,685 individuals; Replication Sample Size: 15,854 individuals); (Region: 11p15.5; Reported Gene(s): KCNQ1; Risk Allele: rs2074238-T); (p-value= 0.00000000000000003).This variant is associated with QT interval.] [GWAS:QT interval]
common in complete genomics
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[PharmGKB:Non-Curated GWAS Results: Whole genome association study identifies polymorphisms associated with QT prolongation during iloperidone treatment of schizophrenia (Initial Sample Size: 183 individuals; Replication Sample Size: NR; Risk Allele: rs4933824-T). This variant is associated with Response to iloperidone treatment (QT prolongation).] [GWAS:Response to iloperidone treatment (QT prolongation)]
common in complete genomics
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23andMe blog Influences QT interval [PharmGKB:Curated Associated with noise-induced hearing loss.] [OMIM:POTASSIUM CHANNEL, VOLTAGE-GATED, ISK-RELATED SUBFAMILY, MEMBER 1;]
common in clinvar
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rs7626962, also known as Ser1103Tyr or S1103Y, is a SNP in the cardiac sodium channel SCN5A gene. Although relatively common (for a rare allele; 10 - 20% of individuals) in those of African ancestry, in all populations the rs7626962(T) allele has been reported to increase the risk for cardiac issues such as long QT syndrome but also arrhythmias and even sudden infant death syndrome. The odds ratio for displaying signs of arrhythmia for anyone carrying a rs7626962(T) allele is reported as 8.7 (CI 3.2 - 23.9) ; as for sudden infant death syndrome, at least in African-ancestry populations, the odds ratio for the same allele is reported as 4.9, leading to an odds ratio of 24 for rs7626962(T;T) homozygotes. This variant meets the criteria published in 2013 by the ACMG regarding incidental findi...
common in complete genomics
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[PharmGKB:Non-Curated GWAS Results: Whole genome association study identifies polymorphisms associated with QT prolongation during iloperidone treatment of schizophrenia (Initial Sample Size: 183 individuals; Replication Sample Size: NR; Risk Allele: rs3924426-T). This variant is associated with Response to iloperidone treatment (QT prolongation).] [GWAS:Response to iloperidone treatment (QT prolongation)]
Magnitude: 0
Repute:Good
References:6
Repute:Good
References:6
common in clinvar
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rs17221854, also known as Arg583Cys or R583C, is a SNP in the KCNQ1 gene on chromosome 11. The rs17221854(T) allele has been reported as associated with long QT syndrome. Additionally, a person who developed QT prolongation and torsade de pointes while taking the drug dofetilide carried this (T) allele, leading the authors to hypothesize that this mutation was responsible for the patient's drug response. This variant meets the criteria published in 2013 by the ACMG regarding incidental findings in exome or genome sequencing, as a variant that they do recommend informing a patient about. [OMIM:LONG QT SYNDROME 1]
Magnitude: 0
Repute:Good
References:8
Repute:Good
References:8
common in complete genomics
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rs28928904, also known as I593R or Ile593Arg, is a SNP in the KCNH2 gene on chromosome 7. A 1996 publication reports that the rs28928904(G) allele is associated with long QT syndrome 2. This variant meets the criteria published in 2013 by the ACMG regarding incidental findings in exome or genome sequencing, as a variant that they do recommend informing a patient about. [OMIM:LONG QT SYNDROME 2]
Magnitude: 0
Repute:Good
References:9
Repute:Good
References:9
common in clinvar
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rs28937316, also known as Arg1644His or R1664H, is a SNP in the cardiac sodium channel SCN5A gene on chromosome 3. Acting in a dominant manner, one copy of a rs28937316(A) allele is considered causative for long QT syndrome 3. This variant meets the criteria published in 2013 by the ACMG regarding incidental findings in exome or genome sequencing, as a variant that they do recommend informing a patient about. [OMIM:LONG QT SYNDROME 3]
common in complete genomics
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[PharmGKB:Non-Curated GWAS results: Common variants at ten loci modulate the QT interval duration in the QTSCD Study. (Initial Sample Size: 15,842 individuals; Replication Sample Size: up to 13,602 individuals); (Region: 6q22.31; Reported Gene(s): PLN; Risk Allele: rs12210810-C); (p-value= 0.00000000000000002).This variant is associated with QT interval.] [GWAS:QT interval]
common in complete genomics
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rs16847548 and rs16856785 strongly associated with QT interval
64 snps
(hide) Redheads
common in clinvar
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rs1805008, known as Arg160Trp or R160W, is one of several SNPs in the MC1R gene associated with red hair color (redheads), in this case in an Irish population although this has also been reported in Icelandic and Dutch populations . The risk allele is rs1805008(T), compared with the wild-type rs1805008(C) allele. blog about designing melanocortin analogs specific to these genotypes. See also OMIM 155555.0005 Melanoma Parkinson's disease [OMIM:SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 2; SHEP2]
normal risk
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rs1805007, known as Arg151Cys or R151C, one of several SNPs in the MC1R gene associated with red hair color (redheads), and in redheaded females, linked to being more responsive to the anesthetics pentazocine, nalbuphine, and butorphanol, often used by dentists The risk allele is rs1805007(T), compared with the wild-type rs1805007(C) allele. The risk allele has also been reported in several studies to be associated with increased risk for melanoma. For example, an odds ratio of 2.94 (CI: 1.04-8.31) has been reported for an Italian population , and similarly an odds ratio of 2.9 has been reported for a Polish population . Blog entry about designing melanocortin analogs specific to these genotypes. See also OMIM 155555.0004 Freckling [OMIM:SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 2; SHEP2]...
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See also Rs1805009
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
normal
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This missense mutation influences red hair color and has been observed in the Spanish maternal ancestry of User:Corpas son.
common in complete genomics
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rs1805006, known as Asp84Glu or D84E, is one of several SNPs in the MC1R gene associated with higher risk of melanoma. The risk allele is rs1805006(A), compared with the wild-type rs1805006(C) allele. Allelic odds ratio for pale skin(P-value)=5.19(<1.0e-5)MC1R*D84E rs1805006 http://genepi.qimr.edu.au/contents/p/staff/Duffyetal_JID_520-528Jan10.pdf See also OMIM 155555.0003 [OMIM:?]
5 snps
(hide) Revised NEO Personality Inventory
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[PharmGKB:Non-Curated GWAS results: Genome-wide association scan for five major dimensions of personality. (Initial Sample Size: 3,972 individuals; Replication Sample Size: 3,903 individuals); (Region: Xp11.3; Reported Gene(s): FUNDC1; Risk Allele: rs6610953-G); (p-value= 0.000006).This variant is associated with Personality dimensions.] [GWAS:Personality dimensions]
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The G allele of SNAP25 gene SNP rs362584 was associated with increased neurotic traits (combined p value = 0.0000522) in a group of 3972 Sardinians, and two smaller replicative samples from the USA and Netherlands (the replicative samples were not significant by themselves, with the Netherlands sample showing considerably less of a trend).full paper in pdf
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[PharmGKB:Non-Curated GWAS results: Genome-wide association scan for five major dimensions of personality. (Initial Sample Size: 3,972 individuals; Replication Sample Size: 3,903 individuals); (Region: 2p22.1; Reported Gene(s): THUMPD2; Risk Allele: rs2540226-T); (p-value= 0.000003).This variant is associated with Personality dimensions.] [GWAS:Personality dimensions]
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The A allele of the CLOCK gene SNP rs6832769 was associated with lessened agreeableness (p = 0.00000871) in a group of 3972 Sardinians. The effect remained significant in the replicative American sample, but failed to achieve significance in the Norwegian sample and third sample (though the combined p value remained significant at 0.000865). full paper in pdf [PharmGKB:Non-Curated GWAS results: Genome-wide association scan for five major dimensions of personality. (Initial Sample Size: 3,972 individuals; Replication Sample Size: 3,903 individuals); (Region: 4q12; Reported Gene(s): CLOCK; Risk Allele: rs6832769-A); (p-value= 0.000002).This variant is associated with Personality dimensions.]
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[PharmGKB:Non-Curated GWAS results: Genome-wide association scan for five major dimensions of personality. (Initial Sample Size: 3,972 individuals; Replication Sample Size: 3,903 individuals); (Region: 19q13.31; Reported Gene(s): ZNF180; Risk Allele: rs644148-G); (p-value= 0.0000009).This variant is associated with Personality dimensions(openness).] [GWAS:Personality dimensions]
5 snps
(hide) SERPINA1
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finds no association between rs11832 and pulmonary emphysema
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finds no association between rs8004738 and pulmonary emphysema
Frequency: 52.7%
References:1
References:1
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finds no association between rs17751769 and pulmonary emphysema
common in clinvar
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finds no association between rs1303 and pulmonary emphysema [OMIM:PI M3] [GWAS:Metabolite levels]
common in clinvar
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finds no association between rs709932 and pulmonary emphysema [OMIM:PI M4]
common in complete genomics
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Alpha 1-antitrypsin deficiency, emphysema, and liver disease. Genetic basis and strategies for therapy. Molecular analysis of the heterogeneity among the P-family of alpha-1-antitrypsin alleles. [OMIM:?]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:5
Repute:Good
References:5
common in complete genomics
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rs28929474, also known as Glu342Lys as well as E366K, is a SNP in the serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1 SERPINA1 gene. This SNP is the one most frequently leading, when homozygous, to the complications of alpha-1 antitrypsin deficiency and the associated high risk of emphysema and liver disease. Between 1 - 2% of US Caucasians are thought to be (heterozygous) carriers for this SNP, leading some associations, like the Alpha-1 Foundation, to call for mass carrier screening. * 23andMe blog rs28929474(T) increases odds of liver disease in cystic fibrosis patients by 4.17 times. (T;T) at both copies of this SNP causes alpha-1 antitrypsin deficiency; note use of opposite strand nomenclature by this company. Genetic polymorphisms and susceptibilit...
Magnitude: 0
Repute:Good
References:2
Repute:Good
References:2
common in complete genomics
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rs28931568 is a SNP representing an amino acid change in the SERPINA1 gene, which encodes alpha-1-antitrypsin (AAT). Carriers of two rs28931568(A) alleles, i.e. homozygotes, are at high risk for emphysema based on the finding of this variant in an affected African-American family. [OMIM:PI M(MINERAL SPRINGS)]
Magnitude: 0
Repute:Good
References:3
Repute:Good
References:3
common in complete genomics
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rs28931569 is a SNP representing an amino acid change in the SERPINA1 gene, which encodes alpha-1-antitrypsin (AAT). Carriers of two rs28931569(C) alleles, i.e. homozygotes, are at high risk for emphysema . [OMIM:PI M(PROCIDA)]
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
common in complete genomics
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rs17580, also known as the S or PiS allele, is a SNP in the SERPINA1 gene. Levels of alpha-1 antitrypsin (encoded by the SERPINA1 gene) may be reduced in carriers of the rs17580(T) allele, but there is no known association with liver disease or cystic fibrosis. The rs17580 PiS variant is most associated with risk of developing COPD, especially in smokers, but it's association with emphysema is variable. See rs28929474 for the most common pathologic SNP (PiZ) in the SERPINA1 gene. Please be careful when interpreting results for this SNP as it is in dbSNP and SNPedia in minus orientation where the risk allele is T, but test results may be in the plus orientation where the risk allele is A (although currently 23andMe reports the risk allele as T). This SNP has an ambiguous flip which can make...
20 snps
(hide) Skin color
probably light-skinned, European ancestry This SNP influences skin pigmentation and indicates indicates light-skinned European ancestry. estimates that the rs1426654(A) allele (light skin pigmentation) spread through the European population around 6,000 - 12,000 years ago. Prior to that, 'European ancestors' were most likely relatively brown-skinned.
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This SNP influences skin pigmentation. The allele, A111T, rs1426654(A), indicates light-skinned european ancestry. It appears as if this SNP is a relatively new one in human evolution; one estimate is that the rs1426654(A) allele, in other words, light skin pigmentation, spread through the European population around 6,000 - 12,000 years ago. Prior to that, 'European ancestors' were most likely relatively brown-skinned. Another study () has concluded that almost individuals carrying the A111T variant can trace ancestry back to a single person who most likely lived at least 10,000 years ago. This SNP is one of three from the SLC24A5 gene that can be analyzed to categorize the ancestry of a person as either European, African, or Asian, based on a 2009 study. The 3 SNPs are: * rs1426654 * rs25...
Generally European; Light skin; Possibly an increased risk of melanoma This SNP is associated with skin, hair, and eye colour, and risk of melanoma. Individuals with the G;G genotype are generally of European descent and have fair skin. In a population-based case-control study investigating a number of pigmentation-related SNPs and their correlation with cutaneous malignant melanoma (CMM) in a Caucasian Australian population, rs16891982 (variant F374L) was found to be associated with odds ratios of 3.44, 2.86, 1.68, and 1.68 for all study subjects (1,738 CMM cases and 4,517 controls); subjects with northern European ancestry (1,438 cases and 3,098 controls); northern European subjects adjusted for hair, eye, and skin colour; and northern European subjects adjusted for the MC1R genotype, r...
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This snp influences skin pigmentation. The allele p.L374F indicates light-skinned european ancestry c.1122C>G, p.Phe374Leu (NCBI dbSNP rs16891982) in SLC45A2 was associated with protection from malignant melanoma (OR, 0.41; 95% CI, 0.24-0.70; P=0.008 after adjustment for multiple testing) An association study conducted on a population of European origin concluded that the rare (in Europeans, at least) allele L374, i.e. rs16891982(C) in dbSNP orientation, significantly increases the possibility of having black hair color, with an odds ratio of around 7. This population-based case-control study investigated a number of pigmentation-related SNPs and their correlation with cutaneous malignant melanoma (CMM) in an Australian population. rs16891982 (variant F374L) was found to be associated w...
normal
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Although the rs26722(T) alllele is relatively rare, at least statistically it seems to be associated with darker eye, hair, and skin color, all other things being equal. A genomewide association study of skin pigmentation in a South Asian population. A genome-wide association study identifies novel alleles associated with hair color and skin pigmentation. Association of the SLC45A2 gene with physiological human hair colour variation. Genome-wide association study of tanning phenotype in a population of European ancestry. Genetic variants in pigmentation genes, pigmentary phenotypes, and risk of skin cancer in Caucasians. Genetic determinants of hair and eye colours in the Scottish and Danish populations. [OMIM:PIGMENTATION OF HAIR, SKIN, AND EYES, VARIATION IN]
3 snps
(hide) SLC6A2
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T allele associated with better response to treatment of ADHD with atomoxetine.
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Trajectories of change in depression severity during treatment with antidepressants. Pharmacogenomics of antidepressant drugs.
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Sexually dimorphic effects of four genes (COMT, SLC6A2, MAOA, SLC6A4) in genetic associations of ADHD: a preliminary study.
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G allele associated with better response to treatment of ADHD with atomoxetine.
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A allele associated with better response to treatment of ADHD with atomoxetine.
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Support for association between ADHD and two candidate genes: NET1 and DRD1.
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(Associated with ADHD.)
Frequency: 72.6%
References:3
References:3
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Norepinephrine transporter and catecholamine-O-methyltransferase gene variants and attention-deficit/hyperactivity disorder symptoms in adults. Further evidence of association between two NET single-nucleotide polymorphisms with ADHD. Lack of association between response of OROS-methylphenidate and norepinephrine transporter (SLC6A2) polymorphism in Korean ADHD. Genetic influences on attention deficit hyperactivity disorder symptoms from age 2 to 3: a quantitative and molecular genetic investigation. Support for association between ADHD and two candidate genes: NET1 and DRD1.
common in complete genomics
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G allele associated with better response to treatment of ADHD with atomoxetine.
normal risk of ADHD
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T allele may be associated with Attention deficit hyperactivity disorder.
Magnitude: 0
Frequency: 98.5%
Repute:Good
References:2
Frequency: 98.5%
Repute:Good
References:2
common in complete genomics
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The data were consistent for rs11568324, suggesting the existence of a rare allele conferring protection for ADHD
normal
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rs5558 (F528C) is a non-synonymous SNP in SLC6A2 (norepinephrine transporter), with a T encoding for Phenylalanine and C encoding the rare Cysteine variant. assoc. w/ major depression Cysteine variant exhibited increased norepinephrine transport, insensitivity to protein kinase C induced down-regulation, and a decrease in desipramine (tricyclic antidepressant) potency
21 snps
(hide) Test Trails A
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non sig. gwas, hit (p = 4 x 10^-6) for Trails A performance [GWAS:Cognitive Performance]
Frequency: 43.4%
References:1
References:1
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non sig. gwas, hit (p = 4 x 10^-6) for Trails A performance [GWAS:Cognitive Performance]
Frequency: 53.6%
References:1
References:1
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non sig. gwas, hit (p = 4 x 10^-6) for Trails A performance [GWAS:Cognitive Performance]
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non sig. gwas, hit (p = 5 x 10^-7) for Trails A performance [GWAS:Cognitive Performance]
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non sig. gwas, hit (p = 4 x 10^-6) for Test Trails A performance [GWAS:Cognitive Performance]
Frequency: 79.6%
References:1
References:1
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non sig. gwas, hit (p = 3 x 10^-7) for Trails A performance [GWAS:Cognitive Performance]
Magnitude: 0
Frequency: 91.1%
Repute:Good
References:1
Frequency: 91.1%
Repute:Good
References:1
common in complete genomics
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non sig. gwas, hit (p = 7 x 10^-6) for Trails A performance [GWAS:Cognitive Performance]
7 snps
(hide) Tetrahydrobiopterin
lower risk of autism
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Examination of tetrahydrobiopterin pathway genes in autism. Examination of association to autism of common genetic variation in genes related to dopamine.
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GTP cyclohydrolase and tetrahydrobiopterin regulate pain sensitivity and persistence. T allele associated with higher tolerance to pain. Do genetic predictors of pain sensitivity associate with persistent widespread pain? T allele associated with higher pain tolerance. GCH1 haplotype determines vascular and plasma biopterin availability in coronary artery disease effects on vascular superoxide production and endothelial function. Part of a haplotype, rs10483639(C)-rs3783641(A)-rs8007267(T), associated with lower levels of tetrahydrobiopterin.
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GTP cyclohydrolase and tetrahydrobiopterin regulate pain sensitivity and persistence. C allele associated with higher tolerance to pain. Polymorphisms in the GTP cyclohydrolase gene (GCH1) are associated with ratings of capsaicin pain. C allele associated with higher tolerance to pain.
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GTP cyclohydrolase and tetrahydrobiopterin regulate pain sensitivity and persistence. T allele associated with higher tolerance to pain. Polymorphisms in the GTP cyclohydrolase gene (GCH1) are associated with ratings of capsaicin pain. T allele associated with higher tolerance to pain.
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Do genetic predictors of pain sensitivity associate with persistent widespread pain? C allele associated with higher pain tolerance. GCH1 haplotype determines vascular and plasma biopterin availability in coronary artery disease effects on vascular superoxide production and endothelial function. Part of a haplotype, rs10483639(C)-rs3783641(A)-rs8007267(T), associated with lower levels of tetrahydrobiopterin.
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GTP cyclohydrolase and tetrahydrobiopterin regulate pain sensitivity and persistence. A allele associated with higher tolerance to pain. Polymorphisms in the GTP cyclohydrolase gene (GCH1) are associated with ratings of capsaicin pain. A allele associated with higher tolerance to pain. Do genetic predictors of pain sensitivity associate with persistent widespread pain? A allele associated with higher pain tolerance. GCH1 haplotype determines vascular and plasma biopterin availability in coronary artery disease effects on vascular superoxide production and endothelial function. Part of a haplotype, rs10483639(C)-rs3783641(A)-rs8007267(T), associated with lower levels of tetrahydrobiopterin.
6 snps
(hide) Tooth Development
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Tooth Development [GWAS:None]
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Tooth Development [GWAS:None]
Frequency: 70.5%
References:1
References:1
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Rs17179670 is a SNP implicated in Tooth Development
3 snps
(hide) TPMT
common in complete genomics
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[PharmGKB:Curated Risk or phenotype-associated allele: Not specified. Phenotype: This SNP was associated with clearance of docetaxel. Study size: 31. Study population/ethnicity: Patients with Non-Small-Cell Lung Carcinoma. Significance metric(s): p = 0.1013 (ANOVA); p = 0.0159 (QMIS); p = 0.0178 (KW) Type of association: PK.]
common in clinvar
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rs1142345 is a SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The risk allele for this SNP is rs1142345(G), and when it is the only variant in the TPMT gene, it encodes the TPMT*3C allele. While still rare, it is more common in African-Americans (2.4% of all alleles) than in Caucasians. Note that if the same allele also carries the rs1800460(A) SNP, the allele is actually a TPMT*3A allele (OMIM). The medicine 6-Mercaptopurine is metabolized by TPMT. Individual differences in TPMT activity associated with this SNP are now used to determine appropriate dosage range and interval for treatment. 23an...
common in complete genomics
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rs1800584 is a rare SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The rs1800584(A) SNP defines the TPMT*4A allele (OMIM). wikipedia thiopurine drugs metabolized by TPMT include azathioprine, mercaptopurine, and thioguanine [PharmGKB:In-Depth This splicing variant results in very low TPMT activity and risk for hematologic toxicity as a result of treatment with thiopurines.]
normal
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rs1800460 is a SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The risk allele for this SNP is rs1800460(A), and when it is the only variation in the TPMT gene, it encodes the TPMT*3B allele. While still rare, it is more common in Caucasians (4.5% of all alleles) than in African-Americans (0.8%). Note that if the same allele also carries the rs1142345(G) SNP, the allele is actually a TPMT*3A allele (OMIM). The medicine 6-Mercaptopurine is metabolized by TPMT. Individual differences in TPMT activity associated with this SNP are now used to determine appropriate dosage range and interval for treatm...
normal for 23andMe appears common for 23andMe users
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rs1800462, also known as A80P, is a rare SNP in the TPMT gene, potentially encoding a variant incapable of detoxifying byproducts of certain antineoplastic and immunosuppressant drugs. In general, individuals must have two nonfunctioning TPMT alleles for the toxicity to be pronounced. The risk allele for this SNP (in orientation to the dbSNP entry) is rs1800462(C), and it encodes the TPMT*2 allele. It may occur at a frequency of 1 in 200 alleles among Caucasians. wikipedia thiopurine drugs metabolized by TPMT include azathioprine, mercaptopurine, and thioguanine [PharmGKB:In-Depth The TPMT:238G>C SNP was cloned from a patient with severe mercaptopurine toxicity. It results in a non-synonymous protein change TPMT:Ala80Pro that has a 100-fold reduction in catalytic activity compared to w...
5 snps
(hide) Triglycerides
lower HDL cholesterol
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The (A) allele of rs326 was associated with risk for lower high-density lipoprotein (HDL) cholesterol plasma levels in 3 independent population samples, including both Caucasians and African-Americans. [PharmGKB:Curated This SNP has been associated with small changes in HDL cholesterol levels. The A allele has been correlated with lower HDL.] [OMIM:LIPOPROTEIN LIPASE; LPL] [GWAS:Triglycerides]
slightly higher risk for gout
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The T allele of rs1260326 has been associated with type 2 diabetes and hypertriglyceridemia. A fine mapping approach indicates that this SNP, rs1260326, shows the strongest association signal with metabolic phenotypes in the region that also harbors the tightly linked (r(2)=0.93) SNP rs780094, which has been previously associated with triglyceride and glucose concentrations. This SNP, rs1260326, encodes a common missense glucokinase regulatory protein gene GCKR variant. gout association, based on Loci related to metabolic-syndrome pathways including LEPR,HNF1A, IL6R, and GCKR associate with plasma C-reactive protein: the Women's Genome Health Study. Polymorphisms of the HNF1A gene encoding hepatocyte nuclear factor-1 alpha are associated with C-reactive protein. The common P446L polymorphi...
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[GWAS:Triglycerides]
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gwas among adults residing on Korcula Island in Croatia, triglycerides, the G allele associated with decreased triglyceride levels<br><br> [PharmGKB:Non-Curated GWAS results: Genome-wide association study of biochemical traits in Korcula Island, Croatia. (Initial Sample Size: 898 individuals; Replication Sample Size: NR); (Region: Xq23; Reported Gene(s): ZCCHC16; Risk Allele: rs5982533-G); (p-value= 0.000007).This variant is associated with Biochemical measures.] [GWAS:Biochemical measures]
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per the 23andMe blog, the minor allele of this SNP (T) was associated with decreased triglycerides {| border='1' |- !SNP !Rarer allele !LDL !HDL !TG |- | rs6544713 || T || + || || |- | rs2650000 || A || + || || |- | rs471364 || C || || - || |- | rs1800961 || T || || - || |- | rs7679 || C || || - || + |- | rs2967605 || T || || - || |- | rs2409722 || T || || || - |- | rs10903129 || A || - || - || - |- | rs6756629 || A || - || + || - |- | rs12670798 || C || + || + || + |- | rs7395662 || A || - || + || + |- | rs174570 || T || - || - || + |- | rs2271293 || A || - || + || - |- | rs2624265 || C || || || + |- | rs2167079 || T || || + || |- | rs9891572 || T || || + || |- | rs4844614 || T || + || || |- | rs5031002 || G || + || || |- |}
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The effect of a novel intergenic polymorphism (rs11774572) on HDL-cholesterol concentrations depends on TaqIB polymorphism in the cholesterol ester transfer protein gene. Forty-three loci associated with plasma lipoprotein size, concentration, and cholesterol content in genome-wide analysis. Investigation of variants identified in caucasian genome-wide association studies for plasma high-density lipoprotein cholesterol and triglycerides levels in Mexican dyslipidemic study samples. Two new Loci for body-weight regulation identified in a joint analysis of genome-wide association studies for early-onset extreme obesity in French and german study groups. [PharmGKB:Non-Curated GWAS results: Common variants at 30 loci contribute to polygenic dyslipidemia. (Initial Sample Size: 19,840 individua...
Frequency: 27.4%
References:6
References:6
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per the 23andMe blog, the minor allele of this SNP (A) was associated with decreased cholesterol and triglycerides {| border='1' |- !SNP !Rarer allele !LDL !HDL !TG |- | rs6544713 || T || + || || |- | rs2650000 || A || + || || |- | rs471364 || C || || - || |- | rs1800961 || T || || - || |- | rs7679 || C || || - || + |- | rs2967605 || T || || - || |- | rs2409722 || T || || || - |- | rs10903129 || A || - || - || - |- | rs6756629 || A || - || + || - |- | rs12670798 || C || + || + || + |- | rs7395662 || A || - || + || + |- | rs174570 || T || - || - || + |- | rs2271293 || A || - || + || - |- | rs2624265 || C || || || + |- | rs2167079 || T || || + || |- | rs9891572 || T || || + || |- | rs4844614 || T || + || || |- | rs5031002 || G || + || || |- |} [PharmGKB:Non-Curated GWAS results: Loci influe...
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[GWAS:None]
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[GWAS:Triglycerides]
Frequency: 31.0%
References:21
References:21
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rs17321515 influences severe hypertriglyceridemia. 132 patients of European ancestry with severe HTG (fasting plasma TG>10 mmol/L), and 351 matched normolipidemic controls [PharmGKB:Non-Curated GWAS Results: Newly identified loci that influence lipid concentrations and risk of coronary artery disease (Initial Sample Size: 8,684 individuals; Replication Sample Size: 5,312-9,707 individuals; Risk Allele: rs17321515-A). This variant is associated with triglyceride levels.] [GWAS:Triglycerides] [GWAS:Triglycerides]
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[PharmGKB:Non-Curated GWAS results: Common variants at 30 loci contribute to polygenic dyslipidemia. (Initial Sample Size: 19,840 individuals; Replication Sample Size: Up to 20,623 individuals); (Region: 2p24.1; Reported Gene(s): APOB; Risk Allele: rs7557067-G); (p-value= 0.000000000009).This variant is associated with Triglycerides.] [GWAS:Triglycerides]
Frequency: 33.6%
References:7
References:7
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per the 23andMe blog, the minor allele of this SNP (C) was associated with increased cholesterol and triglycerides {| border='1' |- !SNP !Rarer allele !LDL !HDL !TG |- | rs6544713 || T || + || || |- | rs2650000 || A || + || || |- | rs471364 || C || || - || |- | rs1800961 || T || || - || |- | rs7679 || C || || - || + |- | rs2967605 || T || || - || |- | rs2409722 || T || || || - |- | rs10903129 || A || - || - || - |- | rs6756629 || A || - || + || - |- | rs12670798 || C || + || + || + |- | rs7395662 || A || - || + || + |- | rs174570 || T || - || - || + |- | rs2271293 || A || - || + || - |- | rs2624265 || C || || || + |- | rs2167079 || T || || + || |- | rs9891572 || T || || + || |- | rs4844614 || T || + || || |- | rs5031002 || G || + || || |- |} [PharmGKB:Non-Curated GWAS results: Loci influe...
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per the 23andMe blog, the minor allele of this SNP (C) was associated with increased triglycerides {| border='1' |- !SNP !Rarer allele !LDL !HDL !TG |- | rs6544713 || T || + || || |- | rs2650000 || A || + || || |- | rs471364 || C || || - || |- | rs1800961 || T || || - || |- | rs7679 || C || || - || + |- | rs2967605 || T || || - || |- | rs2409722 || T || || || - |- | rs10903129 || A || - || - || - |- | rs6756629 || A || - || + || - |- | rs12670798 || C || + || + || + |- | rs7395662 || A || - || + || + |- | rs174570 || T || - || - || + |- | rs2271293 || A || - || + || - |- | rs2624265 || C || || || + |- | rs2167079 || T || || + || |- | rs9891572 || T || || + || |- | rs4844614 || T || + || || |- | rs5031002 || G || + || || |- |} [PharmGKB:Non-Curated GWAS results: Genome-wide association ana...
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This appears to be the snp on the Illumina Human 550 which is closest to rs4420638 [PharmGKB:Non-Curated GWAS results: Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. (Initial Sample Size: 17,815 individuals; Replication Sample Size: NR); (Region: 19q13.32; Reported Gene(s): TOMM40, APOE; Risk Allele: rs439401-G); (p-value= 0.000000002).This variant is associated with Triglycerides.] [GWAS:Triglycerides]
Frequency: 46.0%
References:8
References:8
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Genetic loci associated with plasma concentration of low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, triglycerides, apolipoprotein A1, and Apolipoprotein B among 6382 white women in genome-wide analysis with replication. Investigation of variants identified in caucasian genome-wide association studies for plasma high-density lipoprotein cholesterol and triglycerides levels in Mexican dyslipidemic study samples. Genetics and beyond--the transcriptome of human monocytes and disease susceptibility. Exploring genetic determinants of plasma total cholesterol levels and their predictive value in a longitudinal study. Genome-wide association study of coronary heart disease and its risk factors in 8,090 African Americans: the NHLBI CARe Project. [PharmGKB:Non-Curated GW...
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[PharmGKB:Non-Curated GWAS results: Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. (Initial Sample Size: 17,815 individuals; Replication Sample Size: NR); (Region: 1p31.3; Reported Gene(s): DOCK7; Risk Allele: rs1167998-C); (p-value= 0.000000000002).This variant is associated with Triglycerides.] [GWAS:Triglycerides]
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[PharmGKB:Non-Curated GWAS Results: Newly identified loci that influence lipid concentrations and risk of coronary artery disease (Initial Sample Size: 8,684 individuals; Replication Sample Size: 5,312-9,707 individuals; Risk Allele: rs1748195-C). This variant is associated with triglyceride levels.] [GWAS:Triglycerides]
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per the 23andMe blog, the minor allele of this SNP (A) was associated with decreased LDL cholesterol, increased HDL cholesterol and increased triglycerides {| border='1' |- !SNP !Rarer allele !LDL !HDL !TG |- | rs6544713 || T || + || || |- | rs2650000 || A || + || || |- | rs471364 || C || || - || |- | rs1800961 || T || || - || |- | rs7679 || C || || - || + |- | rs2967605 || T || || - || |- | rs2409722 || T || || || - |- | rs10903129 || A || - || - || - |- | rs6756629 || A || - || + || - |- | rs12670798 || C || + || + || + |- | rs7395662 || A || - || + || + |- | rs174570 || T || - || - || + |- | rs2271293 || A || - || + || - |- | rs2624265 || C || || || + |- | rs2167079 || T || || + || |- | rs9891572 || T || || + || |- | rs4844614 || T || + || || |- | rs5031002 || G || + || || |- |} [Pharm...
metabolic consequences
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rs780094, a SNP in the GCKR gene encoding the glucokinase regulatory protein, contributes to the risk of type-2 diabetes and dyslipidaemia in mulitple populations. The effect on type 2 diabetes is probably mediated through impaired beta cell function rather than through obesity. The rs780094(A) risk allele is associated with the following traits : * higher levels of fasting serum triacylglycerol * impaired fasting and OGTT-related insulin release * dyslipidemia * somewhat reduced risk of type-2 diabetes There may also be an additive effect between this SNP and a SNP known as 'GCK -30A', rs1799884, at least on fasting serum insulin levels. rs780094 influences severe hypertriglyceridemia. 132 patients of European ancestry with severe HTG (fasting plasma TG>10 mmol/L), and 351 matched norm...
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[GWAS:None]
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The hepatocyte growth factor receptor (MET) gene is not associated with refractive error and ocular biometrics in a Caucasian population. [GWAS:Triglycerides]
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The G allele of rs4846914 is associated with higher risk of hypertriglyceridemia. ] [PharmGKB:Non-Curated GWAS results: Common variants at 30 loci contribute to polygenic dyslipidemia. (Initial Sample Size: 19,840 individuals; Replication Sample Size: Up to 20,623 individuals); (Region: 1q42.13; Reported Gene(s): GALNT2; Risk Allele: rs4846914-G); (p-value= 0.00000004).This variant is associated with HDL cholesterol.] [GWAS:HDL cholesterol] [GWAS:Triglycerides]
Frequency: 57.5%
References:2
References:2
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gwas among adults residing on Korcula Island in Croatia, triglycerides, the A allele associated with decreased triglyceride levels<br><br> A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study. [PharmGKB:Non-Curated GWAS results: Genome-wide association study of biochemical traits in Korcula Island, Croatia. (Initial Sample Size: 898 individuals; Replication Sample Size: NR); (Region: 4q23; Reported Gene(s): RAP1GDS1; Risk Allele: rs10516430-A); (p-value= 0.000006).This variant is associated with Biochemical measures.] [GWAS:Biochemical measures]
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[GWAS:Triglycerides]
Frequency: 61.6%
References:5
References:5
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Polygenic determinants of severe hypertriglyceridemia. Genome-wide association analysis of metabolic traits in a birth cohort from a founder population. Genome-wide association studies in an isolated founder population from the Pacific Island of Kosrae. Genetic loci associated with plasma concentration of low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, triglycerides, apolipoprotein A1, and Apolipoprotein B among 6382 white women in genome-wide analysis with replication. Triglyceride level-influencing functional variants of the ANGPTL3, CILP2, and TRIB1 loci in ischemic stroke. [PharmGKB:Non-Curated GWAS Results: Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans (Initial Sample ...
Frequency: 75.2%
References:12
References:12
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[PharmGKB:Non-Curated GWAS results: Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. (Initial Sample Size: 17,815 individuals; Replication Sample Size: NR); (Region: 8p21.3; Reported Gene(s): LPL; Risk Allele: rs10096633-G); (p-value= 0.000000000000000002).This variant is associated with Triglycerides.] [OMIM:LIPOPROTEIN LIPASE; LPL] [GWAS:Triglycerides]
Frequency: 76.1%
References:4
References:4
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[GWAS:Triglycerides]
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[GWAS:Triglycerides]
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gwas among adults residing on Korcula Island in Croatia, triglycerides, the A allele associated with decreased triglyceride levels<br><br> [PharmGKB:Non-Curated GWAS results: Genome-wide association study of biochemical traits in Korcula Island, Croatia. (Initial Sample Size: 898 individuals; Replication Sample Size: NR); (Region: 4q12; Reported Gene(s): USP46; Risk Allele: rs346923-A); (p-value= 0.000002).This variant is associated with Biochemical measures.] [GWAS:Biochemical measures]
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[GWAS:Triglycerides]
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[GWAS:None]
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[GWAS:Triglycerides]
common on affy axiom data
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per the 23andMe blog, the minor allele of this SNP (C) was associated with decreased HDL cholesterol and increased triglycerides {| border='1' |- !SNP !Rarer allele !LDL !HDL !TG |- | rs6544713 || T || + || || |- | rs2650000 || A || + || || |- | rs471364 || C || || - || |- | rs1800961 || T || || - || |- | rs7679 || C || || - || + |- | rs2967605 || T || || - || |- | rs2409722 || T || || || - |- | rs10903129 || A || - || - || - |- | rs6756629 || A || - || + || - |- | rs12670798 || C || + || + || + |- | rs7395662 || A || - || + || + |- | rs174570 || T || - || - || + |- | rs2271293 || A || - || + || - |- | rs2624265 || C || || || + |- | rs2167079 || T || || + || |- | rs9891572 || T || || + || |- | rs4844614 || T || + || || |- | rs5031002 || G || + || || |- |} [PharmGKB:Non-Curated GWAS result...
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per the 23andMe blog, the minor allele of this SNP (T) was associated with decreased cholesterol and increased triglycerides {| border='1' |- !SNP !Rarer allele !LDL !HDL !TG |- | rs6544713 || T || + || || |- | rs2650000 || A || + || || |- | rs471364 || C || || - || |- | rs1800961 || T || || - || |- | rs7679 || C || || - || + |- | rs2967605 || T || || - || |- | rs2409722 || T || || || - |- | rs10903129 || A || - || - || - |- | rs6756629 || A || - || + || - |- | rs12670798 || C || + || + || + |- | rs7395662 || A || - || + || + |- | rs174570 || T || - || - || + |- | rs2271293 || A || - || + || - |- | rs2624265 || C || || || + |- | rs2167079 || T || || + || |- | rs9891572 || T || || + || |- | rs4844614 || T || + || || |- | rs5031002 || G || + || || |- |} rs7115739 and rs174570 http://www.scie...
common on affy axiom data
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Common variation in the beta-carotene 15,15'-monooxygenase 1 gene affects circulating levels of carotenoids: a genome-wide association study. Common lipid-altering gene variants are associated with therapeutic intervention thresholds of lipid levels in older people. Genetics and beyond--the transcriptome of human monocytes and disease susceptibility. [PharmGKB:Non-Curated GWAS results: Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. (Initial Sample Size: 17,815 individuals; Replication Sample Size: NR); (Region: 7q11.23; Reported Gene(s): MLXIPL; Risk Allele: rs2240466-G); (p-value= 0.000000000001).This variant is associated with Triglycerides.] [GWAS:Triglycerides]
Magnitude: 0
Frequency: 77.9%
Repute:Good
References:18
Frequency: 77.9%
Repute:Good
References:18
common on affy axiom data
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rs17145738 influences severe hypertriglyceridemia. 132 patients of European ancestry with severe HTG (fasting plasma TG>10 mmol/L), and 351 matched normolipidemic controls [PharmGKB:Non-Curated GWAS Results: Newly identified loci that influence lipid concentrations and risk of coronary artery disease (Initial Sample Size: 8,684 individuals; Replication Sample Size: 5,312-9,707 individuals; Risk Allele: rs17145738-C). This variant is associated with triglyceride levels.] [GWAS:Triglycerides] [GWAS:Triglycerides]
Magnitude: 0
Frequency: 82.0%
Repute:Good
References:18
Frequency: 82.0%
Repute:Good
References:18
common in complete genomics
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[PharmGKB:Non-Curated GWAS Results: Newly identified loci that influence lipid concentrations and risk of coronary artery disease (Initial Sample Size: 8,589 individuals; Replication Sample Size: 7,440-10,783 individuals; Risk Allele: rs16996148-G). This variant is associated with LDL cholesterol levels.] [GWAS:LDL cholesterol] [GWAS:Triglycerides]
common on affy axiom data
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per the 23andMe blog, the minor allele of this SNP (A) was associated with decreased LDL cholesterol, increased HDL, and decreased triglycerides {| border='1' |- !SNP !Rarer allele !LDL !HDL !TG |- | rs6544713 || T || + || || |- | rs2650000 || A || + || || |- | rs471364 || C || || - || |- | rs1800961 || T || || - || |- | rs7679 || C || || - || + |- | rs2967605 || T || || - || |- | rs2409722 || T || || || - |- | rs10903129 || A || - || - || - |- | rs6756629 || A || - || + || - |- | rs12670798 || C || + || + || + |- | rs7395662 || A || - || + || + |- | rs174570 || T || - || - || + |- | rs2271293 || A || - || + || - |- | rs2624265 || C || || || + |- | rs2167079 || T || || + || |- | rs9891572 || T || || + || |- | rs4844614 || T || + || || |- | rs5031002 || G || + || || |- |} [PharmGKB:Non-Cur...
Magnitude: 0
Frequency: 86.2%
Repute:Good
References:2
Frequency: 86.2%
Repute:Good
References:2
common in complete genomics
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[PharmGKB:Non-Curated GWAS results: Common variants at 30 loci contribute to polygenic dyslipidemia. (Initial Sample Size: 19,840 individuals; Replication Sample Size: Up to 20,623 individuals); (Region: 19p13.11; Reported Gene(s): NCAN,CILP2,PBX4; Risk Allele: rs17216525-T); (p-value= 0.00000000004).This variant is associated with Triglycerides.] [GWAS:Triglycerides]
common on affy axiom data
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[PharmGKB:Non-Curated GWAS Results: Genome-wide scan identifies variation in MLXIPL associated with plasma triglycerides (Initial Sample Size: 2,011 individuals; Replication Sample Size: 10,536 individuals; Risk Allele: rs1558861-A).] [GWAS:None] [GWAS:Triglycerides]
Magnitude: 0
Frequency: 92.0%
Repute:Good
References:7
Frequency: 92.0%
Repute:Good
References:7
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[GWAS:Triglycerides]
Magnitude: 0
Frequency: 93.8%
Repute:Good
References:5
Frequency: 93.8%
Repute:Good
References:5
common in complete genomics
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[PharmGKB:Curated GWAS results: A null mutation in human APOC3 confers a favorable plasma lipid profile and apparent cardioprotection. (Initial Sample Size: 809 individuals; Replication Sample Size: 698 individuals); (Region: 11q23.3; Reported Gene(s): APOA1, APOC3, APOA4, APOA5, DSCAML1; Risk Allele: rs10892151-A); (p-value= 3E-29).This variant is associated with Triglycerides.] [OMIM:APOLIPOPROTEIN C-III; APOC3] [GWAS:Triglycerides]
Magnitude: 0
Frequency: 100.0%
Repute:Good
References:2
Frequency: 100.0%
Repute:Good
References:2
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[GWAS:Triglycerides]
common in clinvar
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[PharmGKB:Curated Phenotype: In a GWAS, this SNP was significantly associated with plasma concentrations of triglycerides. Study size:6382. Study population/ethnicity: Caucasian women. Significance metric(s): P = 4.7 x 10(-11). Type of association: CO; GN] [OMIM:LIPOPROTEIN LIPASE; LPL] [GWAS:HDL cholesterol]
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The rs964184(G;G) genotype is associated with hypertriglyceridemia. [PharmGKB:Non-Curated GWAS results: Common variants at 30 loci contribute to polygenic dyslipidemia. (Initial Sample Size: 19,840 individuals; Replication Sample Size: Up to 20,623 individuals); (Region: 11q23.3; Reported Gene(s): APOA1, APOC3, APOA4, APOA5; Risk Allele: rs964184-G); (p-value= 0.000000000001).This variant is associated with HDL cholesterol.] [GWAS:HDL cholesterol]
common on affy axiom data
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rs3812316, a SNP in the MLXIPL gene that is also known as G771C or Gln241His, has been observed in a study of over 10,000 individuals of different ethnicities to be very significantly associated (p=1.4x10e-10) with plasma triglyceride levels. [PharmGKB:Non-Curated GWAS Results: Genome-wide scan identifies variation in MLXIPL associated with plasma triglycerides (Initial Sample Size: 2,011 individuals; Replication Sample Size: 10,536 individuals; Risk Allele: rs3812316-C).] [GWAS:Triglycerides]
47 snps
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reduced risk (0.59x) of pancreatic cancer
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23andMe reports that the G allele of this SNP appears to lower the risk of pancreatic cancer. Genome-wide association study of pancreatic cancer in Japanese population. [OMIM:?] [GWAS:Pancreatic cancer]
1.33x increased risk of Ulcerative Colitis, but much lower Type 1 Diabetes risk. This raises the risk of Ulcerative Colitis (according to 23andMe), but also greatly lowers the risk of Type 1 Diabetes. It may also affect other autoimmune diseases.
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A genome-wide association study using DNA samples from 1,052 individuals with ulcerative colitis and preexisting data from 2,571 controls, all of European ancestry, concluded that this SNP and several others were associated with altered risk for the disease. [PharmGKB:Non-Curated GWAS results: Ulcerative colitis-risk loci on chromosomes 1p36 and 12q15 found by genome-wide association study. (Initial Sample Size: 1,022 cases, 2,503 controls; Replication Sample Size: 1,387 cases, 1,115 controls); (Region: 6p21.32; Reported Gene(s): BTNL2, HLA-DRA, HLA-DRB5, HLA-DRB1, HLA-DQA1, HLA-DQB1; Risk Allele: rs2395185-?); (p-value= 0.0000000000000001).This variant is associated with Ulcerative colitis.] [OMIM:?] [GWAS:Ulcerative colitis]
Magnitude: 2
Frequency: 53.1%
Repute:Good
References:14
Frequency: 53.1%
Repute:Good
References:14
slightly increased prostate cancer risk
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shows a significantly stronger association with more aggressive forms of prostate cancer (odds ratios (OR) = 1.15; P = 7.7 x 10(-9)). [PharmGKB:Curated GWAS Results: Common sequence variants on 2p15 and Xp11.22 confer susceptibility to prostate cancer (Initial Sample Size: 1,854 cases, 21,372 controls; Replication Sample Size: 8,239 cases, 7,590 controls; Risk Allele: rs721048-A).] [OMIM:EH DOMAIN-BINDING PROTEIN 1; EHBP1] [GWAS:Prostate cancer]
Normal (slightly higher) risk of Basal Cell Carcinoma. Normal risk of this kind of skin cancer.
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2 SNPs located in different regions of chromosome 1 are likely to be associated with increased risk for basal cell carcinoma (BCC), the most common form of skin cancer. *each A at rs7538876 yields a 1.28x increased risk of developing BCC (p = 4.4 x 10e-12) *each G at rs801114 also yields a 1.28x increased odds of developing BCC (p = 5.9 x 10e-12) *2.68x increased risk of BCC for homozygous carriers of both SNPs This study was based on an analysis of ~2,000 Icelandic and Eastern European skin cancer patients (as well as a large number of controls). The authors estimate that approximately 1.6% of all individuals of European ancestry are homozygous for both risk alleles, and thus that percentage of the population is at 2.68x higher risk for BCC compared to individuals who are rs7538876(G;G) a...
Normal risk of Basal Cell Carcinoma. Normal risk for this kind of skin cancer.
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2 SNPs located in different regions of chromosome 1 are likely to be associated with increased risk for basal cell carcinoma (BCC), the most common form of skin cancer. *each A at rs7538876 yields a 1.28x increased risk of developing BCC (p = 4.4 x 10e-12) *each G at rs801114 also yields a 1.28x increased odds of developing BCC (p = 5.9 x 10e-12) *2.68x increased risk of BCC for homozygous carriers of both SNPs This study was based on an analysis of ~2,000 Icelandic and Eastern European skin cancer patients (as well as a large number of controls). The authors estimate that approximately 1.6% of all individuals of European ancestry are homozygous for both risk alleles, and thus that percentage of the population is at 2.68x higher risk for BCC compared to individuals who are rs7538876(G;G) a...
1.6x higher risk for glioma development
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23andMe blog rs2736100 C 1.27 Glioma Lung cancer susceptibility locus at 5p15.33. Common genetic variants on 5p15.33 contribute to risk of lung adenocarcinoma in a Chinese population. Variants in the CDKN2B and RTEL1 regions are associated with high-grade glioma susceptibility. Deciphering the impact of common genetic variation on lung cancer risk: a genome-wide association study. Role of 5p15.33 (TERT-CLPTM1L), 6p21.33 and 15q25.1 (CHRNA5-CHRNA3) variation and lung cancer risk in never-smokers. Individuals susceptible to lung adenocarcinoma defined by combined HLA-DQA1 and TERT genotypes. New insights into susceptibility to glioma. Replication of lung cancer susceptibility loci at chromosomes 15q25, 5p15, and 6p21: a pooled analysis from the International Lung Cancer Consortium. Evaluatio...
~1.5x increased risk for chronic lymphocytic leukemia
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rs872071 is a SNP associated with the interferon regulatory factor 4 IRF4 gene. In a GWAS study including over 1,500 Caucasian patients with chronic lymphocytic leukemia (CLL), the rs872071(G) allele showed the strongest association (p = 1.91 x 10e-20) of all SNPs studied. The reported odds ratio was 1.54. See also: 23andMe blog A subsequent study () has found a similar association extending to another 800+ Spanish and Swedish CLL patients. rs872071 was also seen to be associated with CLL in Hong Kong Chinese (71 patients), with a reported odds ratio of 1.78 (CI: 1.25-2.53). A related hematologic malignancy, Hodgkin's lymphoma, may also be influenced by rs872071. Two case-control series totalling 529 and 2192 patients found an odds ratio of 1.21 (CI: 1.05-1.39, p = 0.009). [PharmGKB:Non-C...
Normal risk of developing bladder cancer. This is the normal risk of bladder cancer, particularly in Europeans and in people who already have tumors with low risk of progression.
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rs710521 is a SNP located in chromosome region 3q38, near the TP63 gene. A study ultimately totaling over 4,000 bladder cancer patients of European ancestry (and 40,000 controls) concluded that individuals carrying two copies of rs710521(A) were at 1.4x increased risk (allele-specific odds ratio = 1.19, p = 1 x 10e-7) for the disease. An additional 1,425 bladder cancer patients, supplemented by a meta-analysis of 5,695 additional cases (and 40,000+ controls), did replicate a (somewhat) increased risk associated with the rs710521(A) allele. The overall odds ratio was 1.18 (OR: 1.12 - 1.25, p < 0.0001). Another study in Chinese populations did not find an increased risk of bladder cancer for this SNP. [PharmGKB:Non-Curated GWAS Results: Sequence variant on 8q24 confers susceptibility to ...
Very slightly higher risk for breast cancer
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rs889312 is a SNP near the MAP3K1 gene. rs889312 was one of the four strongest associating SNPs found in a genome-wide association study of over 4,000 breast cancer samples. . From a DeCode user report, it appears that the risk allele is C; this A;A individual reportedly has 0.93x risk of breast cancer. In a study of 1,267 breast cancer patients, rs889312 heterozygotes and minor allele homozygotes were less likely to be lymph node positive at breast cancer diagnosis (P = 0.044) relative to major allele homozygote carriers. A meta-analysis including 26,015 cases and 33,962 controls concludes that the rs889312(C) allele is clearly a significant - but quite weak - contributor to increased risk for breast cancer. breast cancer *rs2981582, rs3803662, and rs889312) showed weak but significant as...
Frequency: 6.2%
References:18
References:18
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[GWAS:None]
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23andMe reports that rs7579899(A,A) homozygotes are 1.15 times more likely, and (G,G) homozygotes 1.15 times less likely, than (A,G) heterozygotes to develop renal cell carcinoma (a form of kidney cancer). [GWAS:None]
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Detection, imputation, and association analysis of small deletions and null alleles on oligonucleotide arrays. Identification of genes with allelic imbalance on 6p associated with nasopharyngeal carcinoma in southern Chinese. [OMIM:?] [GWAS:Nasopharyngeal Carcinoma]
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Detection, imputation, and association analysis of small deletions and null alleles on oligonucleotide arrays. [OMIM:?] [GWAS:Nasopharyngeal carcinoma]
Frequency: 19.5%
References:4
References:4
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Genetic variant in TP63 on locus 3q28 is associated with risk of lung adenocarcinoma among never-smoking females in Asia. [GWAS:Lung adenocarcinoma]
normal
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rs401681 is a SNP in the CLPTM1-like CLPTM1 gene. The following studies span several types of cancer, and over 30,000 cases and 45,000 controls. deCODE press release reports rs401681 linked to basal cell carcinoma and many cancers for individuals with shorter telomeres, whereas those with long telomeres are at greater risk of melanoma. Neighboring rs2736098 also increases risk of cancer by affecting telomerase reverse transcriptase. The risk of these different cancers conferred by these two SNPs appears to be independent. 23andMe blog rs2736098 and rs401681 linked to many cancers, including susceptibility to pancreatic cancer However, a very large study (encompassing thousands of cases and controls) found no association between rs401681 and either (1) mean telomere length, or, (2) breast c...
Frequency: 20.5%
References:4
References:4
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[GWAS:Follicular lymphoma]
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[GWAS:None]
Frequency: 26.8%
References:1
References:1
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[GWAS:Prostate cancer]
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[OMIM:?] [GWAS:Nasopharyngeal carcinoma]
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[OMIM:?] [GWAS:Testicular germ cell cancer]
Frequency: 30.1%
References:2
References:2
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[GWAS:Prostate cancer]
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23andMe blog each rs4624820(A) increases the odds of testicular cancer by 1.37x [OMIM:?] [GWAS:Testicular germ cell tumor]
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[GWAS:None]
Frequency: 35.4%
References:4
References:4
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[OMIM:?]
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Nasopharyngeal Cancer [OMIM:?] [GWAS:Nasopharyngeal Carcinoma]
Frequency: 36.3%
References:2
References:2
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[GWAS:None]
Frequency: 36.9%
References:9
References:9
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23andMe blog chronic lymphocytic leukemia *rs13397985 G 1.41 [PharmGKB:Non-Curated GWAS Results: A genome-wide association study identifies six susceptibility loci for chronic lymphocytic leukemia (Initial Sample Size: 505 cases, 1,438 controls; Replication Sample Size: 1,024 cases, 1,677 controls; Risk Allele: rs13397985-G). This variant is associated with Chronic lymphocytic leukemia.] [GWAS:None] [GWAS:Chronic lymphocytic leukemia]
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[GWAS:None]
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[GWAS:Glioma]
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[GWAS:Hodgkin's lymphoma]
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[GWAS:None]
Frequency: 40.7%
References:4
References:4
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[GWAS:Prostate cancer]
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[OMIM:?] [GWAS:Nasopharyngeal Carcinoma]
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[GWAS:None]
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[GWAS:Alopecia areata]
Frequency: 45.1%
References:2
References:2
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[GWAS:None]
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[PharmGKB:Non-Curated GWAS results: Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size. (Initial Sample Size: 12,611 individuals; Replication Sample Size: 7,187 individuals); (Region: 3q23; Reported Gene(s): ZBTB38); (p-value= 0.000000000003).This variant is associated with Height.] [OMIM:STATURE QUANTITATIVE TRAIT LOCUS 10; STQTL10] [GWAS:Height] [GWAS:Height]
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news the presence of the G allele was protective against follicular lymphoma, while the presence of the A allele was predictive of an increased risk of developing follicular lymphoma. Dr. Brown said individuals who had the A variant were nearly twice as likely to develop follicular lymphoma. 23andMe blog coverage [OMIM:?] [GWAS:Follicular lymphoma]
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rs4415084 and rs10941679 confer risk for estrogen receptor breast cancer (ER)-positive tumors (OR = 1.27, P = 2.5E-12 for rs10941679) based on a study of 6,145 cases. From a DeCode user report, the risk allele appears to be T; this T;T individual reportedly has a 1.19x increased risk of breast cancer. the two risk SNPs reported in the European population were neither associated with breast cancer risk in our Chinese population A multistage genome-wide association study in breast cancer identifies two new risk alleles at 1p11.2 and 14q24.1 (RAD51L1). Leveraging genetic variability across populations for the identification of causal variants. [PharmGKB:Curated This variant is associated with risk for estrogen receptor (ER)-positive breast cancer.] [OMIM:BREAST CANCER] [GWAS:None]
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Hodgkin lymphoma [GWAS:Hodgkin's lymphoma]
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[OMIM:?] [GWAS:Nasopharyngeal carcinoma]
possible increased risk for neuroblastoma
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SNPs clustered in one region of chromosome 6p22 have been linked to increased risk for the exceedingly rare childhood cancer known as neuroblastoma. A study involving 720 patients determined that rs4712653(C;C) genotypes had increased likelihood of neuroblastoma development (odds ratio 1.96, CI: 1.57 to 2.43, p=7 x 10<sup>-8</sup>). At-risk homozygotes diagnosed with neuroblastoma had, on average, more malignant clinical presentation, more aggressive disease, and poorer long-term survival. For more information on this cluster of SNPs, see rs6939340. Common variations in BARD1 influence susceptibility to high-risk neuroblastoma. [OMIM:NEUROBLASTOMA] [GWAS:None]
Frequency: 51.8%
References:9
References:9
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[GWAS:None]
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[GWAS:None]
possible increased risk for neuroblastoma
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SNPs clustered in one region of chromosome 6p22 have been linked to increased risk for the exceedingly rare childhood cancer known as neuroblastoma. A study involving 720 patients determined that rs6939340(G;G) genotypes had increased likelihood of neuroblastoma development (odds ratio 1.97, CI: 1.58 to 2.45, p=9.3 x 10<sup>-15</sup>). At-risk homozygotes diagnosed with neuroblastoma had, on average, more malignant clinical presentation, more aggressive disease, and poorer long-term survival. Presumably driven primarily by the at-risk homozygotes, the rs6939340(G) allele was considered to be a risk factor, however, there was insufficient data to conclude whether rs6939340(A;G) heterozygotes were actually at any increased risk compared to rs6939340(A;A) 'wild-type' homozygotes. ...
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[GWAS:Prostate cancer]
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[GWAS:None]
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[GWAS:Serum total protein level]
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[GWAS:None]
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[OMIM:?] [GWAS:Breast cancer]
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The T allele at rs798766 is associated with 1.24 higher odds of bladder cancer. [OMIM:?] [GWAS:Urinary bladder cancer]
Frequency: 64.2%
References:5
References:5
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23andMe blog chronic lymphocytic leukemia *rs17483466 G 1.39 Genetic susceptibility for chronic lymphocytic leukemia among Chinese in Hong Kong. [PharmGKB:Non-Curated GWAS Results: A genome-wide association study identifies six susceptibility loci for chronic lymphocytic leukemia (Initial Sample Size: 505 cases, 1,438 controls; Replication Sample Size: 1,024 cases, 1,677 controls; Risk Allele: rs17483466-G). This variant is associated with Chronic lymphocytic leukemia.] [GWAS:None] [GWAS:Chronic lymphocytic leukemia]
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[GWAS:Prostate cancer]
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The A allele appears to protect against Hodgkin lymphoma.
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[GWAS:None]
Frequency: 76.9%
References:1
References:1
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[GWAS:None]
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[GWAS:None]
Frequency: 79.3%
References:1
References:1
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cancer-genetics these snps influence genetic risk for prostate cancer rs2660753 showed a per-allele OR, 1.08 (95% confidence interval, 1.00-1.16; P = 0.06) An initial report of an association with between this SNP and risk for ovarian cancer was not replicated when the same authors expanded the study over 12 studies comprising 4,482 cases (and over 6,000 controls). [GWAS:Prostate cancer]
References:14
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NIH Although the function of this SNP is unknown, further analysis by the CGEMS team found that this region is predominately associated with estrogen receptor-positive breast cancer. From one person's DeCode report, it appears that the risk allele is C (relative risk 1.18 with two copies; apparently this information comes from a study or studies involving 9,335 cases and 10,263 controls). no significant association was observed between rs11249433 and breast cancer risk in this Chinese population Leveraging genetic variability across populations for the identification of causal variants. Performance of common genetic variants in breast-cancer risk models. [PharmGKB:Non-Curated GWAS results: A multistage genome-wide association study in Breast Cancer identifies two new risk alleles at 1p11....
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rs20541 is a C/T polymorphism on the interleukin 13 gene IL13 associated with IgE levels. rs20541 influences the effect of maternal smoking during pregnancy and persistent childhood asthma rs1295685 and rs20541 were significantly associated with elevated IgE levels in pooled analyses. rs2569190(T;T) and rs2569191(C;C) genotypes associated with lower IgE 23andMe blog psoriasis Europeans rs20541(G) 1.27x risk [PharmGKB:Non-Curated GWAS results: Genome-wide scan reveals association of psoriasis with IL-23 and NF-kappaB pathways. (Initial Sample Size: 1,359 cases, 1,400 controls; Replication Sample Size: 5,048 cases, 5,041 controls); (Region: 5q31.1; Reported Gene(s): IL13; Risk Allele: rs20541-G); (p-value= 0.000000000000005).This variant is associated with Psoriasis.] [OMIM:PSORIASIS SUSCEP...
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[GWAS:Chronic lymphocytic leukemia]
Magnitude: 0
Frequency: 19.5%
References:41
Frequency: 19.5%
References:41
normal
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rs13387042(A;A) has an estimated 1.44-fold greater risk of breast cancer than the GG genotype. This initial association was later tested among patients in the Breast Cancer Association Consortium, including 31,510 women with invasive breast cancer, 1101 women with ductal carcinoma in situ (DCIS), and 35,969 controls. In Caucasian women of European origin, each A allele is associated with 1.12 higher odds (CI: 1.09-1.15). This association held regardless of ER or PR status. [PharmGKB:Non-Curated GWAS results: A multistage genome-wide association study in Breast Cancer identifies two new risk alleles at 1p11.2 and 14q24.1 (RAD51L1). (Initial Sample Size: 1,145 cases, 1,142 controls; Replication Sample Size: 8,625 cases, 9,657 controls); (Region: 2q35; Reported Gene(s): Intergenic; Risk Alle...
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rs2072590 is a SNP on chromosome 2q31, in a noncoding region ~5 kb distal to the HOXD3 gene and ~10 kb proximal to HOXD1. A genome-wide association study ultimately including over 10,000 ovarian cancer patients found statistically strong (p = 3.8 × 10e?14) evidence for slightly elevated risk associated with the rs2072590(T) allele, with an odds ratio of 1.20 (CI: 1.14–1.25) as calculated for the serous subtype (of ovarian cancer), though it was significant for the other subtypes as well. [GWAS:None]
Normal risk of aggressive neuroblastoma.
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Each G allele has been associated with an allelic odds ratio of 1.68 (p = 8.65 x 10(-18)) for risk of aggressive neuroblastoma. [OMIM:NEUROBLASTOMA]
normal
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23andMe blog Each copy of a G at this SNP increases the odds of aggressive neuroblastoma by 1.68 times. allelic odds ratio of 1.68 (p = 2.74 x 10(-16)) Chromosome 6p22 locus associated with clinically aggressive neuroblastoma. [OMIM:NEUROBLASTOMA] [GWAS:None]
common in complete genomics
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23andMe blog each rs210138(G) was found to increase the odds of testicular cancer by 1.5x [OMIM:?] [GWAS:Testicular germ cell tumor]
Magnitude: 0
Frequency: 69.9%
Repute:Good
References:3
Frequency: 69.9%
Repute:Good
References:3
common on affy axiom data
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rs12210050 was found to be associated with basal cell carcinoma based on a study by the eMERGE network in which electronic medical records were searched to find clinical associations associated with selected SNPs. [GWAS:Tanning]
common on affy axiom data
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Replication of lung cancer susceptibility loci at chromosomes 15q25, 5p15, and 6p21: a pooled analysis from the International Lung Cancer Consortium. [GWAS:Lung adenocarcinoma]
common on affy axiom data
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lung cancer rs3117582 P = 4.97 x 10(-10) Update in lung cancer 2008. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Role of 5p15.33 (TERT-CLPTM1L), 6p21.33 and 15q25.1 (CHRNA5-CHRNA3) variation and lung cancer risk in never-smokers. [PharmGKB:Non-Curated Common 5p15.33 and 6p21.33 variants influence lung cancer risk. (Initial Sample Size: 1,952 cases, 1,438 controls; Replication Sample Size: 7,579 cases, 8,236 controls); (Region: 6p21.33; Reported Gene: BAT3MSH5; Risk Allele: rs3117582-C) This variant is associated with Lung cancer.] [OMIM:LUNG CANCER SUSCEPTIBILITY 4; LNCR4] [GWAS:Lung adenocarcinoma]
Magnitude: 0
Frequency: 92.0%
Repute:Good
References:6
Frequency: 92.0%
Repute:Good
References:6
common in complete genomics
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According to a 23andMe report, the rs12621278(A;A) genotype is associated with 2.4 times higher risk of progression of prostate cancer. [GWAS:Prostate cancer]
Magnitude: 0
Frequency: 95.6%
Repute:Good
References:2
Frequency: 95.6%
Repute:Good
References:2
81 snps
(hide) Variable number tandem repeat
common in complete genomics
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- rs2227902 and rs3796530 were found to be in 100% LD with a variable number tandem repeat (VNTR) length variant in the REST gene in a sample of 746 elderly Caucasians. Minor alleles (T and A, respectively) at both locations associated with the 4-length VNTR, while common alleles associated with the VNTR 5-length repeat. Carriers of the 4-length VNTR homozygous for the Val66 variant in the BDNF gene performed slightly, but significantly (p = 0.004), better than those without in the general cognitive tests performed in the study. Carriers of the 5-length VNTR and the 66Met BDNF variant had significantly lower g (p = 0.01), but the effect was not as great as the individual effect of the 66Met allele.
1 snp
(hide) Vitamin D
HLA-DRB1*1501 carrier; higher multiple sclerosis risk Rs3135391(C;T) is highly correlated with the HLA-DRB1*1501 allele. There is a 3x higher risk of multiple sclerosis associated with the (C;T) genotype.
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rs3135391 is highly correlated with the HLA-DRB1*1501 allele. The risk allele (T), is associated with a 3 to 6 fold higher risk for developing multiple sclerosis, and is the most significantly associated risk factor for MS. [PMC2892470] In one study, for example, the odds ratio was reported to be 3.04 (p < 1 x 10e-78). The HLA-DRB1*1501 allele has also been associated with other autoimmune diseases, such as systemic lupus erythematosis (SLE) (see) and possibly narcolepsy. The HLA-DRB1*1501 allele is fairly common; for example, it occurs in 15-30% of individuals of Northern European ancestry. [PMC2892470] An interesting series of correlations have been woven together to suggest that a possible way to lower the risk of rs3135388(T) carriers developing multiple sclerosis would be to ensure...
3x higher risk of multiple sclerosis Rs3135388(C;T) is highly correlated with the HLA-DRB1*1501 allele. There is a 3x higher risk of multiple sclerosis associated with the (C;T) genotype.
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rs3135388(T) is highly (> 99%) correlated with the HLA-DRB1*1501 allele; the risk allele (T) is associated with a 3 to 6 fold higher risk for developing multiple sclerosis. The risk per allele (or per haplotype) appears additive. It has also been associated with other autoimmune diseases, such as systemic lupus erythematosis (SLE) (see) and, when linked with DQB1*0602, narcolepsy. The HLA-DRB1*1501 allele is fairly common; for example, it occurs in 15-30% of individuals of Northern European ancestry. Note: most publications refer to the risk allele as rs3135388(A), but in dbSNP and SNPedia orientation, it is rs3135388(T). An interesting series of correlations have been woven together to suggest that a possible way to lower the risk of rs3135388(T) carriers developing multiple sclerosis ...
ex-smokers at 2x higher risk for COPD; supplement with Vitamin D?
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A study of 414 (ex)-smokers older than 50 years concluded that vitamin D levels were reduced by 25% in rs7041](T;T) homozygotes (p<0.0001), and even after correction for age, gender and smoking history, they were also at increased risk for chronic obstructive pulmonary disease (COPD; odds ratio 2.11, CI: 1.20-3.71, p=0.009). They conclude that since vitamin D deficiency occurs frequently in COPD and correlates with its severity, vitamin D supplementation may be warranted in patients with severe COPD, and especially in those carrying rs7041(T) alleles. [OMIM:?] [GWAS:Serum vitamin D-binding protein levels]
if less milk in teenage females, less bone?
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A very small study of 117 healthy European peri- and postmenarcheal girls (14.9 +/- 1.6 years) were followed for 4 years along with their calcium intake. Girls with rs4516035(C;T) and (C;C) genotypes had 13% lower spine mineral content if their milk intakes were below 260 mL/day, compared to either genotype-matched girls with higher milk intakes or to girls with the (T;T) genotype. If this is real, it suggests that rs4516035(C;T) and (C;C) female teens need more milk than rs4516035(T;T) girls to have optimal bone density. rs4516035 and the more aggressive tumour location in head-neck and trunk (OR=1.54, p=0.020)
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[GWAS:Vitamin D levels]
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[PharmGKB:In-Depth Associated with response to bronchodilators]
?
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rs2107301 is a SNP in the vitamin D VDR receptor gene. rs2107301(T;T) homozygotes were associated with an ~2.5x higher risk of prostate cancer compared to homozygote carriers of the more common (C) allele in the 630 Caucasian patients studied.
Higher serum levels of vitamin D
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Levels of 25-hydroxyvitamin D in familial longevity: the Leiden Longevity Study. Concluded that familial longevity was associated with a lower vitamin D levels and a lower frequency of the allelic variation in the CYP2R1 gene. Genome-wide association study of circulating vitamin D levels. This SNP is part of CYP2R1, which encodes a key C-25 hydroxylase that converts vitamin D3 to an active vitamin D receptor ligand. This SNP, along with rs2282679, rs3829251, and rs6599638 accounted for 2.8% of the variance in circulating vitamin D levels. [GWAS:Vitamin D levels]
Frequency: 38.1%
References:5
References:5
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Variants in the vitamin D receptor gene and asthma. Vitamin D receptor polymorphisms are associated with Graves' disease in German and Polish but not in Serbian patients. Asthma families show transmission disequilibrium of gene variants in the vitamin D metabolism and signalling pathway. Polymorphisms in the vitamin D receptor and their associations with risk of schizophrenia and selected anthropometric measures. Vitamin D pathway gene polymorphisms, diet, and risk of postmenopausal breast cancer: a nested case-control study. Optimization of candidate-gene SNP-genotyping by flexible oligonucleotide microarrays; analyzing variations in immune regulator genes of hay-fever samples. Vitamin D receptor gene (VDR) associations with cancer. Genome-wide association with bone mass and geometry in t...
Frequency: 40.9%
References:2
References:2
Intermediate risk of low bone mineral density disorders
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rs1544410, also known as the BsmI polymorphism, is a SNP in the Vitamin D receptor (VDR). Multiple studies examining bone mineral density (BMD) in women have associated the A allele with increased risk of low BMD , , & . Additionally, A meta-analysis of 26 studies estimated a decreased risk of osteoporosis associated with the G;G genotype with an odds ratio of 0.61, 95% CI, 0.40-0.92 . rs1544410 increases susceptibility to Shorter stature for carriers of the A allele [PharmGKB:Curated This variant is associated with etidronate response in Caucasian (Slovenian) postmenopausal women (24 patients), with bb genotype associated with lower increase in bone mineral density (BMD) after bisphosphonate treatments.]
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rs731236 protection from breast cancer (OR=0.80, 95%CI=0.64-0.99; p= 0.047) [PharmGKB:Curated This variant was significantly associated with acquired resistance to clodronate treatment in Caucasian patients with Paget's disease of the bone]
Frequency: 62.8%
References:11
References:11
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Genome-wide association with bone mass and geometry in the Framingham Heart Study. Vitamin D receptor gene polymorphisms and epithelial ovarian cancer risk. CDX2 VDR polymorphism and colorectal cancer. Vitamin D receptor gene haplotypes and susceptibility to HIV-1 infection in injection drug users. Vitamin D receptor gene polymorphisms and haplotypes and postmenopausal breast cancer risk. Association of vitamin D receptor gene variants, adiposity and colon cancer. Modification of the inverse association between dietary vitamin D intake and colorectal cancer risk by a FokI variant supports a chemoprotective action of Vitamin D intake mediated through VDR binding. Circulating 25-hydroxyvitamin D, VDR polymorphisms, and survival in advanced non-small-cell lung cancer. Colon tumor mutations an...
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rs3847987 in the vitamin D pathway was associated with the time to onset of COPD. The SNP is a cytosine-to-adenine switch, and men with two copies of the adenine variant were more likely to develop COPD. The hazard ratio was 1.60, with a 95% confidence interval from 1.26 to 2.05, which was significant at P=0.005. news
Frequency: 82.3%
References:1
References:1
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Vaccine immunogenetics: bedside to bench to population. Personalized vaccines: the emerging field of vaccinomics. Toll-like receptor signaling pathway variants and prostate cancer mortality. Association of polymorphisms in TLR genes and in genes of the Toll-like receptor signaling pathway with cancer risk. [PharmGKB:Curated Heterozygots for this variant -926 bp in promoter region of the TLR3 gene were associated with low antibody and lymphoproliferative responses (p <or= 0.02) to measles vaccination.]
2.47x higher risk for prostate cancer
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rs2238135 is a SNP in the vitamin D VDR receptor gene. rs2238135(G;G) homozygotes were associated with an ~2.5x higher risk of prostate cancer compared to homozygote carriers of the more common (C) allele in the 630 Caucasian patients studied.
common in clinvar
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see rs2282679, a near-perfect proxy for rs4588 Gene-environment interaction effects on the development of immune responses in the 1st year of life. The genetics of chronic obstructive pulmonary disease. Vitamin D pathway gene polymorphisms, diet, and risk of postmenopausal breast cancer: a nested case-control study. The Gc2 allele of the vitamin D binding protein is associated with a decreased postmenopausal breast cancer risk, independent of the vitamin D status. Genetic and environmental determinants of 25-hydroxyvitamin D and 1,25-dihydroxyvitamin D levels in Hispanic and African Americans. Genetic polymorphisms of the vitamin D binding protein and plasma concentrations of 25-hydroxyvitamin D in premenopausal women. A meta-analysis of candidate gene polymorphisms and ischemic stroke in ...
normal
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rs2282679, located in the group-specific component (vitamin D binding protein) GC gene on chromosome 4p12, has been linked by several studies to vitamin D serum concentrations. In both studies, the allele associated with lower vitamin D, and thus the potential for vitamin D insufficiency, is rs2282679(C). Carriers of two such alleles have lower vitamin D than carriers of one allele, who in turn on average have lower vitamin D levels than rs2282679(A;A) individuals. A near-perfect proxy (i.e. substitute) for rs2282679 is reported to be rs4588. [GWAS:Vitamin D levels]
Magnitude: 0
Frequency: 70.8%
Repute:Good
References:1
Frequency: 70.8%
Repute:Good
References:1
common on affy axiom data
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select biomarker trait being 25(OH) vitamin D plasma levels [GWAS:Select biomarker traits]
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Physiogenomic comparison of human fat loss in response to diets restrictive of carbohydrate or fat. Vitamin d pathway genes, diet, and risk of renal cell carcinoma.
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
Magnitude: 0
Repute:Good
References:1
Repute:Good
References:1
38 snps
(hide) Weight management
complex; see details for increased risks
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Several susceptibilities have been linked to rs1042714, a SNP in the ADRB2 gene that is also known as the Q27E SNP. The rs1042714(C) allele encodes the glutamine (Gln; 'Q'), and the rs1042714(G) allele encodes the glutamic acid (Glu; 'E'). A study of 304 patients found that the Glu27 allele led to increased risk for idiopathic venous thromboembolism; the reported odds ratio was 1.40 (CI: 1.09-1.79, p=0.006) for carriers of at least one risk allele. A study of 334 families with at least one child with autism found that increased risk associated with the rs1042714(G;G) homozygous genotype; the odds ratio reported was between 1.33-1.60 (CI: 1.07-2.58). The risk was approximately doubled among mothers who had clinical markers for pregnancy related stress. In a study of 342 patients with type-2...
normal
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rs1042713, also known as Arg16, G16R, and 16Arg>Gly, is a SNP in the adrenergic, beta-2-, surface receptor ADRB2 gene. The rs1042713(G) allele encodes the G/glycine form that is the more common one in most populations, while rs1042713(A) encodes the R/arginine residue at this position of the ADRB2 protein. A study of 1,182 young Scottish asthma patients (age, 3-22 years) concluded that rs1042713(A) alleles are significantly associated with 'exacerbations' of their condition, regardless of treatment regimens (odds ratio 1.30, CI: 1.09-1.55, p=0.003). This didn't hold true for patients using inhalers less than once per day; and it was particularly true for those receiving daily inhaled long- or short-acting beta(2)-agonist treatment (OR, 1.64, CI: 1.22-2.20, p=.001). This may therefore in...
normal fat metabolism; common in clinvar
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rs1801282, also known as Pro12Ala, is a common SNP in the peroxisome proliferator-activated receptor PPARG gene. The more common (C) allele (in dbSNP orientation) encodes the 'Pro' amino acid at this SNP position. rs1801282 has been reported to be associated with metabolic syndrome, but other studies have not been able to replicate any strong or significant effect. The association between type-2 diabetes and SNP rs1801282 is mentioned as being replicated in rs1801282 and risk of cognitive decline in elders? Maybe with diabetes. A ten-year study of 679 male patients with symptomatic coronary artery disease found that rs1801282(G) carriers had a much lower (10 year) cardiovascular risk, with the hazard ratio estimated to be 0.10 (CI: 0.01-0.70, p = 0.02) for ischemic heart disease and 0.24 f...
normal
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rs4994, also known as Trp64Arg or as the Arg64 variant, is a SNP in the ADRB3 gene. The rs4994(C) allele encodes the variant arginine. In a study of 600+ women initially referred for coronary angiography and then followed for 6 years, during which time 115 experienced a heart problem, rs4994(C) individuals were calculated to be at higher risk (adjusted hazard ratio 2.10, CI: 1.05-4.24). This risk was due to subtle increases in risk for all of the individual endpoints, and was only seen in women without obstructive coronary artery disease. Response to Diet and Exercise [PharmGKB:Curated Arg in position 64 associated with olanzapine-induced weight gain] [OMIM:OBESITY, SUSCEPTIBILITY TO]
4 snps
(hide) Yasko Methylation
reduced MAOA activity
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rs6323 (R297R / Arg297Arg) is a SNP in the MAOA (monoamine oxidase A) gene. Monoamine oxidase A degrades serotonin, dopamine, epineprine, and norepinephrine. The G allele encodes for the higher activity form of the enzyme. Subjects with major depressive disorder with the highest activity form of the enzyme (G or G/G) had a significantly lower magnitude of placebo response.
Possible risks. Complex. MTHFR rs1801131 is involved in converting 5-methylfolate (5MTHF) to tetrahydrofolate (THF). Unlike MTHFR C677T, this mutation does not lead to elevated homocysteine levels.
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rs1801131 is a SNP in the MTHFR gene, representing an A>C mutation at mRNA position 1298, resulting in a glu429-to-ala (E429A) substitution (hence this SNP is also known as A1298C or E429A). A diplotype (according to the authors, but perhaps actually a genoset) of rs1801131 and rs1801133 has been linked to increased risk for several types of brain cancer. The highest risk of meningioma was associated with heterozygosity for both MTHFR SNPs (odds ratio 2.11, CI: 1.42-3.12, p=0.002). The corresponding odds ratio for glioma was 1.23 (CI: 0.91-1.66, p=0.02. In general, risks were increased with genotypes associated with reduced MTHFR activity. rs1801131 shows no consistent association with schizophrenia overall in 12 studies totaling 3,000+ patients [PharmGKB:Curated Risk or phenotype-asso...
higher risk for endometrial cancer
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rs4633 is a variant at codon 62 of the COMT gene, however, it does not change the amino acid sequence of the COMT protein. In a study of 150 (Caucasian) cases of endometrial cancer, a significant increase in rs4633(T;T) genotype was observed in patients compared to controls (OR = 2.39, CI: 1.31-4.37, p = 0.004). Furthemore, the frequency of the C-G haplotype of rs4633-rs4680 was significantly higher in controls (p < 0.0001) than in patients. This correlated with lower expression levels of the COMT protein in carriers of these alleles. pubmed 1180576 Schizophrenia Susceptibility Genetic basis for individual variations in pain perception and the development of a chronic pain condition [PharmGKB:Curated On the basis of subjects' pain responsiveness, haplotypes involving rs6269 (A/G), rs46...
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Yasko Methylation Methionine synthase, coded by the MTR gene, has a B12 attached to it. The Methionine synthase takes a methyl group from methyl folate and attaches it to its B12, then it attaches it to a molecule of homocysteine, turning it into methionine, which in turn becomes SAMe. After 1000-2000 times doing this, the B12 gets turned into a useless form, and MTRR turns the B12 back into the useful form so that the molecule of MTR can keep working. The MTRR mutations make this enzyme less active, suggesting a need for more B12.
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Yasko Methylation The product the BHMT gene is central to the ‘short cut’ through the methylation cycle, again helping to convert homocysteine to methionine. The activity of this gene product can be affected by stress, by cortisol levels and may play a role in ADD/ADHD by affecting norepinephrine levels. Yasko believes that believes BHMT-02 and BHMT-04 play a role in the gut environment. Yasko also believes that BHMT-08 is related to the impact that psychological stress has on a patient's attention levels.
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Yasko Methylation Catalyzes the hydrolysis of AdoHcy to adenosine and homocysteine. AdoHcy hydrolysis serves not only to sustain the flux of methionine sulfur toward cysteine, but is believed also to play a critical role in the regulation of biologic methylations. This is one of the SNPs reported by NutraHacker.
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Associated with lean body mass but not fat body mass in a study of ~1,800 Caucasians
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Plays a major role in ketone body metabolism. Defects cause a 3-ketothiolase deficiency. Yasko believes it will cause an increase in gut bugs (particularly clostridia) as well as elevated fatty acid metabolites. This is one of the SNPs reported by NutraHacker.
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Being investigated in Ehlers-Danlos syndrome
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Yasko Methylation The product the BHMT gene is central to the ‘short cut’ through the methylation cycle, again helping to convert homocysteine to methionine. The activity of this gene product can be affected by stress, by cortisol levels and may play a role in ADD/ADHD by affecting norepinephrine levels. Yasko believes that believes BHMT-02 and BHMT-04 play a role in the gut environment. Yasko also believes that BHMT-08 is related to the impact that psychological stress has on a patient's attention levels.
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Yasko Methylation The product the BHMT gene is central to the ‘short cut’ through the methylation cycle, again helping to convert homocysteine to methionine. The activity of this gene product can be affected by stress, by cortisol levels and may play a role in ADD/ADHD by affecting norepinephrine levels. Yasko believes that BHMT-02 and BHMT-04 play a role in the gut environment. Yasko also believes that BHMT-08 is related to the impact that psychological stress has on a patient's attention levels.
Intermediate risk of low bone mineral density disorders
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rs1544410, also known as the BsmI polymorphism, is a SNP in the Vitamin D receptor (VDR). Multiple studies examining bone mineral density (BMD) in women have associated the A allele with increased risk of low BMD , , & . Additionally, A meta-analysis of 26 studies estimated a decreased risk of osteoporosis associated with the G;G genotype with an odds ratio of 0.61, 95% CI, 0.40-0.92 . rs1544410 increases susceptibility to Shorter stature for carriers of the A allele [PharmGKB:Curated This variant is associated with etidronate response in Caucasian (Slovenian) postmenopausal women (24 patients), with bb genotype associated with lower increase in bone mineral density (BMD) after bisphosphonate treatments.]
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rs731236 protection from breast cancer (OR=0.80, 95%CI=0.64-0.99; p= 0.047) [PharmGKB:Curated This variant was significantly associated with acquired resistance to clodronate treatment in Caucasian patients with Paget's disease of the bone]
multiple associations, see details
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rs4680 (Val158Met) is a well studied SNP in the COMT gene. 23andMe blog summarizes them as *rs4680(A) = Worrier. Met, more exploratory, lower COMT enzymatic activity, therefore higher dopamine levels; lower pain threshold, enhanced vulnerability to stress, yet also more efficient at processing information under most conditions *rs4680(G) = Warrior. Val, less exploratory, higher COMT enzymatic activity, therefore lower dopamine levels; higher pain threshold, better stress resiliency, albeit with a modest reduction in executive cognition performance under most conditions Roughly speaking, the predominant wisdom (known colloquially as the warrior/worrier hypothesis; summary at ) posits that people with Val alleles have increased COMT activity and lower prefrontal extracellular dopamine compar...
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Yasko Methylation Methionine synthase, coded by the MTR gene, has a B12 attached to it. The Methionine synthase takes a methyl group from methyl folate and attaches it to its B12, then it attaches it to a molecule of homocysteine, turning it into methionine, which in turn becomes SAMe. After 1000-2000 times doing this, the B12 gets turned into a useless form, and MTRR turns the B12 back into the useful form so that the molecule of MTR can keep working. The MTRR mutations make this enzyme less active, suggesting a need for more B12.
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A and G alleles of rs4343 are strongly associated marking insertion and deletion alleles of ACE I/D respectively. For those looking for the ACE Alu Insertion/Deletion, this is a very good substitute for people searching for ACE Del16. G would mean deletion. A haplotype of rs4311, rs4343, rs699 increases risk of diabetic nephropathy 4x. [PharmGKB:Curated While the ACE:I/D has dbSNP identifiers rs1799752, rs4340, rs13447447 and rs4646994, measurement of a single base at these positions does not give an informative genotype. In Europeans, rs4343 is in complete LD with the ACE:I/D, with the A and G alleles of rs4343 marking the insertion and deletion alleles of ACE:I/D respectively.] [GWAS:Angiotensin-converting enzyme activity]
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[PharmGKB:Curated Risk or phenotype-associated allele: G Phenotype: The GG (Gly/Gly) genotype was associated with lower risk for colorectal cancer. This risk was further lowered in men with low alcohol intake. Study size: Study population/ethnicity: Patients with colorectal cancer from the Physicians' Health Study (PHS) and the Health Professional Follow-up Study (HPFS). Significance metric(s): OR = 0.59 (95% CI, 0.27-1.27); OR = 0.27 (95% CI, 0.09-0.81)(interaction with alcohol) Type of association: CO]
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Yasko Methylation Catalyzes the hydrolysis of AdoHcy to adenosine and homocysteine. AdoHcy hydrolysis serves not only to sustain the flux of methionine sulfur toward cysteine, but is believed also to play a critical role in the regulation of biologic methylations.
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Yasko Methylation Catalyzes the hydrolysis of AdoHcy to adenosine and homocysteine. AdoHcy hydrolysis serves not only to sustain the flux of methionine sulfur toward cysteine, but is believed also to play a critical role in the regulation of biologic methylations. This is one of the SNPs reported by NutraHacker.
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Being investigated in Ehlers-Danlos syndrome
normal
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rs1801394, also known as A66G or Ile22Met, is a SNP in the methionine synthase MTRR gene. This gene encodes one of the two enzymes involved in the production of methionine (the other is MTR). The protein encoded by an rs1801394 allele has a lower affinity for MTR () and is inconsistently associated with homocysteine level, although it is a risk factor for neural tube defects () and Down syndrome () in conditions of higher homocysteine. Based on a study of British patients with primary brain tumors, (1,005 glioma cases and 631 meningioma cases), rs1801394(G;G) individuals were at higher risk for meningioma (odds ratio 1.41, CI: 1.02-1.94). In general, genotypes associated with increased 5,10-methylenetetrahydrofolate levels are associated with elevated risk for these types of brain cancer. ...
Common genotype: normal homocysteine levels
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rs1801133 is a SNP that is relatively common and has been studied for (relatively) a long time. Also known as C677T, Ala222Val, and A222V, it encodes a variant in the MTHFR gene, which encodes an enzyme involved in folate metabolism. Homozygous rs1801133(T;T) individuals have ~30% of the expected MTHFR enzyme activity, and rs1801133(C;T) heterozygotes have ~65% activity, compared to the most common genotype, rs1801133(C;C). This reduced activity (i.e. this SNP) has been linked at least once to each of the following disorders (though not necessarily reproducibly): * autism * cancer, including ** gastric cancer ** lung cancer ** head and neck cancer ** renal cancer * cleft lip and cleft palate * coronary artery disease * dementia * depression * hyperhomocysteinemia * migraine * neural tube d...
common in complete genomics
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No association of single nucleotide polymorphisms in one-carbon metabolism genes with prostate cancer risk. Lack of association of polymorphisms in homocysteine metabolism genes with pseudoexfoliation syndrome and glaucoma.
common in complete genomics
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pancreatic cancer 702 cases and 785 controls *rs162049 P = .0018; OR, 1.33; 95% CI: 1.11-1.60 *rs10380 (His595Tyr) P = .0063; OR, 1.45; 95% CI: 1.11-1.88
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The complex global pattern of genetic variation and linkage disequilibrium at catechol-O-methyltransferase. Influence and interaction of genetic polymorphisms in catecholamine neurotransmitter systems and early life stress on antidepressant drug response.
27 snps