Promethease Report

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 (r²=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. [PharmGKB:Curated This SNP located within SLCO1B1 on chromosome 12 yielded a single strong association of myopathy in a genomewide...

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...

discussed in this blog post as possibly playing a role in coronary heart disease This SNP was also associated with increased risk for coronary artery disease in a Korean population. The association remained significant after adjusting for significant clinical covariates (P=0.001 to 0.024). We identified one risk haplotype (GGGG; P=0.017) and one protective haplotype (AAAA; P=0.007) for development of CAD. Further analysis suggested that the SNPs probably confer susceptibility to CAD in a dominance model (covariates-adjusted P=0.001 to 0.024; OR=2.37 to 1.54). Also found to be significant in a study of 416 Italian myocardial infarction patients. Found to be associated with coronary heart disease in a study of 1360 Chinese Han patients, with an odds ratio of 1.52 (CI: 1.13 - 2.04) for rs2383...

This SNP is in the TCF7L2 gene, and has been linked to type-2 diabetes, breast cancer and aggressive prostate cancer. This SNP is also known as IVS4G>T. is the paper which links it to Breast cancer. It suggests the T allele as increasing risk. 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 ~1000 Hispanic-Americans with reduced insulin secretion as measured by acute insulin response and adjusted for the degree of insulin sensitivity (p = 0.036). In a study of 1,457 prostate cancer case...

This SNP influences skin pigmentation. The allele p.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. 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 * rs2555364 * rs16960620 [OMIM:SOLUTE CARRIER FAMILY 24 (SODIUM/POTASSIUM/CALCIUM EXCHANGER), MEMBER]

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.]

This SNP (C/T) is in 5' region of the HLA-C gene, 35 kb away from transcription initiation in or around the HLA-C gene. 'People with this tiny sequence variation, dubbed rs9264942, appear to have up to 90% less virus in their systems than those who carry other polymorphisms. About 10% of Europeans appear to carry two copies of rs9264942, which leads to an average 90% viral load reduction. About 50% of Europeans carry one copy, which gives a 60% reduction. By comparison, less than 40% of people of African descent appear to carry a single copy of the polymorphism.' Genetic variation may lower HIV load by 90% They are referring to the (C;C) genotype giving a 90% reduction and the (C;T) giving a 60% reduction. dbSNP page This SNP is also reported to account for 6.5% of the 15% variation in vir...

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...

rs3135391 tags the HLA-CRB1*1501 allele, the most significantly associated risk factor for multiple sclerosis. In one study, for example, the odds ratio was reported to be 3.04 (p < 1 x 10e-78).

Lumbar disc herniation (LDH), a form of lumbar disc disease, is one of the most common musculoskeletal diseases. rs1676486, a SNP also known as c.4603C-->T in the COLL11A1 gene (one of 3 Type XI collagen genes), has been implicated in a study of ~800 Japanese patients as being associated with LDH. The risk allele in dbSNP orientation is (A), and the odds ratio associated with the allele is 1.42 (CI: 1.23 - 1.65). [PharmGKB:Curated In independent Japanese populations, the T allele was shown to be associated with Lumbar Disc Herniation.] [OMIM:COLLAGEN, TYPE XI, ALPHA-1; COL11A1]

rs2298566 is a SNP in the MYH15 gene. The risk allele in terms of heart disease is rs2298566(C). 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 possible risk variants (two copies of each of the five SNPs) were assigned a GRS of 5 and those carrying no risk variants a GRS of -5. A high GRS was defined as 3 or higher. Approximately 4% of the white cohort in ARIC...

rs1333048 increases susceptibility to coronary artery disease 1.30 times for heterozygotes (AC) and 1.54 times for homozygotes (CC) rs1333048 2x risk for periodontitis and a confirmation of coronary heart disease spittoon [OMIM:?]

rs17576, also known as Gln279Arg or Q279R, is a SNP in exon 6 of the matrix metalloproteinase-9 MMP9 gene. The rs17576(G) allele encodes the Arg (R). In a study of 385 male veterans with greater than 20 pack-years of cigarette smoking, rs17576(G) allele carriers were at higher risk for chronic obstructive pulmonary disease (COPD). The rs17576(G;G) homozygous genotype was at 3-fold increased risk for COPD. A study of 744 Chinese patients with lung cancer found that the rs17576(G;G) genotype was associated with higher risk of lung cancer with metastasis (adjusted OR, 1.79, CI: 1.03-3.08) compared to the (A;A) genotype. rs17576 is also one of two SNPs in the MMP9 gene associated with increased risk for myocardial infarction, but not coronary artery disease. The relatively weak odds ratios for...

rs499697 the minor, derived allele is associated with curlier hair curl, 0.13 points per G. [GWAS:Common traits (Other)]

rs7250581 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 (G); the odds ratio associated with heterozygotes is 1.06 (CI 0.79-1.43), and for homozygotes, 1.40 (CI 1.05-1.86).

rs2024513 is a SNP in the neurexin-1 NRXN1 gene on chromosome 2p16.3. Based on a case-control study of 700+ Han Chinese patients with schizophrenia, rs2024513(A) was associated with higher risk, at an odds ratio of 1.3 (CI: 1.07 - 1.56, p=0.006).

rs356219, a tagging SNP in the SNCA gene for a Parkinson's disease associated haplotype, predicts the amount of SNCA (alpha-synuclein) mRNA found in post mortem substantia nigra and cerebellum brain tissue. replicates the association of rs356219 with late-onset Parkinson's disease, calculating an odds ratio of 1.3 (CI: 1.13 - 1.5, p=2x10e-4) per rs356219(G) allele among the 1145 patients from northern Spain studied. [OMIM:SYNUCLEIN, ALPHA; SNCA] [GWAS:None]

rs2981745, also known as -93C>T, is a SNP in a gene known as Deleted in Malignant Brain Tumors 1 DMBT1. The (overly descriptive?) name refers to the hypothesis that this gene has a role as a tumor suppressor. A study of 1,195 BRCA1/2 mutation negative German breast cancer families and 1,466 unrelated German controls concluded that rs2981745(T) carriers over the age of 60 are at increased risk for breast cancer, with an odds ratio of 1.66 (CI: 1.21-2.29, p=0.0017). rs2981745 was also said to be tightly linked to rs11523871, which showed the same odds ratios in this study.

C allele is associated with 1.51mg/dl increase in HDL cholesterol (good cholesterol).

rs2207418 is a SNP located in a 'gene desert' region of ch 20p12. In an Amish founder population of 851 individuals, the rs2207418(C) allele was associated with cardiac hypertrophy, increased risk of heart failure (relative risk 1.85, CI: 1.2 - 2.7, p = 0.0019), and increased mortality (hazard risk 1.5, CI: 1.2 - 1.9, p = 0.0004).

news atrial fibrillation rs13376333 in KCNN3, with an odds ratio (OR) of 1.5 per copy of rs13376333(T); CI: 1.40–1.64, p = 1.83 × 10e-21. spitoon [PharmGKB:Curated Risk or phenotype-associated allele: T . Phenotype: This variant is associated with lone atrial fibrillation. Study size: 1,335 cases; 12,844 referants. Study population/ethnicity: Cases-German AF Network, Heart and Vascular Health Study, the Cleveland Clinic and Massachusetts General Hospital. Significance metric(s): overall combined odds ratio = 1.52, 95% CI 1.40-1.64, P = 1.83 x 10(-21) . Type of association: CO;GN] [OMIM:?] [GWAS:Atrial fibrillation]

rs2274223 is a SNP in the phospholipase C, epsilon 1 PLCE1 gene. In a large study of Han Chinese esophageal cancer patients [specifically esophageal squamous cell carcinoma (ESCC)], the rs2274223(G) allele was associated with greater risk (odds ratio 1.43, p = 7.4 x 10e-56).In this same study [http://www.nature.com/ng/journal/vaop/ncurrent/ris/ng.648.ris, rs2274223(G) was also associated with greater risk for gastric cancer (aka stomach cancer), with an odds ratio of 1.55 (1.74 x 10e-39). [OMIM:?] [GWAS:None]

rs10050860 is one of several SNPs in the ERAP1 gene that has been shown in a large (over 1,000 Caucasian patients) study to be associated with ankylosing spondylitis. The odds ratio is 0.71 (p=7.7x10e-9).

rs4959039 is a SNP located within the Class I HLA-G region of chromosome 6. Independently of the influence of the (nearby) HLA-DRB1*1501 allele, the rs4959039(G) was shown to be associated with increased risk for multiple sclerosis in a study of ~2,300 patients.

rs1126497, also known as Thr115Met, is a SNP in the epithelial cell adhesion molecule EPCAM gene. In a study of case control study of 1643 individuals with breast cancer and 1818 control subjects in Eastern and Southern Chinese populations, the rs1126497(T) allele was associated with a 1.4x increased risk (CI: 1.16-1.57), and it was also associated with early breast cancer onset (p=0.0023).

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.

rs2549782 is a SNP in the endoplasmic reticulum aminopeptidase 2 ERAP2 gene. A case-control study of 1103 Chilean maternal-fetal dyads and 1637 unpaired African American samples (836 maternal, 837 fetal) concluded that the fetal minor allele rs2549782(G) was associated with 1.3x increased risk (CI: 1.075-1.619) for preeclampsia in the African American population (p = 0.009), but not in the Chilean population.

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...

rs187116, also known as +4883G>A, is a SNP in the CD44 gene. A presentation at the 2010 American Society of Clinical Oncology meeting based on ~100 patients reported this SNP as being significantly associated with more aggressive gastric cancer. In dbSNP orientation, the risk allele is rs187116(C); patients carrying at least one rs187116(C) had a significantly shorter median time-to-recurrence (TTR) of 2.1 years compared to 7.0 years TTR for rs187116(T;T) patients (p = 0.036, log-rank test).[http://www.asco.org/ASCOv2/Meetings/Abstracts?&vmview=abst_detail_view&confID=72&abstractID=1689]

[GWAS:Conduct disorder (case status)]

Common genetic variability in ESR1 and EGF in relation to endometrial cancer risk and survival. Development of predictive models of proliferative vitreoretinopathy based on genetic variables: the Retina 4 project.

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. 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. [PharmGKB:Curated SNP is associated with tamoxifen-induced changes...