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rs660895

From SNPedia

Orientationplus
Stabilizedplus
Geno Mag Summary
(A;A) 0 normal
(A;G)
(G;G) 2.5 6x higher risk of rheumatoid arthritis
ReferenceGRCh38 38.1/141
Chromosome6
Position32609603
is asnp
is mentioned by
dbSNPrs660895
ebirs660895
HLIrs660895
Exacrs660895
Varsomers660895
Maprs660895
PheGenIrs660895
hapmaprs660895
1000 genomesrs660895
hgdprs660895
ensemblrs660895
gopubmedrs660895
geneviewrs660895
scholarrs660895
googlers660895
pharmgkbrs660895
gwascentralrs660895
openSNPrs660895
23andMers660895
23andMe allrs660895
SNP Nexus

SNPshotrs660895
SNPdbers660895
MSV3drs660895
GWAS Ctlgrs660895
GMAF0.2089
Max Magnitude2.5
? (A;A) (A;G) (G;G) 28

This SNP, along with SNPs rs6910071 and rs3817964, is a tag SNP for the HLA-DRB1*0401 allele.

The HLA-DRB1*0401 allele has been associated with higher risk for rheumatoid arthritis, and in particular, rheumatoid vasculitis. The association is seen particularly for individuals carrying two copies of, i.e. homozygous for, the allele. The reported odds ratio for rs660895(G;G) homozygotes is 6.2 (CI: 1.01 - 37.9). [PMID 15529352]

The risk for rheumatoid arthritis may be higher for individuals carrying one copy (one "dose") of the HLA-DRB1*0401 allele, if they also carry a different HLA-DRB1 risk allele. In particular, *0401/*0404 individuals are reported to have an odds ratio for rheumatoid vasculitis of 4.1 (CI: 1.1 - 16.2), and *0401/*0101 individuals have an odds ratio of 4.0 (CI: 1.4 - 11.6). [PMID 15529352]

  • (A;A) is 0 dose of HLA-DRB1*0401
  • (A;G) is 1 dose of HLA-DRB1*0401
GWAS snp
PMID [PMID 17804836OA-icon.png]
Trait Rheumatoid arthritis
Title TRAF1-C5 as a risk locus for rheumatoid arthritis--a genomewide study
Risk Allele
P-val 1E-108
Odds Ratio 3.62 [NR]

[PMID 24270849OA-icon.png] rs660895 was found to be associated with rheumatoid arthritis based on a study by the eMERGE network in which electronic medical records were searched to find clinical associations associated with selected SNPs.

GWAS snp
PMID [PMID 22197929]
Trait
Title A genome-wide association study in Han Chinese identifies multiple susceptibility loci for IgA nephropathy.
Risk Allele G
P-val 4E-20
Odds Ratio 1.3400 None


[PMID 22355377OA-icon.png] Caucasian and asian specific rheumatoid arthritis risk Loci reveal limited replication and apparent allelic heterogeneity in north indians


[PMID 15747258OA-icon.png] A high-resolution linkage-disequilibrium map of the human major histocompatibility complex and first generation of tag single-nucleotide polymorphisms.


[PMID 18438406OA-icon.png] Genetic determinants of ulcerative colitis include the ECM1 locus and five loci implicated in Crohn's disease.


[PMID 19116921OA-icon.png] Different patterns of associations with anti-citrullinated protein antibody-positive and anti-citrullinated protein antibody-negative rheumatoid arthritis in the extended major histocompatibility complex region.


[PMID 19143813OA-icon.png] Confirmation of HLA class II independent type 1 diabetes associations in the major histocompatibility complex including HLA-B and HLA-A.


[PMID 19143815OA-icon.png] MHC fine mapping of human type 1 diabetes using the T1DGC data.


[PMID 19458352OA-icon.png] Primary biliary cirrhosis associated with HLA, IL12A, and IL12RB2 variants.


[PMID 20017995OA-icon.png] A principal-components-based clustering method to identify multiple variants associated with rheumatoid arthritis and arthritis-related autoantibodies.


[PMID 20018015OA-icon.png] Elastic-net regularization approaches for genome-wide association studies of rheumatoid arthritis.


[PMID 20018024OA-icon.png] On the association between rheumatoid arthritis and classical HLA class I and class II alleles predicted from single-nucleotide polymorphism data.


[PMID 20018025OA-icon.png] Genome-wide analysis of haplotype interaction for the data from the North American Rheumatoid Arthritis Consortium.


[PMID 20018053OA-icon.png] A genome-wide association scan for rheumatoid arthritis data by Hotelling's T2 tests.


[PMID 20018057OA-icon.png] Detecting single-nucleotide polymorphism by single-nucleotide polymorphism interactions in rheumatoid arthritis using a two-step approach with machine learning and a Bayesian threshold least absolute shrinkage and selection operator (LASSO) model.


[PMID 20018067OA-icon.png] A two-stage search strategy for detecting multiple loci associated with rheumatoid arthritis.


[PMID 20018071OA-icon.png] Allelic based gene-gene interactions in rheumatoid arthritis.


[PMID 20018077OA-icon.png] Incorporating biological knowledge in the search for gene x gene interaction in genome-wide association studies.


[PMID 20018080OA-icon.png] Effects of covariates and interactions on a genome-wide association analysis of rheumatoid arthritis.


[PMID 20018081OA-icon.png] Assessment of gene-covariate interactions by incorporating covariates into association mapping.


[PMID 20369022OA-icon.png] Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations.


[PMID 20797713] Endometriosis and autoimmune disease: association of susceptibility to moderate/severe endometriosis with CCL21 and HLA-DRB1.


GET Evidence
rs660895
aa_change
aa_change_short
impact pathogenic
qualified_impact Insufficiently evaluated pathogenic
overall_frequency 0.185484
summary



[PMID 23961418OA-icon.png] Association of the HLA locus and TNF with type I autoimmune hepatitis susceptibility in New Zealand Caucasians


[PMID 22807207] Association between Parkinson's disease and the HLA-DRB1 locus.


[PMID 23223422OA-icon.png] Identification of the NF-kappaB activating protein-like locus as a risk locus for rheumatoid arthritis.


[PMID 23678157] Integrative analyses for functional mechanisms underlying associations for rheumatoid arthritis.