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rs10499194

From SNPedia

(T;T) protective against rheumatoid arthritis
Orientationplus
Stabilizedplus
Geno Mag Summary
(C;C) 0 normal
(T;T) 2 protective against rheumatoid arthritis for asians
Make rs10499194(C;T)
ReferenceGRCh38 38.1/141
Chromosome6
Position137681500
is asnp
is mentioned by
dbSNPrs10499194
ebirs10499194
HLIrs10499194
Exacrs10499194
Varsomers10499194
Maprs10499194
PheGenIrs10499194
hapmaprs10499194
1000 genomesrs10499194
hgdprs10499194
ensemblrs10499194
gopubmedrs10499194
geneviewrs10499194
scholarrs10499194
googlers10499194
pharmgkbrs10499194
gwascentralrs10499194
openSNPrs10499194
23andMers10499194
23andMe allrs10499194
SNP Nexus

SNPshotrs10499194
SNPdbers10499194
MSV3drs10499194
GWAS Ctlgrs10499194
GMAF0.1745
Max Magnitude2
? (C;C) (C;T) (T;T) 28
[PMID 17982456OA-icon.png] 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.

[PMID 19417005OA-icon.png] 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)

GWAS
SNP rs10499194
PubMedID [PMID 17982456OA-icon.png]
Condition Rheumatoid arthritis
Gene TNFAIP3, OLIG3
Risk Allele C
pValue 1.00E-009
OR 1.33
95% CI 1.15-1.52


[PMID 19401279] Susceptibility variants for rheumatoid arthritis in the TRAF1-C5 and 6q23 loci: a meta-analysis

[PMID 19565500OA-icon.png] Variants in TNFAIP3, STAT4, and C12orf30 loci associated with multiple autoimmune diseases are also associated with juvenile idiopathic arthritis

OMIM180300
DescRHEUMATOID ARTHRITIS; RA
Variant
Relatedalso



[PMID 20112363] The association of a nonsynonymous single-nucleotide polymorphism in TNFAIP3 with systemic lupus erythematosus and rheumatoid arthritis in the Japanese population


[PMID 19366996OA-icon.png] Association of the 6q23 region with the rate of joint destruction in rheumatoid arthritis



[PMID 18794853OA-icon.png] Common variants at CD40 and other loci confer risk of rheumatoid arthritis.


[PMID 18853133OA-icon.png] Gene variants influencing measures of inflammation or predisposing to autoimmune and inflammatory diseases are not associated with the risk of type 2 diabetes.


[PMID 18987647OA-icon.png] Rheumatoid arthritis: a view of the current genetic landscape.


[PMID 19165918OA-icon.png] Genetic variants near TNFAIP3 on 6q23 are associated with systemic lupus erythematosus.


[PMID 19169254OA-icon.png] Genome-wide scan reveals association of psoriasis with IL-23 and NF-kappaB pathways.


[PMID 19292917OA-icon.png] Analysis of TNFAIP3, a feedback inhibitor of nuclear factor-kappaB and the neighbor intergenic 6q23 region in rheumatoid arthritis susceptibility.


[PMID 19321514] 6q23 polymorphisms in rheumatoid arthritis Spanish patients.


[PMID 19387456OA-icon.png] Meta-analysis and imputation identifies a 109 kb risk haplotype spanning TNFAIP3 associated with lupus nephritis and hematologic manifestations.


[PMID 19439038OA-icon.png] Complex genetic association of 6q23 with autoimmune rheumatic conditions.


[PMID 19445664OA-icon.png] Association of common polymorphisms in known susceptibility genes with rheumatoid arthritis in a Slovak population using osteoarthritis patients as controls.


[PMID 19474294OA-icon.png] Potential etiologic and functional implications of genome-wide association loci for human diseases and traits.


[PMID 19674979OA-icon.png] Overlap of disease susceptibility loci for rheumatoid arthritis and juvenile idiopathic arthritis.


[PMID 19849816OA-icon.png] Genetics of rheumatic disease.


[PMID 20018027OA-icon.png] Conditional analysis of the major histocompatibility complex in rheumatoid arthritis.


[PMID 20439292] Genetic variants in the prediction of rheumatoid arthritis.


[PMID 20511617] Association of the TNFAIP3 rs5029939 variant with systemic sclerosis in the European Caucasian population.


[PMID 22402800] Associations between TNFAIP3 gene polymorphisms and rheumatoid arthritis: a meta-analysis.


GET Evidence
rs10499194
aa_change
aa_change_short
impact pathogenic
qualified_impact Insufficiently evaluated pathogenic
overall_frequency 0.1875
summary



[PMID 23161053] TNFAIP3 gene polymorphisms confer risk for Behcet's disease in a Chinese Han population


[PMID 23450725OA-icon.png] Susceptibility to childhood-onset rheumatoid arthritis: investigation of a weighted genetic risk score that integrates cumulative effects of variants at five genetic loci.


[PMID 26005883] Lack of association of TNFAIP3 and JAK1 with Behçet's disease in the European population