Have questions? Visit https://www.reddit.com/r/SNPedia

rs6920220

From SNPedia

rheumatoid arthritis
Orientationplus
Stabilizedplus
Geno Mag Summary
(A;A) 3.5 1.7x risk of Rheumatoid Arthritis
(A;G) 3 1.2x risk Rheumatoid Arthritis
(G;G) 0 normal
ReferenceGRCh38 38.1/141
Chromosome6
Position137685367
is asnp
is mentioned by
dbSNPrs6920220
ebirs6920220
HLIrs6920220
Exacrs6920220
Varsomers6920220
Maprs6920220
PheGenIrs6920220
hapmaprs6920220
1000 genomesrs6920220
hgdprs6920220
ensemblrs6920220
gopubmedrs6920220
geneviewrs6920220
scholarrs6920220
googlers6920220
pharmgkbrs6920220
gwascentralrs6920220
openSNPrs6920220
23andMers6920220
23andMe allrs6920220
SNP Nexus

SNPshotrs6920220
SNPdbers6920220
MSV3drs6920220
GWAS Ctlgrs6920220
GMAF0.1047
Max Magnitude3.5
? (A;A) (A;G) (G;G) 28
CPMC Logo.png

This SNP has been recognized by the Coriell Personalized Medicine Collaborative ICOB.
Additional information is available here

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). [PMID 17554300OA-icon.png]

[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)


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

GWAS snp
PMID [PMID 18794853OA-icon.png]
Trait Rheumatoid arthritis
Title Common variants at CD40 and other loci confer risk of rheumatoid arthritis
Risk Allele
P-val 2E-9
Odds Ratio 1.24 [1.16-1.32]
GWAS snp
PMID [PMID 17982456OA-icon.png]
Trait Rheumatoid arthritis
Title Two independent alleles at 6q23 associated with risk of rheumatoid arthritis
Risk Allele
P-val 9.9999999999999995E-8
Odds Ratio 1.22 [NR]


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

OMIM612378
DescSYSTEMIC LUPUS ERYTHEMATOSUS, SUSCEPTIBILITY TO, 13; SLEB13
Variant
Relatedalso
OMIM180300
DescRHEUMATOID ARTHRITIS; RA
Variant
Relatedalso



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

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

GWAS snp
PMID [PMID 20453842OA-icon.png]
Trait Rheumatoid arthritis
Title Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk lock
Risk Allele A
P-val 9E-13
Odds Ratio 1.22 [1.16-1.29]

[PMID 20921970] A genetic marker at the OLIG3/TNFAIP3 locus associates with methotrexate continuation in early inflammatory polyarthritis: results from the Norfolk Arthritis Register

[PMID 21120996OA-icon.png] Most common single-nucleotide polymorphisms associated with rheumatoid arthritis in persons of European ancestry confer risk of rheumatoid arthritis in African Americans

GWAS snp
PMID [PMID 21297633OA-icon.png]
Trait
Title Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47
Risk Allele A
P-val 8E-17
Odds Ratio 1.1400 [1.09-1.20]

[PMID 18625055OA-icon.png] Lack of association or interactions between the IL-4, IL-4Ralpha and IL-13 genes, and rheumatoid arthritis.

[PMID 18794857OA-icon.png] Rheumatoid arthritis susceptibility loci at chromosomes 10p15, 12q13 and 22q13.

[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 19180477OA-icon.png] Genetic risk factors for rheumatoid arthritis differ in Caucasian and Korean populations.

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

[PMID 19838195OA-icon.png] A large-scale replication study identifies TNIP1, PRDM1, JAZF1, UHRF1BP1 and IL10 as risk loci for systemic lupus erythematosus.

[PMID 19956648OA-icon.png] Pathway analysis of GWAS provides new insights into genetic susceptibility to 3 inflammatory diseases.

[PMID 20017963OA-icon.png] Representation of genetic association via attributable familial relative risks in order to identify polymorphisms functionally relevant to rheumatoid arthritis.

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

[PMID 20231195] Lack of association between the rs6920220 (G/A) polymorphism of the 6q23 region and biopsy-proven giant cell arteritis.

[PMID 20353580OA-icon.png] Evaluation of the rheumatoid arthritis susceptibility loci HLA-DRB1, PTPN22, OLIG3/TNFAIP3, STAT4 and TRAF1/C5 in an inception cohort.

[PMID 20426808OA-icon.png] AntEpiSeeker: detecting epistatic interactions for case-control studies using a two-stage ant colony optimization algorithm.

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

[PMID 20444755OA-icon.png] Investigation of rheumatoid arthritis susceptibility genes identifies association of AFF3 and CD226 variants with response to anti-tumour necrosis factor treatment.

[PMID 20617138OA-icon.png] Association of TNFAIP3 polymorphism with susceptibility to systemic lupus erythematosus in a Japanese population.

[PMID 20973039] Most common SNPs associated with rheumatoid arthritis in subjects of European ancestry confer risk of rheumatoid arthritis in African-Americans.

[PMID 21383967OA-icon.png] Meta-analysis of genome-wide association studies in celiac disease and rheumatoid arthritis identifies fourteen non-HLA shared loci.

[PMID 21833526] A Tunisian case-control association study of a 6q polymorphism in rheumatoid arthritis.

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


GET Evidence
rs6920220
aa_change
aa_change_short
impact pathogenic
qualified_impact Insufficiently evaluated pathogenic
overall_frequency 0.117188
summary



GWAS snp
PMID [PMID 23128233OA-icon.png]
Trait Inflammatory bowel disease
Title Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
Risk Allele A
P-val 1E-21
Odds Ratio 1.10 [1.064-1.141]


[PMID 22328738OA-icon.png] Comprehensive assessment of rheumatoid arthritis susceptibility loci in a large psoriatic arthritis cohort.


[PMID 22798268] Rheumatoid arthritis-associated polymorphisms at 6q23 are associated with radiological damage in autoantibody-positive RA.


[PMID 22843550] Genetic variation and alterations of genes involved in NFkappaB/TNFAIP3- and NLRP3-inflammasome signaling affect susceptibility and outcome of colorectal cancer.

GWAS snp
PMID [PMID 24449572OA-icon.png]
Trait Rheumatoid arthritis
Title Novel rheumatoid arthritis susceptibility locus at 22q12 identified in an extended UK genome-wide association study.
Risk Allele
P-val 3E-8
Odds Ratio 1.23 [1.14-1.32]