rs10488631
| Orientation | plus |
| Stabilized | plus |
| Geno | Mag | Summary |
|---|---|---|
| (C;C) | 3 | 2x increased risk of developing SLE; 3.2x increased risk of developing primary biliary cirrhosis; and 3.4x increased risk of developing Sjögren's syndrome |
| (C;T) | 2 | 2x increased risk of developing SLE; 1.6x increased risk of developing primary biliary cirrhosis; and 1.7x increased risk of developing Sjögren's syndrome |
| (T;T) | 1 | Normal risk of developing SLE, primary biliary cirrhosis, and Sjögren's syndrome |
| Reference | GRCh38 38.1/141 |
| Chromosome | 7 |
| Position | 128954129 |
| Gene | TNPO3 |
| is a | snp |
| is | mentioned by |
| dbSNP | rs10488631 |
| dbSNP (classic) | rs10488631 |
| ClinGen | rs10488631 |
| ebi | rs10488631 |
| HLI | rs10488631 |
| Exac | rs10488631 |
| Gnomad | rs10488631 |
| Varsome | rs10488631 |
| LitVar | rs10488631 |
| Map | rs10488631 |
| PheGenI | rs10488631 |
| Biobank | rs10488631 |
| 1000 genomes | rs10488631 |
| hgdp | rs10488631 |
| ensembl | rs10488631 |
| geneview | rs10488631 |
| scholar | rs10488631 |
| rs10488631 | |
| pharmgkb | rs10488631 |
| gwascentral | rs10488631 |
| openSNP | rs10488631 |
| 23andMe | rs10488631 |
| SNPshot | rs10488631 |
| SNPdbe | rs10488631 |
| MSV3d | rs10488631 |
| GWAS Ctlg | rs10488631 |
| GMAF | 0.05418 |
| Max Magnitude | 3 |
| ? | (C;C) (C;T) (T;T) | 28 |
|---|---|---|
|
| ||
rs10488631, a SNP located 3' of the IRF5 gene, has been reported as a possibly causative SNP for systemic lupus erthymatosus (SLE), based on a study of ~700 Swedish patients. The risk allele is rs10488631(C), with a reported odds ratio of 2.07 (CI: 1.63-2.62, p = 9x10e-10).[PMID 18063667]
The C allele is also associated with primary biliary cirrhosis, with each C increasing the odds about 1.6 times. [PMID 20639879
] [PMID 20639880]
Each C allele increases risk of Sjögren's syndrome by 1.7 times. [PMID 20861858]
[PMID 19092842] SLE rs10488631 and rs7582694
| GWAS snp | |
|---|---|
| PMID | [PMID 18204098] |
| Trait | Systemic lupus erythematosus |
| Title | Association of systemic lupus erythematosus with C8orf13-BLK and ITGAM-ITGAX |
| Risk Allele | C |
| P-val | 1.9999999999999999E-11 |
| Odds Ratio | NR NR |
| GWAS snp | |
|---|---|
| PMID | [PMID 19458352]
|
| Trait | Primary biliary cirrhosis |
| Title | Primary Biliary Cirrhosis Associated with HLA, IL12A, and IL12RB2 Variants |
| Risk Allele | G |
| P-val | 2E-7 |
| Odds Ratio | 1.52 [1.30-1.78] |
| GWAS snp | |
|---|---|
| PMID | [PMID 20383147]
|
| Trait | Systemic sclerosis |
| Title | Genome-wide association study of systemic sclerosis identifies CD247 as a new susceptibility locus |
| Risk Allele | C |
| P-val | 2E-13 |
| Odds Ratio | 1.50 [1.35-1.67] |
[PMID 19854706] Association of IRF5 polymorphisms with activation of the interferon alpha pathway
| GWAS snp | |
|---|---|
| PMID | [PMID 20453842]
|
| Trait | Rheumatoid arthritis |
| Title | Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk lock |
| Risk Allele | C |
| P-val | 4E-11 |
| Odds Ratio | 1.19 [NR] |
| GWAS snp | |
|---|---|
| PMID | [PMID 20639880]
|
| Trait | Primary biliary cirrhosis |
| Title | Genome-wide meta-analyses identify three loci associated with primary biliary cirrhosis |
| Risk Allele | C |
| P-val | 3E-10 |
| Odds Ratio | 1.63 [NR] |
| GWAS snp | |
|---|---|
| PMID | [PMID 21408207]
|
| Trait | |
| Title | Differential Genetic Associations for Systemic Lupus Erythematosus Based on Anti-dsDNA Autoantibody Production |
| Risk Allele | C |
| P-val | 7E-18 |
| Odds Ratio | 1.9200 [1.66-2.22] |
[PMID 21807777] Preferential Association of Interferon Regulatory Factor 5 Gene Variants with Seronegative Rheumatoid Arthritis in 2 Swedish Case-Control Studies
| GWAS snp | |
|---|---|
| PMID | [PMID 21779181]
|
| Trait | |
| Title | Identification of novel genetic markers associated with clinical phenotypes of systemic sclerosis through a genome-wide association strategy. |
| Risk Allele | |
| P-val | 8E-7 |
| Odds Ratio | 1.6300 [1.34-1.98] |
| GWAS snp | |
|---|---|
| PMID | [PMID 21750679]
|
| Trait | |
| Title | Genome-wide scan identifies TNIP1, PSORS1C1, and RHOB as novel risk loci for systemic sclerosis. |
| Risk Allele | C |
| P-val | 4E-7 |
| Odds Ratio | 1.3500 [1.20-1.51] |
[PMID 22440820] IRF5 polymorphism predicts prognosis in patients with systemic sclerosis
[PMID 17412832] Three functional variants of IFN regulatory factor 5 (IRF5) define risk and protective haplotypes for human lupus.
[PMID 17568788] Opposed independent effects and epistasis in the complex association of IRF5 to SLE.
[PMID 18285424] Interferon regulatory factor 5 (IRF5) gene variants are associated with multiple sclerosis in three distinct populations.
[PMID 18579578] A risk haplotype of STAT4 for systemic lupus erythematosus is over-expressed, correlates with anti-dsDNA and shows additive effects with two risk alleles of IRF5.
[PMID 18668568] Association of the IRF5 risk haplotype with high serum interferon-alpha activity in systemic lupus erythematosus patients.
[PMID 18843782] Different genetic effects of interferon regulatory factor 5 (IRF5) polymorphisms on systemic lupus erythematosus in a Korean population.
[PMID 19109131] Cutting edge: autoimmune disease risk variant of STAT4 confers increased sensitivity to IFN-alpha in lupus patients in vivo.
[PMID 19838195] A large-scale replication study identifies TNIP1, PRDM1, JAZF1, UHRF1BP1 and IL10 as risk loci for systemic lupus erythematosus.
[PMID 20112383] Genetic variants and disease-associated factors contribute to enhanced interferon regulatory factor 5 expression in blood cells of patients with systemic lupus erythematosus.
[PMID 21379322] Risk alleles for systemic lupus erythematosus in a large case-control collection and associations with clinical subphenotypes.
[PMID 21506939] Replicated association of 17q12-21 with susceptibility of primary biliary cirrhosis in a Japanese cohort.
[PMID 23372721] The Systemic Lupus Erythematosus IRF5 Risk Haplotype Is Associated with Systemic Sclerosis
[PMID 22328738] Comprehensive assessment of rheumatoid arthritis susceptibility loci in a large psoriatic arthritis cohort.
| GWAS snp | |
|---|---|
| PMID | [PMID 24871463]
|
| Trait | Systemic lupus erythematosus |
| Title | GWAS identifies novel SLE susceptibility genes and explains the association of the HLA region. |
| Risk Allele | C |
| P-val | 2E-13 |
| Odds Ratio | 1.83 [1.684-1.99] |
[PMID 26092158] IRF5, PTPN22, CD28, IL2RA, KIF5A, BLK and TNFAIP3 genes polymorphisms and lupus susceptibility in a cohort from the Egypt Delta; relation to other ethnic groups
[PMID 31916109] Defining genetic risk factors for scleroderma-associated interstitial lung disease : IRF5 and STAT4 gene variants are associated with scleroderma while STAT4 is protective against scleroderma-associated interstitial lung disease.
