rs2488457
| Orientation | minus |
| Stabilized | minus |
| Geno | Mag | Summary |
|---|---|---|
| (C;C) | 0 | common/normal |
| (C;G) | 1.5 | Slightly increased (~1.5x) risk for certain autoimmune diseases in some populations |
| (G;G) | 1.7 | Slightly increased (~1.7x) risk for certain autoimmune diseases in some populations |
| Reference | GRCh38 38.1/141 |
| Chromosome | 1 |
| Position | 113872746 |
| Gene | AP4B1-AS1, PTPN22 |
| is a | snp |
| is | mentioned by |
| dbSNP | rs2488457 |
| dbSNP (classic) | rs2488457 |
| ClinGen | rs2488457 |
| ebi | rs2488457 |
| HLI | rs2488457 |
| Exac | rs2488457 |
| Gnomad | rs2488457 |
| Varsome | rs2488457 |
| LitVar | rs2488457 |
| Map | rs2488457 |
| PheGenI | rs2488457 |
| Biobank | rs2488457 |
| 1000 genomes | rs2488457 |
| hgdp | rs2488457 |
| ensembl | rs2488457 |
| geneview | rs2488457 |
| scholar | rs2488457 |
| rs2488457 | |
| pharmgkb | rs2488457 |
| gwascentral | rs2488457 |
| openSNP | rs2488457 |
| 23andMe | rs2488457 |
| SNPshot | rs2488457 |
| SNPdbe | rs2488457 |
| MSV3d | rs2488457 |
| GWAS Ctlg | rs2488457 |
| GMAF | 0.2916 |
| Max Magnitude | 1.7 |
rs2488457, known in the literature as c.-1123C>G, represents a variant in the upstream promoter region of the PTPN22 gene on chromosome 1. In at least some studies and in some populations, the minor allele is linked to slightly increased risk for autoimmune diseases such as Crohn's disease, type-1 diabetes, multiple sclerosis, rheumatoid arthritis, lupus, and celiac disease.
| ? | (C;C) (C;G) (G;G) | 28 |
|---|---|---|
|
| ||
[PMID 22197427] PTPN22 and myasthenia gravis: replication in an Italian population and meta-analysis of literature data
[PMID 17000021] No independent role of the -1123 G>C and+2740 A>G variants in the association of PTPN22 with type 1 diabetes and juvenile idiopathic arthritis in two Caucasian populations.
[PMID 17934143] Further evidence of a primary, causal association of the PTPN22 620W variant with type 1 diabetes.
[PMID 18075792
] PTPN22: its role in SLE and autoimmunity.
[PMID 18252225] On the use of general control samples for genome-wide association studies: genetic matching highlights causal variants.
[PMID 18578611] Associations of protein tyrosine phosphatase nonreceptor 22 (PTPN22) gene polymorphisms with susceptibility to Graves' disease in a Japanese population.
[PMID 19180477] Genetic risk factors for rheumatoid arthritis differ in Caucasian and Korean populations.
[PMID 19956096] rs2476601 T allele (R620W) defines high-risk PTPN22 type I diabetes-associated haplotypes with preliminary evidence for an additional protective haplotype.
[PMID 19956101] Overview of the Rapid Response data.
[PMID 19956106] Analysis of 19 genes for association with type I diabetes in the Type I Diabetes Genetics Consortium families.
[PMID 20722033] The susceptibility loci juvenile idiopathic arthritis shares with other autoimmune diseases extend to PTPN2, COG6, and ANGPT1.
[PMID 21193990] A PTPN22 promoter polymorphism -1123G>C is associated with RA pathogenesis in Chinese.
[PMID 22396730] No association of PTPN22 polymorphisms with susceptibility to ocular Behcet's disease in two Chinese Han populations.
[PMID 23025987] Recipient PTPN22 -1123 C/C genotype predicts acute graft-versus-host disease after HLA fully matched unrelated bone marrow transplantation for hematologic malignancies.
[PMID 23456301] Association of PTPN22 gene (rs2488457) polymorphism with ulcerative colitis and high levels of PTPN22 mRNA in ulcerative colitis.
[PMID 25073032] Association Between a Gain-of-Function Variant of PTPN22 and Rejection in Liver Transplantation
[PMID 25781893] STAT4 rs7574865 G/T and PTPN22 rs2488457 G/C Polymorphisms Influence the Risk of Developing Juvenile Idiopathic Arthritis in Han Chinese Patients
[PMID 27888068] Associations of single nucleotide polymorphisms of PTPN22 and Ctla4 genes with the risk of allergic rhinitis in a Chinese Han population.
| ClinVar | |
|---|---|
| Risk | Rs2488457(G;G) rs2488457(T;T) |
| Alt | Rs2488457(G;G) rs2488457(T;T) |
| Reference | Rs2488457(C;C) |
| Significance | Other |
| Disease | Diabetes mellitus |
| Variation | info |
| Gene | PTPN22 AP4B1-AS1 |
| CLNDBN | Diabetes mellitus, insulin-dependent, susceptibility to |
| Reversed | 1 |
| HGVS | NC_000001.10:g.114415368G>C |
| CLNSRC | OMIM Allelic Variant |
| CLNACC | RCV000009465.2, |
