rs1893217
| Orientation | minus |
| Stabilized | minus |
| Geno | Mag | Summary |
|---|---|---|
| (C;C) | 2 | Somewhat increased (~2x) risk for Crohn's disease |
| (C;T) | 1.4 | Slightly increased (1.4x) risk for Crohn's disease |
| (T;T) | 0 | common/normal |
| Reference | GRCh38 38.1/141 |
| Chromosome | 18 |
| Position | 12809341 |
| Gene | PTPN2 |
| is a | snp |
| is | mentioned by |
| dbSNP | rs1893217 |
| dbSNP (classic) | rs1893217 |
| ClinGen | rs1893217 |
| ebi | rs1893217 |
| HLI | rs1893217 |
| Exac | rs1893217 |
| Gnomad | rs1893217 |
| Varsome | rs1893217 |
| LitVar | rs1893217 |
| Map | rs1893217 |
| PheGenI | rs1893217 |
| Biobank | rs1893217 |
| 1000 genomes | rs1893217 |
| hgdp | rs1893217 |
| ensembl | rs1893217 |
| geneview | rs1893217 |
| scholar | rs1893217 |
| rs1893217 | |
| pharmgkb | rs1893217 |
| gwascentral | rs1893217 |
| openSNP | rs1893217 |
| 23andMe | rs1893217 |
| SNPshot | rs1893217 |
| SNPdbe | rs1893217 |
| MSV3d | rs1893217 |
| GWAS Ctlg | rs1893217 |
| GMAF | 0.118 |
| Max Magnitude | 2 |
| ? | (C;C) (C;T) (T;T) | 28 |
|---|---|---|
|
| ||
linked to Crohn's disease and type-1 diabetes
| GWAS snp | |
|---|---|
| PMID | [PMID 19430480 ]
|
| Trait | Type 1 diabetes |
| Title | Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes |
| Risk Allele | |
| P-val | 4E-15 |
| Odds Ratio | NR NR |
[PMID 19951419] Confirmation of the genetic association of CTLA4 and PTPN22 with ANCA-associated vasculitis
[PMID 20222910] Susceptibility loci reported in genome-wide association studies are associated with Crohn's disease in Canadian children
| GWAS snp | |
|---|---|
| PMID | [PMID 20190752]
|
| Trait | Celiac disease |
| Title | Multiple common variants for celiac disease influencing immune gene expression |
| Risk Allele | G |
| P-val | 3E-10 |
| Odds Ratio | 1.17 [1.12-1.23] |
[PMID 21179116] An autoimmune-associated variant in PTPN2 reveals an impairment of IL-2R signaling in CD4(+) T cells
| GWAS snp | |
|---|---|
| PMID | [PMID 21383967]
|
| Trait | |
| Title | Meta-Analysis of Genome-Wide Association Studies in Celiac Disease and Rheumatoid Arthritis Identifies Fourteen Non-HLA Shared Loci |
| Risk Allele | G |
| P-val | 5E-12 |
| Odds Ratio | None None |
[PMID 17554260] Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes.
[PMID 18252225] On the use of general control samples for genome-wide association studies: genetic matching highlights causal variants.
[PMID 18556337] Impact of diabetes susceptibility loci on progression from pre-diabetes to diabetes in at-risk individuals of the diabetes prevention trial-type 1 (DPT-1).
[PMID 18987646] The expanding genetic overlap between multiple sclerosis and type I diabetes.
[PMID 19073967] Shared and distinct genetic variants in type 1 diabetes and celiac disease.
[PMID 20722033] The susceptibility loci juvenile idiopathic arthritis shares with other autoimmune diseases extend to PTPN2, COG6, and ANGPT1.
[PMID 22021207] Crohn's disease-associated polymorphism within the PTPN2 gene affects muramyl-dipeptide-induced cytokine secretion and autophagy.
| GWAS snp | |
|---|---|
| PMID | [PMID 23128233]
|
| Trait | Inflammatory bowel disease |
| Title | Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. |
| Risk Allele | G |
| P-val | 3E-26 |
| Odds Ratio | 1.17 [1.127-1.216] |
| GWAS snp | |
|---|---|
| PMID | [PMID 21102463]
|
| Trait | Crohn's disease |
| Title | Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. |
| Risk Allele | G |
| P-val | 1E-14 |
| Odds Ratio | 1.25 [1.18-1.32] |
[PMID 24127071] Associations between PTPN2 polymorphisms and susceptibility to ulcerative colitis and Crohn's disease: a meta-analysis
[PMID 23518806] Association between the PTPN2 gene and Crohn's disease: dissection of potential causal variants
[PMID 24480412] PTPN2 rs1893217 single-nucleotide polymorphism is associated with risk of Behçet's disease in a Chinese Han population
[PMID 22960018] Investigation of the vitamin D receptor gene (VDR) and its interaction with protein tyrosine phosphatase, non-receptor type 2 gene (PTPN2) on risk of islet autoimmunity and type 1 diabetes: the Diabetes Autoimmunity Study in the Young (DAISY).
[PMID 26928573] The Clinical Relevance of the IBD-Associated Variation within the Risk Gene Locus Encoding Protein Tyrosine Phosphatase Non-Receptor Type 2 in Patients of the Swiss IBD Cohort.
[PMID 32031616] Presence of PTPN2 SNP rs1893217 Enhances the Anti-inflammatory Effect of Spermidine.
