rs5743289
From SNPedia
| Orientation | plus |
| Stabilized | plus |
| Geno | Mag | Summary |
|---|---|---|
| (C;C) | 0 | common on affy axiom data |
| (C;T) | 1 | Perhaps increased risk for certain autoinflammatory disorders |
| (T;T) | 1 | Perhaps increased risk for certain autoinflammatory disorders |
| Reference | GRCh38 38.1/141 |
| Chromosome | 16 |
| Position | 50722863 |
| Gene | NOD2 |
| is a | snp |
| is | mentioned by |
| dbSNP | rs5743289 |
| dbSNP (classic) | rs5743289 |
| ClinGen | rs5743289 |
| ebi | rs5743289 |
| HLI | rs5743289 |
| Exac | rs5743289 |
| Gnomad | rs5743289 |
| Varsome | rs5743289 |
| LitVar | rs5743289 |
| Map | rs5743289 |
| PheGenI | rs5743289 |
| Biobank | rs5743289 |
| 1000 genomes | rs5743289 |
| hgdp | rs5743289 |
| ensembl | rs5743289 |
| geneview | rs5743289 |
| scholar | rs5743289 |
| rs5743289 | |
| pharmgkb | rs5743289 |
| gwascentral | rs5743289 |
| openSNP | rs5743289 |
| 23andMe | rs5743289 |
| SNPshot | rs5743289 |
| SNPdbe | rs5743289 |
| MSV3d | rs5743289 |
| GWAS Ctlg | rs5743289 |
| GMAF | 0.07668 |
| Max Magnitude | 1 |
aka c.2798+158C>T
This quite common variant has been linked to several autoinflammatory disorders, but it appears to be quite a complex interaction that is still not well understood (and only affects a small fraction of the people who carry it anyway). OMIM provides the best summary of the findings to date.
| ? | (C;C) (C;T) (T;T) | 28 |
|---|---|---|
|
| ||
| GWAS snp | |
|---|---|
| PMID | [PMID 18758464 ]
|
| Trait | Inflammatory bowel disease |
| Title | Loci on 20q13 and 21q22 are associated with pediatric-onset inflammatory bowel disease |
| Risk Allele | T |
| P-val | 4.0000000000000001E-10 |
| Odds Ratio | 1.46 [1.29-1.64] |
| GWAS snp | |
|---|---|
| PMID | [PMID 17804789]
|
| Trait | Crohn's disease |
| Title | Genome-wide association study for Crohn's disease in the Quebec Founder Population identifies multiple validated disease loci |
| Risk Allele | |
| P-val | 6.0000000000000001E-17 |
| Odds Ratio | NR NR |
| GWAS snp | |
|---|---|
| PMID | [PMID 17447842]
|
| Trait | Crohn's disease |
| Title | Novel Crohn disease locus identified by genome-wide association maps to a gene desert on 5p13.1 and modulates expression of PTGER4 |
| Risk Allele | |
| P-val | 9.9999999999999995E-7 |
| Odds Ratio | NR NR |
[PMID 17068223] A genome-wide association study identifies IL23R as an inflammatory bowel disease gene.
[PMID 19843337] Investigation of innate immunity genes CARD4, CARD8 and CARD15 as germline susceptibility factors for colorectal cancer.
[PMID 24394805] Genetic susceptibility and genotype–phenotype association in 588 Danish children with inflammatory bowel disease.
| ClinVar | |
|---|---|
| Risk | rs5743289(G;G) Rs5743289(T;T) |
| Alt | rs5743289(G;G) Rs5743289(T;T) |
| Reference | Rs5743289(C;C) |
| Significance | Other |
| Disease | INFLAMMATORY BOWEL DISEASE 1 (CROHN DISEASE) Blau syndrome YAO SYNDROME |
| Variation | info |
| Gene | NOD2 |
| CLNDBN | INFLAMMATORY BOWEL DISEASE 1 (CROHN DISEASE), SUSCEPTIBILITY TO Blau syndrome YAO SYNDROME, SUSCEPTIBILITY TO |
| Reversed | 0 |
| HGVS | NC_000016.9:g.50756774C>T |
| CLNSRC | OMIM Allelic Variant |
| CLNACC | RCV000004962.5, RCV000416486.1, RCV000416489.1, |
