rs1050152
| Orientation | plus |
| Stabilized | plus |
| Geno | Mag | Summary |
|---|---|---|
| (C;C) | 0 | normal |
| (C;T) | 2 | 2.1x increased risk of Crohn's disease |
| (T;T) | 2.1 | 2.1x increased risk of Crohn's disease |
| Reference | GRCh38 38.1/141 |
| Chromosome | 5 |
| Position | 132340627 |
| Gene | LOC553103, SLC22A4 |
| is a | snp |
| is | mentioned by |
| dbSNP | rs1050152 |
| dbSNP (classic) | rs1050152 |
| ClinGen | rs1050152 |
| ebi | rs1050152 |
| HLI | rs1050152 |
| Exac | rs1050152 |
| Gnomad | rs1050152 |
| Varsome | rs1050152 |
| LitVar | rs1050152 |
| Map | rs1050152 |
| PheGenI | rs1050152 |
| Biobank | rs1050152 |
| 1000 genomes | rs1050152 |
| hgdp | rs1050152 |
| ensembl | rs1050152 |
| geneview | rs1050152 |
| scholar | rs1050152 |
| rs1050152 | |
| pharmgkb | rs1050152 |
| gwascentral | rs1050152 |
| openSNP | rs1050152 |
| 23andMe | rs1050152 |
| SNPshot | rs1050152 |
| SNPdbe | rs1050152 |
| MSV3d | rs1050152 |
| GWAS Ctlg | rs1050152 |
| GMAF | 0.1846 |
| Max Magnitude | 2.1 |
| ? | (C;C) (C;T) (T;T) | 28 |
|---|---|---|
|
| ||
rs1050152, a SNP in the SLC22A4 gene known as L503F, has been associated with an autoimmune disease, in this case, Crohn's disease, odds ratio = 2.1 (CI = 1.31–3.39, p = 0.002), based on a study of 203 cases and 200 controls. The risk allele is rs1050152(T).[PMID 15107849]
A nearby SNP (rs2631367) in the promoter region of the SLC22A5 gene defines a haplotype along with rs3792876, with odds ratio reported as similar for either SNP or the haplotype. Referring to the TC risk haplotype, the population risk attributable to heterozygotes was 19%, and for homozygous haplotype carriers, 27%.[PMID 15107849]
[PMID 21061378] Two independent genetic factors responsible for the associations of the IBD5 locus with Crohn's disease in the Czech population
[PMID 21122496] OCTN1 variant L503F is associated with familial and sporadic inflammatory bowel disease
[PMID 21674708] Two independent genetic factors responsible for the associations of the IBD5 locus with Crohn's disease in the Czech population
[PMID 21695374] Haplotype in the IBD5 region is associated with refractory Crohn's disease in Slovenian patients and modulates expression of the SLC22A5 gene
[PMID 22606245
] Evolutionary Dynamics of Co-Segregating Gene Clusters Associated with Complex Diseases
| ClinVar | |
|---|---|
| Risk | Rs1050152(T;T) |
| Alt | Rs1050152(T;T) |
| Reference | Rs1050152(C;C) |
| Significance | Non-pathogenic |
| Disease | SLC22A4 POLYMORPHISM |
| Variation | info |
| Gene | SLC22A4 LOC553103 |
| CLNDBN | SLC22A4 POLYMORPHISM |
| Reversed | 0 |
| HGVS | NC_000005.9:g.131676320C>T |
| CLNSRC | OMIM Allelic Variant UniProtKB (protein) |
| CLNACC | RCV000006106.2, |
[PMID 15843420] DLG5 variants do not influence susceptibility to inflammatory bowel disease in the Scottish population.
[PMID 15955786] Polymorphisms in the DLG5 and OCTN cation transporter genes in Crohn's disease.
[PMID 16796743] Evidence for the association of the SLC22A4 and SLC22A5 genes with type 1 diabetes: a case control study.
[PMID 17667713] Analysis of candidate genes on chromosomes 5q and 19p in celiac disease.
[PMID 17786191] rs1004819 is the main disease-associated IL23R variant in German Crohn's disease patients: combined analysis of IL23R, CARD15, and OCTN1/2 variants.
[PMID 18064451] IL4 in the 5q31 context: association studies of type 1 diabetes and rheumatoid arthritis in the Spanish population.
[PMID 18698678] Replication of interleukin 23 receptor and autophagy-related 16-like 1 association in adult- and pediatric-onset inflammatory bowel disease in Italy.
[PMID 18715515] Lack of evidence for association of primary sclerosing cholangitis and primary biliary cirrhosis with risk alleles for Crohn's disease in Polish patients.
[PMID 18756601] OCTN and CARD15 gene polymorphism in Chinese patients with inflammatory bowel disease.
[PMID 19141711] Functional genetic variation in the basal promoter of the organic cation/carnitine transporters OCTN1 (SLC22A4) and OCTN2 (SLC22A5).
[PMID 23474282] Expression Quantitative Trait Loci Analysis Identifies Associations Between Genotype and Gene Expression in Human Intestine
[PMID 23127916] Polymorphisms in OCTN1 and OCTN2 transporters genes are associated with prolonged time to progression in unresectable gastrointestinal stromal tumours treated with imatinib therapy
[PMID 24415875] Susceptibility to ulcerative colitis in Hungarian patients determined by gene-gene interactions
[PMID 22875622] Association between imatinib transporters and metabolizing enzymes genotype and response in newly diagnosed chronic myeloid leukemia patients receiving imatinib therapy.
[PMID 22957492] Pathway analysis of a genome-wide association study of ileal Crohn's disease.
