Variant Annotations
PharmGKB variant annotations provide information about variant-drug pairs based on individual PubMed publications. Each annotation represents information from a single paper and the goal is to report the information that the author states, not an interpretation of the paper. The PMID for supporting PubMed publications is found in the "Evidence" field.
Information presented, including study size, allele frequencies and statistics is taken directly from the publication. However, if the author does not correct p-values in cases of multiple hypotheses, curators may apply a Bonferroni correction. Curators attempt to report study size based on the actual number of participants used for the calculation of the association statistics, so the number may vary slightly from what is reported in the abstract of the paper. OMB Race Category information is derived from the paper and mapped to standardized categories. Category definitions may be found by clicking on the "OMB Race Category" link.
There are 3 annotations for this variant. Register or sign in to see them.
VIP Variant in NR1I2
One variant, rs3814055 (-25385 C>T, AF364606) has been studied by several researchers, for both disease risk and pharmacogenomics impact, with conflicting results. The C allele has been associated with Inflammatory Bowel Diseases (IBD) [Article:16472590] in a European population; the T allele, as part of the haplotype rs3814055 T; rs6784598 C; rs2276707 C was associated with a risk for ulcerative colitis (UC) (but not rs3814055 T in alone) in a Spanish population [Article:17828778]. Other studies did not find any association between this NR1I2 polymorphism (in linkage disequilibrium with rs1523127) and IBD, Crohn's disease (CD), UC [Articles:17047126, 18381611]. Lambda et al [Article:17925385] found the T allele had lower NR1I2 expression in male livers (that would be associated with lower CYP3A4 induction and metabolism). Consistent with this finding, in a study of 91 kidney transplants, the -25385 C allele was part of a haplotype where the bioavailability of cyclosporine was significantly less than other haploytpes (indicating that there was increased metabolism of cyclosporine) [Article:20107201]. On the other hand, Zhang [Article:11668216] found for the -25385 T allele (and -24113 A allele) a 2-fold higher ERMBT after rifampin treatment (indicating greater metabolism).
All results remain to be validated.
| Key Publications: | |
|---|---|
| Drugs / Other Molecules |
Drug (2)
|
| Diseases | Colitis, Ulcerative Crohn Disease Inflammatory Bowel Diseases |
Appendix
Genomic Variant & GenBank ID: 45005C>T on AF364606
mRNA Variant & GenBank ID: 705C>T on NM_003889.3
GoldenPath Position: chr3:120982725
Connected Diseases
Publications related to rs3814055 at chr3:119500035: 7
Cross-References
- UCSC Golden Path:
- chr3:119500035
- dbSNP:
- rs3814055
- ALFRED:
- SI393119A
- HapMap:
- rs3814055
- JSNP:
- IMS-JST174284
Platform Availability
- Illumina