rs6784598

This variant is located in the NR1I2 gene.

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GWAS Catalog Trait Associations (1)

Genome-wide significant associations (p < 5×10⁻⁸) from the NHGRI-EBI GWAS Catalog.

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Research that mentions this SNP (2)

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Investigation of associations between the pregnane-X receptor gene (NR1I2) and Crohnʼs disease in Canadian children using a gene-wide haplotype-based approach
AssociationN=1,001Devendra K. Amre et al.(2008)· Inflammatory Bowel Diseases

A case-control and family-based study of 270 Canadian children with Crohn's disease, 336 controls, and 395 parents found no significant associations between the NR1I2 gene (pregnane-X receptor) and pediatric CD susceptibility using eight tag-SNPs (rs1523127, rs16830505, rs2461823, rs2461818, rs6785049, rs3732359, rs1054190, rs3814057). Only rs2461823 showed marginal association (P=0.05), but this did not survive multiple testing correction. No haplotype associations were detected (omnibus P=0.61).

Traits studied:Crohn's diseaseInflammatory bowel disease
PubMedDOIMetascience Observatory
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Role of the PXR gene locus in inflammatory bowel diseases
AssociationN=1,246Alfonso Martínez et al.(2007)· Inflammatory Bowel Diseases

A case-control study of 365 UC and 331 CD patients versus 550 controls in a Spanish population found that the PXR gene locus (specifically a risk haplotype rs3814055*T//rs6784598*C//rs2276707*C) was significantly associated with extensive ulcerative colitis (OR=1.66, 95% CI 1.20-2.30, P=0.001). The study also identified an epistatic interaction between PXR -25385C/T and MDR1 rs3789243, where carriers of risk alleles at both loci showed increased susceptibility to extensive UC.

Traits studied:Crohn's diseaseExtensive ulcerative colitisInflammatory bowel diseaseLeft-sided ulcerative colitisUlcerative colitis
PubMedDOIMetascience Observatory

About NR1I2

This gene product belongs to the nuclear receptor superfamily, members of which are transcription factors characterized by a ligand-binding domain and a DNA-binding domain. The encoded protein is a transcriptional regulator of the cytochrome P450 gene CYP3A4, binding to the response element of the CYP3A4 promoter as a heterodimer with the 9-cis retinoic acid receptor RXR. It is activated by a range of compounds that induce CYP3A4, including dexamethasone and rifampicin. Several alternatively spliced transcripts encoding different isoforms, some of which use non-AUG (CUG) translation initiation codon, have been described for this gene. Additional transcript variants exist, however, they have not been fully characterized. [provided by RefSeq, Jul 2008]

View all NR1I2 variants →

Gene information from NCBI Gene. Variant classifications from ClinVar.

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