rs3732359

This is a downstream gene variant variant in the NR1I2 gene.

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GWAS Catalog Trait Associations (7)

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

total cholesterol measurement

Jee YH et al. “Genome-wide association studies in a large Korean cohort identify quantitative trait loci for 36 traits and illuminate their genetic architectures.” Nature Communications 16(1):4935 (2025)
Allele A
OR 0.02
p 9.0e-35
N 928,679
Large GWAS
multi-ancestry
Graham SE et al. “The power of genetic diversity in genome-wide association studies of lipids.” Nature 600(7890):675-679 (2021)
Allele A
OR 0.02
p 6.0e-26
N 1,320,016
Large GWAS
European

low density lipoprotein cholesterol measurement

Jee YH et al. “Genome-wide association studies in a large Korean cohort identify quantitative trait loci for 36 traits and illuminate their genetic architectures.” Nature Communications 16(1):4935 (2025)
Allele A
OR 0.02
p 9.0e-22
N 928,679
Large GWAS
multi-ancestry
Graham SE et al. “The power of genetic diversity in genome-wide association studies of lipids.” Nature 600(7890):675-679 (2021)
Allele A
OR 0.01
p 6.0e-15
N 1,320,016
Large GWAS
European
Richardson TG et al. “Evaluating the relationship between circulating lipoprotein lipids and apolipoproteins with risk of coronary heart disease: A multivariable Mendelian randomisation analysis.” Plos Medicine 17(3):e1003062 (2020)
Allele A
OR 0.02
p 5.0e-12
N 440,546
Large GWAS
European
Koskeridis F et al. “Pleiotropic genetic architecture and novel loci for C-reactive protein levels.” Nature Communications 13(1):6939 (2022)
Allele A
OR 0.01
p 2.0e-17
N 361,194
Large GWAS
European

body weight

Sakaue S et al. “A cross-population atlas of genetic associations for 220 human phenotypes.” Nature Genetics 53(10):1415-1424 (2021)
Allele A
OR 0.01
p 5.0e-14
N 525,535
Large GWAS
multi-ancestry

body mass index

Jee YH et al. “Genome-wide association studies in a large Korean cohort identify quantitative trait loci for 36 traits and illuminate their genetic architectures.” Nature Communications 16(1):4935 (2025)
Allele A
OR 0.01
p 2.0e-13
N 928,679
Large GWAS
multi-ancestry
Sakaue S et al. “A cross-population atlas of genetic associations for 220 human phenotypes.” Nature Genetics 53(10):1415-1424 (2021)
Allele A
OR 0.01
p 1.0e-11
N 523,818
Large GWAS
multi-ancestry
Harris BHL et al. “New role of fat-free mass in cancer risk linked with genetic predisposition.” Scientific Reports 14(1):7270 (2024)
Allele A
OR 0.02
p 2.0e-8
N 342,566
Large GWAS
European

non-high density lipoprotein cholesterol measurement

Graham SE et al. “The power of genetic diversity in genome-wide association studies of lipids.” Nature 600(7890):675-679 (2021)
Allele G
OR 0.02
p 2.0e-11
N 1,320,016
Large GWAS
European

omega-6 polyunsaturated fatty acid measurement

Zoodsma M et al. “A genetic map of human metabolism across the allele frequency spectrum.” Nature Genetics 57(10):2445-2455 (2025)
Allele A
OR 0.02
p 1.0e-10
N 450,015
Large GWAS
multi-ancestry

total lipids in lipoprotein particles measurement

Zoodsma M et al. “A genetic map of human metabolism across the allele frequency spectrum.” Nature Genetics 57(10):2445-2455 (2025)
Allele A
OR 0.02
p 1.0e-10
N 450,015
Large GWAS
multi-ancestry
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Research that mentions this SNP (1)

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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

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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