rs339331

This is a intron variant variant in the RFX6 gene.

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GWAS Catalog Trait Associations (6)

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

prostate carcinoma

Ishigaki K et al. “Large-scale genome-wide association study in a Japanese population identifies novel susceptibility loci across different diseases.” Nature Genetics 52(7):669-679 (2020)
Allele C
OR 0.82
p 5.0e-20
N 109,347
Large GWAS
East Asian
Emami NC et al. “A Large-Scale Association Study Detects Novel Rare Variants, Risk Genes, Functional Elements, and Polygenic Architecture of Prostate Cancer Susceptibility.” Cancer Research 81(7):1695-1703 (2021)
Allele C
OR 1.10
p 4.0e-10
N 208,253
Large GWAS
European
Takata R et al. “12 new susceptibility loci for prostate cancer identified by genome-wide association study in Japanese population.” Nature Communications 10(1):4422 (2019)
Allele C
OR 1.22
p 9.0e-15
N 15,770
Large GWAS
East Asian
Wang M et al. “Large-scale association analysis in Asians identifies new susceptibility loci for prostate cancer.” Nature Communications 6:8469 (2015)
Allele C
OR 1.28
p 4.0e-11
N 7,394
Large GWAS
East Asian
Takata R et al. “Genome-wide association study identifies five new susceptibility loci for prostate cancer in the Japanese population.” Nature Genetics 42(9):751-4 (2010)
Allele C
OR 1.22
p 2.0e-12
N 4,969
Large GWAS
East Asian

phospholipids in small HDL measurement

Zoodsma M et al. “A genetic map of human metabolism across the allele frequency spectrum.” Nature Genetics 57(10):2445-2455 (2025)
Allele C
OR 0.02
p 2.0e-13
N 450,015
Large GWAS
multi-ancestry

total lipids in small HDL measurement

Zoodsma M et al. “A genetic map of human metabolism across the allele frequency spectrum.” Nature Genetics 57(10):2445-2455 (2025)
Allele C
OR 0.02
p 2.0e-13
N 450,015
Large GWAS
multi-ancestry

concentration of small HDL 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 C
OR 0.02
p 5.0e-12
N 450,015
Large GWAS
multi-ancestry

cholesterol in small HDL measurement

Zoodsma M et al. “A genetic map of human metabolism across the allele frequency spectrum.” Nature Genetics 57(10):2445-2455 (2025)
Allele C
OR 0.01
p 1.0e-11
N 450,015
Large GWAS
multi-ancestry
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Research that mentions this SNP (2)

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A functional variant in TP63 at 3q28 associated with bladder cancer risk by creating an miR‐140‐5p binding site
AssociationN=6,832Meilin Wang et al.(2016)· International Journal of Cancer

A three-stage fine mapping study of the 3q28 bladder cancer susceptibility locus identified rs35592567 in the 3'-UTR of TP63 as a functional causal variant. The T allele was significantly associated with decreased bladder cancer risk (OR=0.82, 95% CI=0.75-0.90, P=9.797×10⁻⁶). Functional studies showed the variant affects miR-140-5p binding, regulating TP63 post-transcriptional levels and affecting bladder cancer cell proliferation, migration, and invasion.

Traits studied:Bladder cancer
PubMedDOIMetascience Observatory
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A genome-wide association study of prostate cancer in West African men
AssociationN=932Michael Blaise Cook et al.(2014)· Human Genetics

Genome-wide association study of 474 prostate cancer cases and 458 controls from West African men identified a novel prostate cancer susceptibility locus at 10p14 marked by rs7918885 (p=1.29×10⁻⁷), localized to an intron of the lncRNA gene RP11-543F8.2. A stratified analysis by Gleason score revealed additional associations including rs34575154 in PCDHA1 at 5q31.3 (p=3.66×10⁻⁸) for high-grade disease and rs985081 at Xq28 (p=8.66×10⁻⁹) for low-grade disease. Validation in the African Ancestry Prostate Cancer GWAS Consortium showed limited replication, with only rs2993385 at 10p14 reaching nominal significance (p<0.05), highlighting population-specific genetic architecture.

Traits studied:Prostate cancerProstate cancer (high-grade/Gleason score ≥7)Prostate cancer (low-grade/Gleason score <7)
PubMedDOIMetascience Observatory

About RFX6

The nuclear protein encoded by this gene is a member of the regulatory factor X (RFX) family of transcription factors. Studies in mice suggest that this gene is specifically required for the differentiation of islet cells for the production of insulin, but not for the differentiation of pancreatic polypeptide-producing cells. It regulates the transcription factors involved in beta-cell maturation and function, thus, restricting the expression of the beta-cell differentiation and specification genes. Mutations in this gene are associated with Mitchell-Riley syndrome, which is characterized by neonatal diabetes with pancreatic hypoplasia, duodenal and jejunal atresia, and gall bladder agenesis.[provided by RefSeq, Sep 2010]

View all RFX6 variants →

Gene information from NCBI Gene. Variant classifications from ClinVar.

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