rs6939861

This is a regulatory region variant variant in the TFEB gene.

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GWAS Catalog Trait Associations (2)

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

sex hormone-binding globulin measurement

Ruth KS et al. “Using human genetics to understand the disease impacts of testosterone in men and women.” Nature Medicine 26(2):252-258 (2020)
Allele G
OR 0.01
p 3.0e-16
N 180,094
Large GWAS
European
Harrison S et al. “Testosterone and socioeconomic position: Mendelian randomization in 306,248 men and women in UK Biobank.” Science Advances 7(31) (2021)
Allele G
OR 1.18
p 1.0e-10
N 104,632
Major Consortium StudyLarge GWAS
European

testosterone measurement

Venkatesh SS et al. “Genome-wide analyses identify 25 infertility loci and relationships with reproductive traits across the allele frequency spectrum.” Nature Genetics 57(5):1107-1118 (2025)
Allele A
OR 0.02
p 4.0e-13
N 235,096
Large GWAS
European
Ruth KS et al. “Using human genetics to understand the disease impacts of testosterone in men and women.” Nature Medicine 26(2):252-258 (2020)
Allele A
OR 0.03
p 2.0e-12
N 194,453
Large GWAS
European
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Research that mentions this SNP (1)

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SNP interactions of PGC with its neighbor lncRNAs enhance the susceptibility to gastric cancer/atrophic gastritis and influence the expression of involved molecules
AssociationN=2,228Zhi Lv et al.(2018)· Cancer Medicine

A case-control study of 2,228 northern Chinese subjects examined SNP interactions between the PGC gene (7 SNPs) and neighboring long noncoding RNA genes (7 SNPs) on gastric cancer and atrophic gastritis susceptibility. The study identified 15 pairwise SNP interactions (5 with AG risk, 10 with GC risk), with two GC-related interactions surviving Bonferroni correction: PGC rs6939861 with lnc-C6orf-132-1 rs7749023 (P=0.049) and rs7747696 (P=0.007, OR=2.06).

Traits studied:Atrophic gastritisGastric cancer
PubMedDOIMetascience Observatory

About TFEB

Enables DNA-binding transcription factor activity; enzyme binding activity; and transcription cis-regulatory region binding activity. Involved in several processes, including antibacterial innate immune response; cellular response to amino acid starvation; and positive regulation of metabolic process. Located in cytosol and lysosomal membrane. Is active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

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Gene information from NCBI Gene. Variant classifications from ClinVar.

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