Expressive

rs12363342 (MS4A15): Multi-Tissue eQTL Variant

Key takeaways

  • rs12363342 reduces MS4A15 expression in ovary tissue based on population-level gene expression data
  • The same variant is linked to reduced MS4A8 expression in skeletal muscle, the statistically strongest signal found
  • In esophageal and subcutaneous fat tissue, the variant is associated with modest increases in CCDC86 expression
  • These are gene-expression effects in a population study, not clinical diagnoses or disease risk predictions
  • No clinical trait associations for this variant are reported in the provided studies

Key takeaways

  • rs12363342 reduces MS4A15 expression in ovary tissue based on population-level gene expression data
  • The same variant is linked to reduced MS4A8 expression in skeletal muscle, the statistically strongest signal found
  • In esophageal and subcutaneous fat tissue, the variant is associated with modest increases in CCDC86 expression
  • These are gene-expression effects in a population study, not clinical diagnoses or disease risk predictions
  • No clinical trait associations for this variant are reported in the provided studies

What the research says Expression-QTL data from GTEx v11 (953 donors, FDR<0.05) identifies rs12363342 as a variant that predicts gene activity levels across multiple tissues; the alternate allele is linked to reduced expression of MS4A15 (membrane-spanning 4-domain subfamily A, member 15) in ovary and reduced expression of the related MS4A8 in skeletal muscle GTEx Portal. The same variant is also linked to modestly increased expression of CCDC86 (coiled-coil domain containing 86) in esophageal gastroesophageal junction and subcutaneous adipose tissue GTEx Portal. A provided GWAS methodology study (Loya et al., Nature Genetics 2025) analyzed approximately 405,000 UK Biobank individuals using the Quickdraws algorithm but does not enumerate specific associations for this variant in the available text.

Reported associations

  • MS4A15 expression (ovary): The alternate allele is associated with reduced expression (slope -0.46, p=2.4e-6) GTEx Portal
  • MS4A8 expression (skeletal muscle): The alternate allele is associated with reduced expression (slope -0.21, p=1.2e-13) GTEx Portal
  • CCDC86 expression (esophageal gastroesophageal junction): The alternate allele is associated with increased expression (slope +0.12, p=5.4e-5) GTEx Portal
  • CCDC86 expression (subcutaneous adipose): The alternate allele is associated with increased expression (slope +0.09, p=1.6e-4) GTEx Portal

Evidence quality All specific evidence for rs12363342 comes from GTEx v11 eQTL analyses (953 donors, FDR<0.05 - meaning fewer than 5% of reported signals are expected to be false positives by chance). eQTL findings describe regulatory effects on gene activity levels rather than direct links to clinical outcomes or disease risk. The strongest signal is the MS4A8 skeletal muscle association (p=1.2e-13); the MS4A15 ovary (p=2.4e-6) and CCDC86 adipose (p=1.6e-4) associations are more modest but remain within the FDR threshold. The provided GWAS methodology study (Loya et al., Nature Genetics 2025, approximately 405,000 UK Biobank samples) does not enumerate specific findings for this variant in the available text, so clinical trait associations and independent replication data are absent from the provided materials.

Tissue-specific expression effects

  • MS4A15: Reduced expression in ovary tissue GTEx Portal
  • MS4A8: Reduced expression in skeletal muscle GTEx Portal
  • CCDC86: Increased expression in esophageal gastroesophageal junction and subcutaneous adipose tissue GTEx Portal

Lifestyle considerations No lifestyle considerations on file for this variant.

Frequently asked questions

What is rs12363342?

rs12363342 is a single nucleotide variant (a single-letter change in the DNA code) located in the MS4A15 gene region. Population-level data from GTEx links it to changes in gene activity levels across several tissues.

What does the MS4A15 gene do?

MS4A15 belongs to the membrane-spanning 4-domain subfamily A, a family of proteins that span cell membranes and are thought to be involved in cell signaling. Its specific biological role is not fully characterized in the provided research.

Which tissues are affected by rs12363342?

Based on GTEx v11 population data, the variant is associated with reduced expression of MS4A15 in ovary tissue, reduced expression of the related MS4A8 in skeletal muscle, and increased expression of CCDC86 in esophageal and subcutaneous fat tissues.

Is rs12363342 linked to any disease?

The provided studies do not report specific disease or clinical trait associations for rs12363342. The available evidence is limited to gene expression effects from population-level eQTL analyses, which describe regulatory mechanisms rather than clinical outcomes.

What is an eQTL and why does it matter?

An eQTL (expression quantitative trait locus) is a genomic location where a genetic variant is statistically linked to differences in how much of a gene is produced in a given tissue. eQTLs reveal potential regulatory mechanisms but do not directly indicate disease risk.