rs11860299 (POLR3E): Brain Expression Variant
Key takeaways
- rs11860299 is at the POLR3E locus, identified in large-scale East Asian genome-wide association studies.
- The alternative allele is linked to increased expression of ENSG00000274460 in brain cerebellum tissue (expression slope +0.62, 953 GTEx donors).
- The same allele is also linked to increased expression of EEF2K in cultured fibroblast cells (expression slope +0.32, 953 GTEx donors).
- Korean and Japanese biobanks studying hundreds of thousands of participants form the primary evidence base for this locus.
Key takeaways
- rs11860299 is at the POLR3E locus, identified in large-scale East Asian genome-wide association studies.
- The alternative allele is linked to increased expression of ENSG00000274460 in brain cerebellum tissue (expression slope +0.62, 953 GTEx donors).
- The same allele is also linked to increased expression of EEF2K in cultured fibroblast cells (expression slope +0.32, 953 GTEx donors).
- Korean and Japanese biobanks studying hundreds of thousands of participants form the primary evidence base for this locus.
What the research says Two large East Asian GWAS (genome-wide association studies that scan millions of genetic variants across thousands of participants to find trait associations) provide the primary evidence context for this locus: a Korean cohort of 153,950 individuals analyzed 36 quantitative traits including metabolic, hematological, and anthropometric measures and discovered 301 previously unreported loci, while a cross-population atlas of 220 phenotypes in a Japanese biobank (n = 179,000), extended through meta-analysis with UK Biobank and FinnGen (combined n = 628,000), identified approximately 5,000 new loci across those populations. Specific phenotypic association data for rs11860299 are not detailed in the available study excerpts, so trait-level claims should be treated as preliminary. GTEx eQTL analysis (which links genetic variants to tissue-specific differences in gene expression - the process by which genes produce functional molecules) shows that the alternative allele at rs11860299 is associated with increased expression of ENSG00000274460 in brain cerebellum tissue and increased expression of EEF2K in cultured fibroblast cells GTEx Portal.
Reported associations
- Gene expression in brain cerebellum - ENSG00000274460: The alternative allele is associated with increased expression of ENSG00000274460 in brain cerebellum tissue (eQTL slope +0.62, p = 1.0e-4, n = 953 GTEx donors) GTEx Portal
- Gene expression in cultured fibroblasts - EEF2K: The alternative allele is associated with increased expression of EEF2K in cultured fibroblast cells (eQTL slope +0.32, p = 1.2e-6, n = 953 GTEx donors) GTEx Portal
Evidence quality The GTEx eQTL evidence rests on 953 donors at FDR (false discovery rate - a statistical threshold that limits the proportion of spurious findings) below 0.05, providing moderate-confidence support for the two tissue-specific expression associations reported here. The EEF2K fibroblast signal (p = 1.2e-6) is statistically more robust than the ENSG00000274460 brain cerebellum signal (p = 1.0e-4). The two GWAS studies underlying the broader evidence base cover large East Asian discovery cohorts - 153,950 Korean participants and 179,000 Japanese participants, with meta-analyses extending to 628,000 individuals - but specific phenotypic association results for rs11860299 are not available from the provided study excerpts, so trait-level associations must be treated as preliminary. No conflicting findings were identified among the available data sources, though the evidence base for clinical trait associations is limited at this time.
Tissue-specific expression effects
- ENSG00000274460: Increased expression in brain cerebellum tissue; the alternative allele is associated with higher expression at this genomic locus GTEx Portal
- EEF2K: Increased expression in cultured fibroblast cells; the alternative allele is associated with higher EEF2K expression in this cell type GTEx Portal
Lifestyle considerations No lifestyle considerations on file for this variant.
Frequently asked questions
What is rs11860299 associated with?
GTEx data from 953 donors show that this variant's alternative allele is linked to increased expression of ENSG00000274460 in brain cerebellum tissue and increased EEF2K expression in cultured fibroblast cells. Specific clinical trait associations are under ongoing investigation in large East Asian genome-wide studies.
Which populations have been studied for rs11860299?
Primary evidence comes from Korean and Japanese biobank studies, with meta-analyses also incorporating European cohorts from the UK Biobank and FinnGen, reaching a combined sample of about 628,000 individuals.
What does eQTL mean for this variant?
An eQTL (expression quantitative trait locus) is a genetic variant associated with measurable differences in how much a gene is expressed in a specific tissue. GTEx data show rs11860299 acts as an eQTL in brain cerebellum tissue and in cultured fibroblast cells.
How large were the studies that investigated rs11860299?
A Korean cohort study included 153,950 individuals analyzed for 36 quantitative traits, and a Japanese biobank study covered 179,000 individuals across 220 phenotypes, with meta-analyses extending to about 628,000 participants combined.
How strong is the evidence for rs11860299?
The GTEx eQTL evidence is based on 953 donors at a controlled false discovery rate below 0.05, providing moderate confidence for the expression associations. Broader clinical trait associations from large GWAS are preliminary, as specific effect data for this variant are not yet detailed in the available study excerpts.