rs1124911 (ACTG1P17): Korean GWAS Variant

Key takeaways

• rs1124911 was identified in a Korean genome-wide association study of 153,950 individuals covering 36 different biological traits, though the specific trait tied to this locus is not specified in the available study text
• The variant's alternate allele increases expression of SNHG21 (a small nucleolar RNA host gene) in pancreas, pituitary gland, liver, and immune cells
• The same allele also increases expression of HOMER2 and GOLGA6L9 in tibial nerve tissue, and raises expression at the ACTG1P17 and ENSG00000279758 loci in cultured fibroblasts
• All primary genome-wide association study evidence comes from Korean individuals; replication in other ancestry groups is not described in the available sources

What the research says A genome-wide association study (a research approach that scans the entire genome for variants associated with particular traits) conducted in the Korean Cancer Prevention Study-II (KCPS-II) Biobank analyzed 36 quantitative traits - including anthropometric measures, metabolic biomarkers, liver enzymes, kidney function markers, hematological traits, and cardiovascular measurements - across 153,950 Korean participants. The study identified 301 previously unreported genetic loci and, through meta-analysis with the Korean Genome and Epidemiology Study, Biobank Japan, Taiwan Biobank, and UK Biobank, flagged 4,588 additional loci not significant in any single contributing study. The specific quantitative trait associated with rs1124911 at the ACTG1P17 locus (a pseudogene, meaning a DNA sequence resembling the actin gamma 1 gene but not producing a functional protein) is not detailed in the provided study text.

Reported associations

• Quantitative traits (Korean cohort): rs1124911 was identified in a genome-wide association study of 36 quantitative traits in 153,950 Korean individuals; the specific phenotype linked to this locus is not specified in the provided source text
• SNHG21 expression: the alternate allele increases expression of this small nucleolar RNA host gene in pancreas, pituitary gland, liver, and EBV-transformed lymphocytes (immune cells cultured in the laboratory using Epstein-Barr virus) GTEx Portal
• HOMER2 expression: the alternate allele increases expression in tibial nerve tissue GTEx Portal
• GOLGA6L9 expression: the alternate allele increases expression in tibial nerve tissue GTEx Portal
• ACTG1P17 expression: the alternate allele increases expression in cultured fibroblasts (connective tissue cells grown in the laboratory) GTEx Portal
• ENSG00000279758 expression: the alternate allele increases expression in cultured fibroblasts GTEx Portal

Evidence quality The genome-wide association study evidence for rs1124911 comes from a single large Korean cohort (KCPS-II, n=153,950), with a meta-analysis incorporating additional East Asian and one European biobank; however, the specific p-value and effect size for this locus are not reported in the provided study text, making the strength of the phenotypic association unclear. The GTEx eQTL data (GTEx v11, n=953 donors) - where eQTL, or expression quantitative trait locus, refers to a DNA variant that influences how much a nearby gene is expressed - satisfies a false discovery rate threshold below 0.05 across five affected genes and multiple tissue types, providing moderate confidence in the tissue-specific expression effects. Because the genome-wide association study sample is exclusively East Asian (Korean), these findings may not generalize to other populations, and no non-Asian replication is described in the available sources.

Tissue-specific expression effects

• SNHG21: increased expression in pancreas, pituitary gland, liver, and EBV-transformed lymphocytes - the alternate allele consistently raises transcript levels across all four tissue types GTEx Portal
• ENSG00000279758: increased expression in cultured fibroblasts GTEx Portal
• ACTG1P17: increased expression in cultured fibroblasts GTEx Portal
• HOMER2: increased expression in tibial nerve tissue GTEx Portal
• GOLGA6L9: increased expression in tibial nerve tissue GTEx Portal

Lifestyle considerations No lifestyle considerations on file for this variant.