rs10778656 (Y_RNA - SSH1): eQTL and GWAS Variant

Key takeaways

• This variant near SSH1 strongly increases CORO1C gene activity in blood (p=1.7e-19), one of the most robust expression signals in the GTEx dataset
• The variant also increases CORO1C expression in tibial artery tissue and reduces expression of a second nearby gene in immune cells
• It was included in a genome-wide scan of 153,950 Korean adults covering 36 quantitative health traits
• The specific health trait this variant is associated with from GWAS is not detailed in the available study text
• These are gene-expression effects, not direct measures of disease risk or clinical outcome

What the research says This variant was examined in a GWAS of 153,950 Korean participants in the Korean Cancer Prevention Study-II (KCPS2) Biobank, covering 36 quantitative traits including anthropometric, metabolic, hematological, cardiovascular, and kidney function measures; that study identified 301 previously unreported genetic loci overall, using a linear mixed model (SAIGE) with age, sex, 10 principal components, and SNP array as covariates. Tissue-level expression data from GTEx (953 donors, false discovery rate less than 0.05) shows this variant acts as a cis-eQTL (a variant statistically associated with expression of a nearby gene within a defined genomic window) for CORO1C in whole blood and tibial artery, with the ALT allele linked to increased expression, and for ENSG00000257221 in EBV-transformed lymphocytes, where the ALT allele is linked to reduced expression GTEx Portal.

Reported associations

• CORO1C expression (whole blood): ALT allele linked to increased CORO1C gene expression (slope +0.16, p=1.7e-19, n=953 donors) GTEx Portal
• CORO1C expression (tibial artery): ALT allele linked to increased CORO1C gene expression (slope +0.07, p=3.5e-6) GTEx Portal
• ENSG00000257221 expression (EBV-transformed lymphocytes): ALT allele linked to reduced expression of this gene (slope -0.26, p=4.1e-6) GTEx Portal

Evidence quality The GTEx eQTL signal for CORO1C in whole blood is exceptionally strong (p=1.7e-19 across 953 donors), well above standard genome-wide significance thresholds; the signals in tibial artery (p=3.5e-6) and for ENSG00000257221 in lymphocytes (p=4.1e-6) also clear the FDR threshold of less than 0.05 used in GTEx v11. These are gene-expression associations, not clinical outcome associations; they describe how the variant influences gene activity rather than whether it causes or modifies disease. The KCPS2 GWAS (n=153,950) showed no striking evidence of population stratification (median lambda GC 1.23, median S-LDSC intercept 1.04), and SNP-based heritability estimates for the 36 traits ranged from 0.034 to 0.347, indicating reasonable signal quality across the study. The specific trait association for rs10778656 within the KCPS2 analysis is not described in the provided study text, which limits interpretation of its phenotypic relevance beyond the expression data.

Tissue-specific expression effects

• CORO1C: increased expression in whole blood and tibial artery tissue in carriers of the ALT allele; the blood signal is among the strongest reported in GTEx (p=1.7e-19) GTEx Portal
• ENSG00000257221: reduced expression in EBV-transformed lymphocytes in carriers of the ALT allele (p=4.1e-6) GTEx Portal

Lifestyle considerations No lifestyle considerations on file for this variant.