Integrative single-cell eQTL and GWAS analyses identify cell-type-specific regulatory mechanisms underlying ESCC susceptibility.

Interpreting genetic risk variants within their relevant cellular contexts remains a central challenge in esophageal squamous cell carcinoma (ESCC), a malignancy with a substantial inherited component. We integrate single-cell RNA sequencing with genotype data to generate a cell-type-resolved expression quantitative trait loci (sc-eQTL) map spanning epithelial, immune, and stromal compartments in ESCC tissues. Most regulatory effects are highly cell-type-specific and largely undetectable in bulk transcriptomic analyses. Integration with ESCC genome-wide association studies reveals significant enrichment of risk variants in defined cellular populations, most prominently within invasive epithelial cells. Cell-type-specific transcriptome-wide association, Mendelian randomization, and colocalization analyses prioritize RPS3A as a susceptibility gene whose genetically regulated expression colocalizes with ESCC risk variants and increases during malignant progression. Fine-mapping identifies cooperative enhancer-promoter variants influencing RPS3A expression, and integrative functional analyses implicate RPS3A in alternative splicing programs. These results establish a cell-type-resolved regulatory framework for interpreting inherited susceptibility in ESCC.