An East Asian blood eQTL meta-analysis highlights ancestry-matched eQTL resources for complex-trait genetics

Abstract

Abstract Expression quantitative trait loci (eQTLs) link genetic variation to gene regulation and complex traits, yet population-scale blood eQTL resources remain limited in East Asian populations. We mapped cis-eQTLs in 1,005 Chinese individuals and meta-analysed them with a Japanese cohort to generate an East Asian whole-blood resource (MAEEA; n = 2,024). MAEEA identified ∼2.8 million cis-eQTL associations involving 13,376 eGenes, with lead effects showing external concordance, including in an independent East Asian cohort. For East Asian complex traits, MAEEA showed greater utility than larger non–East Asian eQTL resources for heritability partitioning and candidate gene–trait prioritization; reciprocal analyses using phenotype-matched European GWAS were consistent with ancestry matching contributing to these differences. Highly differentiated eQTL SNPs showed evidence consistent with recent positive selection, and trait-associated eQTL SNPs were enriched for elevated population differentiation. These findings expand East Asian regulatory genetic resources and support ancestry-matched eQTL data for complex-trait interpretation.