The OneK1K cohort consists of single-cell RNA sequencing (scRNA-seq) data from 1.27 million peripheral blood mononuclear cells (PMBCs) collected from 982 donors. We developed a framework for the classification of individual cells, and by combining the scRNA-seq data with genotype data, we mapped the genetic effects on gene expression in each of 14 immune cell types and identified 26,597 independent cis–expression quantitative trait loci (eQTLs).