Single-cell RNA sequencing identifies celltype-specific cis-eQTLs and co-expression QTLs

Genome-wide association studies have identified thousands of genetic variants that are associated with disease1. Most of these variants have small effect sizes, but their downstream expression effects, so-called expression quantitative trait loci (eQTLs), are often large2 and celltype-specific3–5. To identify these celltype-specific eQTLs using an unbiased approach, we used single-cell RNA sequencing to generate expression profiles of ~25,000 peripheral blood mononuclear cells from 45 donors. We identified previously reported cis-eQTLs, but also identified new celltype-specific cis-eQTLs. Finally, we generated personalized co-expression networks and identified genetic variants that significantly alter co-expression relationships (which we termed ‘co-expression QTLs’). Single-cell eQTL analysis thus allows for the identification of genetic variants that impact regulatory networks. Single-cell RNA sequencing (scRNA-seq) of ~25,000 peripheral blood mononuclear cells from 45 donors identifies new celltype-specific cis-eQTLs and genetic variants that significantly alter co-expression relationships (‘co-expression QTLs’).