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 disease. Most of these variants have small effect sizes, but their downstream expression effects, so-called expression quantitative trait loci (eQTLs), are often large and celltype-specific. 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.


KEYWORDS: Gene expression, Gene expression profiling, Gene regulation

year of publication



  • Nature Genetics


  • van der Wijst, MGP
  • Brugge, H
  • de Vries, DH
  • Franke, LH
  • Swertz, MA
  • Deelen, P

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