Rare and common genetic variants shape single-cell immune gene expression

Understanding the genetic basis of gene expression can shed light on the regulatory mechanisms underlying complex traits and diseases^1,2. Single-cell-resolved measures of RNA levels and single-cell expression quantitative trait loci have revealed genetic regulation that drives cell states and types across diverse tissues³. Here we describe phase 1 of TenK10K, which leverages single-cell RNA sequencing data from more than 5 million cells across 28 immune cell types, along with matched whole-genome sequencing data from 1,925 individuals. This provides power to detect associations for rare and low-frequency genetic variants that have largely been uncharacterized in their impact on cell-specific gene expression. We map the effects of both common and rare variants in a cell-type-specific manner using a recent method that increases power by modelling single cells directly rather than aggregated 'pseudobulk' counts. We identify putative common regulatory variants for 83% of all 21,404 genes tested and cumulative rare-variant signals for 47% of those genes. We explore how genetic effects vary across cell types and states, develop a framework to determine the degree of single-cell expression quantitative trait loci cell-type specificity and show that about half of the effects are observed only in one or a few cell types. By integrating our results with functional annotations and disease information, we further characterize the likely molecular modes of action for many disease-variant associations. Finally, we explore the effects that genetic variants have on gene expression across continuous cell states, and effects that vary cell-state abundance directly.