Genotypes were imputed with EAGLE57 and filtered for MAF > 0.2, resulting in a total of 189,322 SNPs. Cell type proportions were calculated as number of cells for each cell type divided by the number of total cells for each person. Linear regression was used to test associations between each genetic variant and cell-type proportion with the Matrix eQTL software58. Cis-eQTL mapping was conducted in each cell type separately. All genes with at least 50 UMI counts in 20% of the individuals in all PBMCs were tested for each cell type, resulting in a total of 4,555 genes. Variance-stabilized and log-normalized gene expression was calculated using the ‘rlog’ function of the DESeq2 package54. All variants within a window of 100kbp of each gene were tested with linear regression using Matrix eQTL58. Batch information for each sample as well as the first 3 principal components of the expression matrix were used as covariates.
