For the replication of trans-eQTLs in scRNA-seq, we used unpublished data of PBMCs from 1,139 unrelated individuals in two cohorts generated using the 10X Chromium platform: OneK1K (N=982) and 1M-scBloodNL (N=157). The data were processed using the Cell Ranger Single Cell Software Suite v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) and aligned using STAR62 implementation within Cell Ranger Single Cell Software Suite . Cells were demultiplexed and doublets removed before performing cell type classification. We combined the data in a meta-analysis within each of the eight available cell types: B-cells, CD4+ T-cells, CD8+ T-cells, classical monocytes, non-classical monocytes, dendritic cells, natural killer cells and plasma cells. See Supplementary Note for methodological details.
