for eQTS analyses are outlined in Supplementary Note and Supplementary Table 13. ExAC pLI scores used for Figure 2 originate from: ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3.1/functional_gene_constraint/fordist_cleaned_exac_r03_march16_z_pli_rec_null_data.txt. Genotype reference files used for harmonizing discovery datasets for meta-analysis originate from here: ftp://share.sph.umich.edu/1000genomes/fullProject/2012.03.14/GIANT.phase1_release_v3.20101123.snps_indels_svs.genotypes.refpanel.ALL.vcf.gz.tgz. Gene model used for gene annotations originates from ENSEMBL v71 (ftp://ftp.ensembl.org/pub/release-71/gtf/homo_sapiens/Homo_sapiens.GRCh37.71.gtf.gz). FANTOM TF annotations used for eQTS enrichment analyses originate from: http://fantom.gsc.riken.jp/5/sstar/Browse_Transcription_Factors_hg19. CHIP-seq data used for cis-eQTL overlap originates from https://www.chicp.org/. Protein-protein interaction data used for trans-eQTL mechanism enrichment analyses originate from: https://www.intomics.com/inbio/map/api/get_data?file=InBio_Map_core_2016_09_12.tar.gz. Hi-C data used for trans-eQTL mechanism enrichment is deposited in GEO (GM12878, GEO accession GSE63525). Curated gene sets used for enrichment analyses (Gene Ontology sets, ENCODE CHiP-X and CheA CHiP-X TF targets, TRANSFAC and JASPAR PWMs, ARCHS4 tissue expression, TargetScan miRNA target predictions, Tarbase miRNA validated targets) were downloaded from Enrichr web site (https://maayanlab.cloud/Enrichr/#stats). Gene expression summaries and meta-data from GTEx v7 originate from: https://gtexportal.org/home/. Gene expression summaries from BIOS are available in Source Data 1 and also in BIOS Omics Atlas (http://bbmri.researchlumc.nl/atlas/#data). Mean cell counts for eight immune cell types from 1M-scBloodNL cohort are available in Source Data 2. Per-cohort individual-level genotype and gene expression data is governed by respective biobanks and access can be requested according to procedures established
