Primary genotype and gene expression data was analyzed by individual cohorts participating in the study and our study analyzed summary statistics. Full summary statistics of the eQTLGen cis-eQTL, trans-eQTL and eQTS meta-analyses are available on the eQTLGen website, www.eqtlgen.org, which was built using the MOLGENIS framework73. We also provide cis-eQTL files formatted for use in SMR, MAFs, and replication statistics for cis-eQTLs, trans-eQTLs and eQTSs. Per-cohort summary statistics for discovery cohorts can be made available after approval of an analysis proposal in eQTLGen and with agreement of the cohort PIs, contact corresponding authors for further information. Trait-associated variants were collected from EBI GWAS Catalogue (https://www.ebi.ac.uk/gwas/; accessed on 21 November 2016), NIH GWAS Catalogue (now hosted by EBI GWAS Catalogue: https://www.ebi.ac.uk/gwas/) and Immunobase (www.immunobase.org; accessed 26 April 2016; now hosted by Open Targets: https://genetics.opentargets.org/immunobase). Sources of numerous GWAS summary statistics used 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
