Individual cohorts participating in the study followed the analysis plans as specified in our analysis cookbooks (https://github.com/molgenis/systemsgenetics/wiki/eQTL-mapping-analysis-cookbook-(eQTLGen); https://github.com/molgenis/systemsgenetics/wiki/eQTL-mapping-analysis-cookbook-for-RNA-seq-data; https://github.com/molgenis/systemsgenetics/wiki/QTL-mapping-analysis-cookbook-for-Affymetrix-expression-arrays) or with slight alterations as described in the Methods and Supplementary Note. Tools and source codes used for genotype harmonization, identification of sample mix-ups, eQTL mapping, meta-analyses and calculation of PGSs are available at https://github.com/molgenis/systemsgenetics/. Tools used for primary analyses were written in Java (v6, v7, v8; www.java.com). Plink v1.0.7 (https://zzz.bwh.harvard.edu/plink/) and v1.90 (https://www.cog-genomics.org/plink/1.9/) was used for clumping and pruning. Downstream analyses and plots were done with R (v3.4.4, v3.6.1, v4.0.0; https://cran.r-project.org/) using packages data.table v1.12 (https://cran.r-project.org/web/packages/data.table/), tidyverse v1.2.1 (https://cran.r-project.org/web/packages/tidyverse/), broom v0.5.1 package (https://cran.r-project.org/web/packages/broom/), pheatmap v1.0.12 package (https://cran.r-project.org/web/packages/pheatmap/), GeneOverlap v1.18.0 (https://bioconductor.org/packages/release/bioc/html/GeneOverlap.html). Power analyses were conducted by R package pwr v1.3–0 (https://cran.r-project.org/web/packages/pwr/). scRNA-seq analyses made use of 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 its implementation of STAR aligner. ToppGene web tool (https://toppgene.cchmc.org/) was used for some interpretative enrichment analyses, as well as GeneNetwork web tool (https://genenetwork.nl/). Decon2 framework was (https://github.com/molgenis/systemsgenetics/tree/master/Decon2) used for predicting cell counts in BIOS data. We formatted our cis-eQTLs into the BESD format using SMR (https://cnsgenomics.com/software/smr/#Overview).