To maximize the potential of eQTL-based analyses of the brain, we combined and rigorously harmonized brain RNA-sequencing (RNA-seq) and genotype data from 14 different cohorts, including 8,613 RNA-seq samples from all major brain eQTL studies, and publicly available samples from the European Nucleotide Archive (ENA). We created a gene co-regulation network based on 8,544 RNA-seq samples covering different brain regions and performed cis- and trans-eQTL analyses of up to 2,683 individuals of European ancestry (EUR), with replication in up to 319 individuals of African ancestry (AFR). We made inferences on the brain cell types in which eQTLs operate and systematically conducted MR and co-localization analyses to find shared genetic effects between eQTLs and 31 brain-related GWAS traits. Our analyses prioritize probable causal genes and reveal cell type-dependent eQTLs that may be associated with disease risk (Fig. 1).
