Prior to clumping (r2=0.2, 500kb window), each set of SNPs was filtered for variants with fewer than five hundred individuals present in the meta-analysis. We also report results of analyses of unfiltered SNPs (Supplementary Figure 8). eQTL annotation was performed using previously published eQTL results (Supplementary Table 2), including eQTLs derived from 10 regions of the brain and whole blood from GTEx v7 (GTEx Consortium et al. 2017), a meta-eQTL analysis of brain cortex tissue (Kim et al. 2014), as well as CD4+ T cells and CD14+ monocytes (Raj et al. 2014). To assess eQTL enrichment, 1000 randomly ascertained SNPs sets were generated using SNPsnap (Pers, Timshel, and Hirschhorn 2015), sampled without replacement (replacement is allowed only when not enough matched SNPs are available) from the European catalogue of 1000 Genomes SNPs, and matched for minor allele frequency (± 5%), gene density (± 50%), distance to nearest gene (within a 1000kb window), and LD buddies (± 50%) at r2=0.8.
