In detail, we used the following tests for the four classes of genetic variation: a) GWAS loci: INRICH100 was used to assess if the 108 SCZ-associated PGC SCZ2 GWAS loci (with a 20 kb window added both upstream and downstream) tended to hit the 693 differentially expressed genes (DEG) more than expected by chance loci. These random loci were generated by permutation of the associated loci within the genome, but matched to the associated loci in terms of the number of SNPs, SNP density, and the number of overlapping genes; background SNPs for matching were taken from the full imputed list of 9.4 million SNPs tested for SCZ association. After intersecting with DLPFC-expressed genes from this paper, there were 87 loci spanning one or more genes, encompassing a total of 489 genes. 10,000 permutations were performed. b) CNV regions: INRICH was also utilized to test if the 12 SCZ-associated CNV regions (without any additional genomic window) tended to hit the differentially expressed genes more than expected by randomly generated regions in the genome matched to the associated regions in terms
