To identify the top independent associations within genomic regions, which include multiple associations for a single gene across tissues, or multiple nearby genes, we partitioned genic associations into 58 groups defined based on genomic proximity and applied stepwise forward conditional analysis within each group (Supplementary Table 1). In total, 67 non-MHC genes remained genome-wide significant after conditioning (Table 1; Figure 2a,b). The largest signal was identified in the CMC-DLPFC GREX data (24 genes; Figure 2c), followed by the Putamen (7 genes). Nineteen out of 67 genes did not lie within 1 Mb of a previously genome-wide significant GWAS locus22 (shown in bold, Table 1); of these, 5/19 genes were within 1 Mb of a locus which approached genome-wide significance (p < 5 × 10−07). The remaining 14 genes all fall within nominally significant PGC-SCZ GWAS loci (p < 8 × 10−04), but did not reach genome-wide significance.
