To assess the enrichment of sets of functionally related genes, we used MAGMA v1.0320 on the CLOZUK + PGC meta-analysis summary statistics. From these, we excluded the xMHC region for its complex LD and the X chromosome given its smaller sample size. In the resulting data, gene-wide P values were calculated by combining the P values of all SNPs inside genes after accounting for LD and outliers. This was performed allowing for a window of 35 kb upstream and 10 kb downstream of each gene to capture the signal of nearby SNPs that could fall in regulatory regions69,70. Next, we calculated competitive gene set P values on the gene-wide P values after accounting for gene size, gene set density and LD between genes. For multiple-testing correction in each gene set collection, an FWER71 was computed using 100,000 resamplings.
