In addition, we explored the specificity of the enrichment for common SCZ variants by testing the enrichment of each module with common variants for Alzheimer’s disease (AD)120, a neurodegenerative brain disorder, and rheumatoid arthritis (RA)121. Summary statistics were downloaded from publically available datasets for AD (http://web.pasteur-lille.fr/en/recherche/u744/igap/igap_download.php) and RA (http://plaza.umin.ac.jp/~yokada/datasource/software.htm). For each GWAS dataset, SNPs were ‘clumped’ using Plink 1.9 (https://www.cog-genomics.org/plink2) and samples of European ancestry from the 1000 genomes project phase 3, using the following settings: threshold of significance for disease-associated SNPs P value = 5 × 10−8, r2 = 0.6, and a window of 500 kb. Enrichment of modules with AD and RA loci was tested using INRICH as described in the “Overlaps with genetic associations” section.
