For all analyses, gene-wise p-values were calculated as the aggregate of the mean and smallest p-value of SNPs annotated to Ensembl gene locations using MAGMA v1.06 (Supplementary Methods and Results) (37). Gene set analysis was performed in MAGMA (Supplementary Methods and Results). Further analyses were performed to assess the enrichment of associated genes with expression-specificity profiles from tissues (Genotype-Tissue Expression project, version 7) and broadly-defined (“level 1”) and narrowly-defined (“level 2”) mouse brain cell-types (38, 39). Analyses were performed in MAGMA following previously described methods with minor modifications, with Bonferroni-correction for significance (Supplementary Methods) (38). Similar analyses can be performed in LDSC-SEG – we report MAGMA results, which reflect specificity of expression across the range, whereas LDSC-SEG compares the top 10% of the range with the remainder (40). Results using LDSC are included in the Supplementary Tables.
