We used FUMA v1.5.2 (Watanabe, Taskesen, van Bochoven, & Posthuma, 2017) to identify independent, genome-wide significant risk loci, annotate variants, and perform gene-wise analyses via MAGMA (de Leeuw, Mooij, Heskes, & Posthuma, 2015). We used the default FUMA parameters to define “independent significant single-nucleotide polymorphisms (SNPs)” as those that reached genome-wide significance (p < 5e−8) and were independent of each other at r 2 < 0.6, and “lead SNPs” as those SNPs that were independent of each other at r 2 < 0.1. “Genomic risk loci” were defined by merging linkage disequilibrium (LD) blocks of independent significant SNPs within a 250-kb distance. We performed gene mapping in FUMA using positional mapping (based on ANNOVAR annotations), expression quantitative trait locus mapping (using GTEx V8 [Aguet et al., 2017], CommonMind [Huckins et al., 2019], and Braineac [Trabzuni et al., 2011] data), and chromatin interaction mapping. We also performed the MAGMA gene, gene-set, and gene expression analyses (using GTEx V8 data).
