We used FUMA v1.5.217 to identify independent, genome-wide significant risk loci, annotate variants, and perform gene-wise analyses via MAGMA18. We used the default FUMA parameters to define “independent significant SNPs” as those which reached genome-wide significance (p < 5e-8) and were independent of each other at r2 < 0.6, and “lead SNPs” as those SNPs that were independent of each other at r2 < 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 (eQTL) mapping (using GTEx V819, CommonMind20, and Braineac21 data), and chromatin interaction mapping. We also performed the MAGMA gene, gene-set, and gene expression analyses (using GTEx V8 data).
