Chunk #56 — Methods — Functional mapping and annotation

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Genome-wide association analyses identify 95 risk loci and provide insights into the neurobiology of post-traumatic stress disorder.

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We used the SNP2GENE module in FUMA25 v1.4.1 (https://fuma.ctglab.nl) to annotate and visualize GWAS results. The complete set of parameters used for FUMA analysis are shown in the Supplementary Note. Independent genomic risk loci were identified (r2 < 0.6, calculated using ancestry-appropriate KGP3 reference genotypes). SNPs within risk loci were mapped to protein coding genes using positional mapping (10-kb window), eQTL mapping (GTEx v8 brain tissue99, BRAINEAC100, and CommonMind101 data sources), and chromatin interaction mapping (PsychENCODE102 and HiC103,104 of brain tissue types) methods. Chromatin interactions and eQTLs were plotted in circos plots. SNPs were annotated to functional annotation databases including ANNOVAR105, CADD28, and RegulomeDB29.