We performed meta-analysis across the EA and AA GWAS samples in COGA (referred to as within COGA meta analysis) in METAL using an inverse-variance weighting fixed effects approach (Willer et al., 2010). We focus on the meta analysis results, as there was not sufficient sample size to focus on ancestry specific results. Genomic control was applied in METAL to all GWAS results. We utilized the publicly available online tool FUMA (Functional Mapping and Annotation of Genome-Wide Association Studies) (Watanabe et al., 2017) to evaluate cis-acting chromatin interactions and expression quantitative trait loci (eQTLs). Gene-based test results are provided for genes with p-values less than the adjusted alpha, based on a correction of 18,012 protein-coding genes (0.05/18012=2.78×10−6). Genetic background for linkage disequilibrium (LD) was based on the observed LD patterns in each ancestry sample. For meta-analysis results, we used LD from the full 1000 genomes reference panel (The 1000 Genomes Project Consortium, 2015).
