Gene-based association analysis was performed using Multi-marker Analysis of GenoMic Annotation (MAGMA)49, which uses a multiple regression approach to detect multi-marker effects that account for SNP p values and LD between markers. We used the default setting (no window around genes) to consider 18,575 autosomal genes for the analysis, with p < 2.69 × 10−6 (0.05/18,575) considered GWS. For each population, we used the respective population from the 1000 Genomes Project phase 3 as the LD reference.
