SNPTEST (Marchini et al., 2007) v2.5.2 was used to conduct association analyses under an additive model only including markers with a minimum MAF of 0.005 and INFO of 0.5. Post GWAS filtering was performed using ancestry specific HWE (p > 10−6) and sample size based MAFs. Instead of using a fixed MAF threshold for each group, the minimum observed minor allele count (MAC) was used. Previous research has shown a MAC of ~40 is robust for most association analyses performed in GWAS (Bigdeli et al., 2014). Post filtered GWAS results were meta-analyzed using METAL (Marchini et al., 2007; Willer et al., 2010) which implements a fixed effect model and inverse variance weighting based on sample size. Markers available for fewer than 1,000 individuals after meta-analysis were excluded. Estimation of genomic inflation (λ, λ1,000) for within super-population GWAS and meta-analyses was performed in R (R Core Team, 2016). False Discovery Rate (FDR) analysis was performed using the “q-value” package (https://github.com/jdstorey/qvalue) using Bioconductor 3.2 (Huber et al., 2015). To define genomic bins for follow-up, we started with all markers with a q
