We simulated individual-level genotypes of EUR, EAS and AFR populations using HAPGEN237 with ancestry-matched 1KG Phase 336 super-population samples as the reference panel. We grouped CEU, IBS, FIN, GBR and TSI into the EUR super-population, CDX, CHB, CHS, JPT and KHV into the EAS super-population, and ACB, ASW, LWK, MKK and YRI into the AFR super-population. To calculate the genetic map (cM) and recombination rate (cM/Mb) for each super-population, we downloaded the maps and rates for their constituent subpopulations (Data availability), linearly interpolated the genetic map and recombination rate at each position (Code availability), and averaged the genetic maps and recombination rates across the subpopulations within each super-population. We simulated 320K EUR samples, 100K EAS samples and 100K AFR samples, and confirmed that the allele frequencies and LD patterns of the simulated genotypes were highly similar to those of the 1KG reference panels. We note, however, that while highly scalable, genotypes simulated by HAPGEN2 may not fully capture the complex population structure within and across ancestry groups. We saved 20K samples for each of the three populations as the target
