Mb on chromosome 16 of the 1000 genomes reference panel using minimac [55]. To evaluate the quality of each imputed SNP we calculated Rsq. We excluded imputed SNPs with Rsq<0.9 for SNPs with allele frequency <0.5%, Rsq<0.8 for SNPs with allele frequency >0.5–1%, Rsq<0.7 for SNPs with allele frequency >1–3%, Rsq<0.6 for SNPs with allele frequency >3–5%, and Rsq<0.5 for SNPs with allele frequency >5%. Given the large reference panel this resulted in high imputation quality [51]. To calculate pairwise correlation between variants we used the 1000 Genomes Project data, specifically we used 61 African Americans from the South-west (ASW) and 65 European Americans (Utah residents with Northern and Western European ancestry from the CEPH collection, CEU).
