To increase coverage, and thus improve power for fine-mapping loci, all PAGE individuals who were successfully genotyped on MEGA were subsequently imputed into the 1000 Genomes phase 3 data release39. Imputation was conducted at the University of Washington Genetic Analysis Center. Genotype data that passed the above quality control filters were phased with SHAPEIT240 and imputed into 1000 Genomes phase 3 reference data using IMPUTE version 2.3.241. Segments of the genome that are known to contain gross chromosomal anomalies were filtered out of the final files of the genotype probabilities. Imputed sites were excluded if the IMPUTE information score was less than 0.4. A total of 39,723,562 imputed SNPs passed quality control measures (for further details see Supplementary Information 3).
