We estimated the LD information of GWAS variants in each LD block using five super-populations (AFR, AMR, EAS, EUR and SAS) from the 1KGP reference panel. Since LDetect only contains LD block information for three continental populations, we assigned the five 1KGP super-populations to them (mapping EUR and AMR to European population, EAS and SAS to Asian population, and AFR to African population). For each 1KGP super-population, we only retained biallelic variants and discarded sites with MAF = 0. To accelerate the process, we further divided the VCF genotype file into LD block-wise files. We mapped test variants to corresponding variants in the reference panel according to identical coordinates and alleles, and harmonized complementary alleles for reverse strands. We used the PAINTOR (26) framework to calculate pairwise Pearson correlation coefficients between each variant in the LD block and block-wise LD matrix.
