Imputation was performed remotely using the Michigan Imputation Server (see URLs). A total of 39,235,157 SNPs and 47,045,346 variants were imputed from the HRC and 1000 Genomes Phase 3 (v5) reference panels, respectively. An imputation quality threshold of r2 >0.5 was subsequently applied to both imputation datasets prior to association testing. This resulted in 15,501,516 and 13,589,949 variants available for association analysis derived from HRC- and 1000 Genomes-based imputation, respectively.
