used, each target dataset was imputed separately to 1000 Genomes by using SHAPEIT2 [40] followed by Minimac3 [41]. Before imputation, variants with A/T or C/G alleles, missing rates >5%, MAF < 3%, and HWE P-values < 0.0001 were excluded. Imputed variants with R2 ≥ 0.30 and MAF ≥ 1% were included in all analyses. Indiana Biobank samples were genotyped using Illumina Infinium Global Screening Array (GSA, Illumina, San Diego, CA) by Regeneron (Tarrytown, NY). Variants with missing rate >5%, MAF < 1%, HWE P-value < 1E−10 among cases and 1E−6 in controls were excluded as reported previously [42]. Population stratification was then estimated using the SNPRelate package [43] from Bioconductor [44]. Indiana Biobank data were also imputed to 1000 Genomes using the Michigan Imputation Server (https://imputationserver.sph.umich.edu/index.html#!pages/home) [41]. Imputed variants with R2 < 0.30 and MAF < 1% were excluded.
