Genome lift-over was performed for the Illumina dataset to map the SNPs using the Human Genome version 19 (hg19). Shapeit.v2 was used for phasing genotype data [44]. Imputation was performed using Impute v2.3.2 and 1000 Genome Project as the reference panel [45,46]. After the imputation, variants with Infor Score <0.5 were removed. Before imputation, there were 1,013,952 SNPs in the Illumina dataset and 1,714,384 SNPs in the Affymetrix dataset. After imputation, there were 11,065,735 SNPs in the Illumina dataset and 9,218,475 SNPs in the Affymetrix dataset. We pooled both datasets and removed variants with a genotype missing rate > 5%, HWE P<1.0 x 10−5, and MAF < 1%. A total of 7,169,107 SNPs were used for subsequent analyses.

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