PCA plot, we excluded subjects who fell outside the JPT and CHB clusters (Figure S1). We then excluded SNPs with a MAF of or SNPs with Hardy-Weinberg equilibrium (HWE) test P-value (Fisher's exact test). Ultimately, we obtained genotype data on 480,103 SNPs for 11,696 subjects who had also completed the questionnaire. Genotype imputation was then performed using a two-step procedure in MACH 1.0. The JPT and CHB data obtained from the Phase II HapMap database (release 24) were used as references. In the first step, crossover and error rate maps were estimated using 500 subjects who were randomly selected from the GWAS data. In the second step, genotype imputation of all subjects was conducted using the crossover and error rate maps estimated in the first step. We excluded imputed SNPs with MAFs of or values of and obtained SNP genotype data for 2,312,503 SNPs.
