First, 906,600 SNPs were genotyped for 2,126 Japanese subjects by Genome-Wide Human SNP Array 6.0 (Affymetrix, Santa Clara, CA) according to the manufacturer's instructions. As for the Present GWAS population, 839 POAG patients and 708 controls were selected after performing the quality control (QC) as described (Supporting Information S1). To exclude the potential inclusion of genetically related subjects into the population, identity-by-descent (IBD) estimates were performed for all possible combinations by PLINK v1.07 (http://pngu.mgh.harvard.edu/ ,purcell/plink/). In total, 6 POAG patients and 22 controls were assumed to be in first-degree relationships or in relationships with a few more-distant relatives, and were thus excluded from the Present GWAS population. Finally, the Present GWAS population ended up with 833 POAG patients, comprised of 330 HPG and 503 NPG patients, and 686 controls. Population stratification for the present GWAS population was examined by principal component analysis using EIGENSTRAT software v3.0 (http:// genepath.med.harvard.edu/,reich/Software.htm). As for the reference genomic population, the four HapMap populations (CEU, YRI, JPT, and CHB) were simultaneously applied to EIGENSTRAT. The generated cluster plots indicated that our POAG and control population was genetically clustered within the JPT population, and there was no outlier sample ( Figure S6 ). We performed SNP quality control for the population on the autosomal SNPs based on the following QC filters: (i) call rate per SNPs in case and control samples $95%, (ii) minor allele frequency (MAF) in case and control samples $1%, and (iii) Hardy-Weinberg equilibrium (HWE) in control samples P$0.001. Consequently, we analyzed the remaining 653,519 SNPs for the Present GWAS population.