To manage and analyze all of the genotype data, we used our in-house Genoika Server System (SASA Plus Co., Ltd., Fukuoka, Japan), which was well improved from the system used in the Previous GWAS [10, 30] by the same system engineers. In addition, to manage the Previous GWAS data effectively, the Labo Server System (World Fusion Co., Ltd.) was used simultaneously. The Genoika Server System comes with PLINK v1.07 (http://pngu.mgh.harvard.edu/,purcell/plink/), the R program v 2.9.2 and 2.10.1 (http://www.r-project.org/), EIGEN-STRAT software v3.0 (http://genepath.med.harvard.edu/ ,reich/Software.htm), and Haploview 4.2 (http://www.broad institute.org/scientific-community/science/programs/medical-andpopulation-genetics/haploview/haploview) built in, and all the analyses were performed by use of this system. In addition, Microsoft Office Excel 2003 (Microsoft Corporation, Redmond, WA) was used for preparing the data sets and statistical analysis. The frequency of alleles in the case and control samples was compared by use of the basic allele test. The odds ratio (OR) and the upper and lower limit of the 95% confidence interval (CI) of each SNP were calculated for the allele possessing a higher frequency in the case samples than in the control samples. The HWE was evaluated by the chi-square test. Q-Q plots were generated by ranking the observed values from minimum to maximum and plotting them against their expected chisquare values using the ''snpMatrix'' package ver 1.14.6 in the R program (http://www.r-project.org/). We applied the Mantel-Haenszel test [19] to combine the data derived from the two data sets in order to reduce potential negative effects arising from the biases in age and female/male ratio among the populations (Table  S6 ). Figure S1 Q-Q plots for the Present GWAS. Quantilequantile (Q-Q) plots for the Present GWAS of POAG (A), HPG (B), and NPG (C) were generated by ranking the observed chisquare values from minimum to maximum and plotting them against their expected values. Genomic inflation factors (l) are also shown. These plots were created using the R-package snpMatrix. (PDF) Figure S2 LD plots in the 9p21 locus. LD plots were generated from the Present GWAS data. The SNPs applied to these plots and the span of the region are the same as shown in Figure 2B . Upper and lower plots indicate the value of pairwise D9 and r2, respectively. The positions of 5 SNPs, which passed the Bonferroni correction threshold in the Present GWAS, are drawn in vertical dashed lines. These LD plots were generated using Haploview v4. Figure S6 Population stratification analysis. Population stratification analysis by EIGENSTRAT in the Present GWAS data set. POAG samples separated with HPG and NPG groups were applied. The version of HapMap reference data is release22 (Build36). Since Control, NPG, HPG, and HapMap JPT samples were tightly overlapped, only the plots for NPG (yellow cross) are visible. (PDF)