GPA-MDS: A Visualization Approach to Investigate Genetic Architecture among Phenotypes Using GWAS Results

Figure 2

Design of simulation study. Each box indicates a GWAS study and -axis represents the SNP index. The gray box within each box indicates risk SNPs. In this study, we considered five phenotypes and of the SNPs were assumed to be risk SNPs for each phenotype. We further assumed that of risk SNPs were shared between phenotypes 1 and 2 and also between phenotypes 3 and 4 to generate pleiotropic structure. Phenotype 5 did not share any risk SNPs with any other phenotypes as a negative control.