We first evaluated SNP prioritization performance of GPA. Specifically, after the two data sets were simulated, we obtained the p-value for each SNP in each disease using a test with one degree of freedom. Then we analyzed the simulated data using our GPA method in the following four modes: 1. analyzing the two diseases separately without the annotation data; 2. analyzing the two diseases separately with the annotation data; 3. analyzing the two diseases jointly without the annotation data; and 4. analyzing the two diseases jointly with the annotation data. In each mode, we compared the order of the local FDR obtained using GPA against the actual risk status of the SNPs to calculate the area under the receiver operating characteristic curve (AUC) as a measure of risk SNP prioritization accuracy. The left panel of Figure 1 shows the AUCs from the four modes with and (results for other scenarios are shown in Figures S10-S20 in Text S1). Because all the simulation parameters were the same for the two diseases, only the results for the first disease are shown. We
