of the eQTL annotation. This made the EM algorithm converge in fewer iterations, resulting in the minor differences between the estimated parameters in Table 4 and those in Table 2. With the local FDR , GPA identified 724 and 977 risk SNPs for BPD and SCZ, respectively. Clearly, the enrichment of eQTL is high with fold (s.e. 0.152) and the enrichment of TFBS is moderate with (s.e. 0.063). These results demonstrate that GPA is able to incorporate multiple annotation datasets for prioritization of GWAS results with good effects.
