In Phase 2, SNPs with p <1.0 × 10−3 in either EAs or AAs, or in the EA-AA meta-analysis, were tested for association in the SAGE dataset using identical statistical models (3,381 SNPs from the Sympcountadj model, 3,323 from the case-control model). Results from Phases 1 and 2 were combined within population groups by meta-analysis. The threshold for evaluating a SNP in Phase 2 was chosen to minimize false negatives, assuming that an equally strong effect observed in the Phase 2 sample would result in a GWS meta-analysis result. Based on the combined Phase 1+2 meta-analysis, we selected 153 SNPs (Sympcountadj, N=34; case-control, N=84; CIP, N=39) for further replication in Phase 3 based on a cutoff of p < 1.0×10−4 (four SNPs met this criterion for more than one trait).
