Table III presents the top independent SNPs from the cross sample meta analysis, which included all of the COGA and S4S samples (N = 15,112). We present two sets of results, the cross sample meta analysis results for the top 3 SNPs identified in the within COGA meta analysis (to test if initial SNPs replicated); and the actual top SNPs identified in the cross sample meta analysis (to test if the increased sample resulted in additional signals). For each of the top genome-wide significant SNPs identified in the within COGA meta analysis (rs2376620, rs2433198, rs12928255), the effect was reduced in the cross sample meta analysis and these SNPs were no longer genome-wide significant. Of the top SNPs in the cross-sample meta analysis, none were significant at the genome-wide threshold. Overall, the larger cross sample meta-analysis did not support replication of SNPs identified in the primary within COGA meta analysis.
