New genome-wide significant genes associated with AD in the vicinity of recently reported single SNP genome-wide significant hits[9], [19].

Gene-wide p-values are shown for those genes with p<2.5×10−6 for which the best single-SNP p-value in that gene is greater than 5×10−8 in the combined Stage 1 and Stage 2 sample. Previously reported genes[4]–[8] ± 0.5 Mb around them are excluded. Gene-wide p-values in the combined Stage 1 and Stage 2 sample obtained by combining the p-values from the Stage 1 with those from the Stage 2 using Fisher's method. The LD between rs1476679 (chr7∶100,004,446) reported by IGAP [9] and the best SNP in ZNF3 is r2 = 0.16. The LD between rs10838725 (chr11: 47,557,871) reported by IGAP [9] and the best SNPs in the region on chr 11 in the table are r2 = 0.3 and 0.88 for NDUFS3 and MTCH2 respectively.