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

<p>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<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094661#pone.0094661-Harold1" target="_blank">[4]</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094661#pone.0094661-Seshadri1" target="_blank">[8]</a> ± 0.5 Mb around them are excluded.</p><p>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 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094661#pone.0094661-Lambert2" target="_blank">[9]</a> and the best SNP in ZNF3 is r² = 0.16. The LD between rs10838725 (chr11: 47,557,871) reported by IGAP <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094661#pone.0094661-Lambert2" target="_blank">[9]</a> and the best SNPs in the region on chr 11 in the table are r² = 0.3 and 0.88 for <i>NDUFS3</i> and <i>MTCH2</i> respectively.</p

New genome-wide significant genes associated with AD.

<p>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<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094661#pone.0094661-Harold1" target="_blank">[4]</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094661#pone.0094661-Seshadri1" target="_blank">[8]</a> ± 0.5 Mb around them are excluded.</p><p>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.</p

Linkage disequilibrium structure of <i>TP53INP1</i> gene.

<p>The SNPs which are significant at 10⁻⁴ level are circled in red.</p

Overrepresentation of significant loci, excluding regions of 0.5[4]–[8] and Stage 1 IGAP genes[9], [19] containing genome-wide significant SNPs.

<p>The observed number of genes is calculated by combining significant loci within 0.5 Mb into one signal. The APOE region is excluded (CHR19; 44,411,940–46,411,945bp). The total number of genes after exclusions is 24,849.</p

Linkage disequilibrium structure of <i>IGHV1-67</i> gene ±5 kb.

<p>The SNPs which are significant at 10⁻⁴ level are circled in red.</p