Fig. 6: AD GWAS SNPs and AD eQTLs are strongly associated with regions of H4K16ac changes.

a–c, Manhattan plots showing the 260 AD SNP regions (vertical lines) in all chromosomes overlapped with H4K16ac changes (color-coded circles) for each of the three classes in Fig. 5a–c. The y axis indicates the –log₁₀(P) of the SNP with the strongest AD association within each SNP region (P values are from the International Genomics of Alzheimer’s project (IGAP)⁴¹). d, Bar plot showing the significance (–log₁₀(P)) of the association between the AD SNP regions and each of the three classes of H4K16ac changes assessed by INRICH. Black dotted horizontal line denotes the threshold of significance (P < 0.05). e, Representative UCSC Genome browser track view showing a cluster of AD SNPs (top) within a SNP region associated with disease-specific class of H4K16ac change (bottom; highlighted in pink) at the NME8 locus. f, Heatmap of Bonferroni adjusted P values for sampling-based analysis of H4K16ac peak overlap (three classes of changes) with temporal cortex (TX) eQTLs from Zou et al.⁴³ eQTLs are split into those from AD cases (TX_AD), non-AD but with other brain pathologies (TX_CTL), and combined conditions (TX_ALL). g, Overlap analysis with TX eQTLs from Zou et al.⁴³ using GREGOR.