Among the 118 AD-related DMPs, we selected 7 DMPs to be validated based on their genomic location in or near genes relevant to brain function or AD pathology, including some of the candidate hotspots, i.e., HAND2, HOXA3, HIST1H3E, NXN, PAX3, RBMS1, and RHOB. All the selected genes were successfully validated by bisulfite cloning sequencing since a significant correlation was shown between the 450K array data and methylation levels obtained by bisulfite cloning sequencing (Additional file 1: Table S3). Here, HOXA3 is linked to Alzheimer disease.