APOE and Alzheimer disease: In the cerebellum there was the highest levels of methylation (marginal mean = 93%), with lower levels in the hippocampus (marginal mean = 85%), and the lowest levels in the frontal lobe (marginal mean = 77%) of AD brain compared to controls. There was a complex interaction among the presence of the APOE ε4 allele, AD status, and DNA methylation levels in the APOE CpG islands. AD-specific methylation differences were mainly attributed to the ε3/ε4 heterozygous subjects