29 5′ UTRs were differentially methylated at Braak III; 37 5′ UTRs were differentially methylated at Braak V/VI, including hypomethylation of Alzheimer's disease risk genes AMY1A and FMR1 within dark regions in their 5′ UTR at Braak V/VI. Here, FMR1 is linked to early-onset autosomal dominant Alzheimer disease.