Using a complex of new analytical paradigms that integrates transcriptomes and methylomes of normal controls, AD patients, and “AD-in-dish” models, we identified a set of previously unexplored FUS-specific AD genes (COL2A1, CAPN3, COL14A1, STAT5A, and SPOCK3) and their epigenetic characteristics, which may provide new insights into the molecular pathology of AD. Here, COL2A1 is linked to Alzheimer disease.