APP and Alzheimer disease: A number of the identified cCRE-targeted DEGs have been implicated in neurodegenerative diseases, including genes involved in AD pathogenesis such as MAPK3, APP, and FAM107B in excitatory neuron cluster 1 (Exc1), MYO1E and APOE in microglial cluster 1 (Micro1), and BIN1 in oligodendrocyte cluster 4 (Oligo4) (Fig. 5d, Additional file 2: Table S10).