CHRNE and Alzheimer disease: These 52 CpG sites and their 32 neighboring genes may affect AD risk, including previous GWAS [28, 35, 44–52] and/or TWAS studies [6–9] identified genes (NDUFS2, FCER1G, BIN1, CD2AP, EPHA1, TP53INP1, CCDC6, TSPAN14, PLEKHA1, MS4A6A, CHRNE, SLC24A4, TBX6, YPEL3, TMEM106B, STX4, and CNN2), six genes located within 500 kb of known AD susceptibility variants [28, 35, 45, 49] (LRRFIP2, GAL3ST4, EPHX2, MAPK3, COASY, and MPO) and nine novel genes reported in this study (CNIH4, THUMPD3, SERPINB9, MTUS1, CISD1, FRAT2, CCDC88B, FES, and SSH2).