Seven of these loci involve novel intronic variants that have not been previously implicated in genetic association studies of AD or related endophenotypes: rs116580059 near SCIN for APOE in TX fraction (rs116580059-APOETX (SCIN)), rs11845003-APOETX (NPAS3), rs116726862-Aβ40TX (SLC9A9), rs148028977-Aβ40TX (RFX7), rs34805055-Aβ40TX (STRN4), rs77785770-Aβ40TX (KCNN2) and rs9890231-Aβ40TBS (ITGB4). Here, APOE is linked to Alzheimer disease.