At Alzheimer’s disease (AD) risk loci, qQTL analysis revealed complex regulatory architecture including variance effects at PITRM1, lower-quantile-specific effects at TMEM106B partially explained by APOE ε4 interactions, and coordinated epigenetic regulation at loci harboring CHRNE/SCIMP/RABEP1. This evidence concerns the gene PITRM1 and early-onset autosomal dominant Alzheimer disease.