In the case of the association between rs117934759 and PTPN12 expression in microglia (Fig. 2d; LRT—P = 1.72 × 10−16, q = 4.14 × 10−14), the eQTL association was strongly influenced by Alzheimer’s disease (AD) samples (ADinteraction, P = 1.11 × 10−10). The gene discussed is PTPN12; the disease is early-onset autosomal dominant Alzheimer disease.