We demonstrated the utility of this approach by showing: the genomic regions we identified are enriched for SNP heritability for intelligence test performance and brain-related disorders; the genes we identified are enriched for neurologically relevant gene ontology terms and genes causing neurogenetic disorders and the existence of an intron-3 retaining transcript of APOE, the usage of which is correlated with Alzheimer’s disease pathology and APOE-ε4 status. The gene discussed is APOE; the disease is early-onset autosomal dominant Alzheimer disease.