Feature interpretability analyses using LIME and SHAP identified reproducible biomarkers across omic layers, including SNPs in MYH11, FOXP1, MAPK10, and SYN3; methylation changes in CDX2 and DHX58; and altered ceramide lipid CER.D19.1.24.0 levels, all previously associated with AD-related pathology. This evidence concerns the gene SYN3 and Alzheimer disease.