We identified largely sex-specific PD-associated changes in DNA modification in 434 unique genes, including genes previously implicated in PD, including PARK7 (DJ-1), SLC17A6 (VGLUT2), PTPRN2 (IA-2β), and NR4A2 (NURR-1), as well as genes involved in developmental pathways, neurotransmitter packaging and release, and axon/neuron projection guidance. Here, PTPRN2 is linked to Parkinson disease.