These data potentially link epigenetic regulation of genes related to LRRK2 and endolysosomal sorting (RAB32 and AGAP1), and genes involved in neuroinflammation, the inflammasome, and neurodevelopment with early changes in PD and suggest that there are significant shifts between 5mC and 5hmC associated with PD in genes not captured by standard methods. Here, AGAP1 is linked to Parkinson disease.