We investigated whether the genes associated with PD risk via expression or splicing changes could be acting through regulation of methylation. A total of 134 CpG sites passed FDR correction and conditional analysis in the substantia nigra (mapping to 107 unique genes), and 116 CpG sites survived FDR correction and conditional analysis in substantia nigra (mapping to 93 unique genes) (eTable 6 in Supplement 7). Of the MWAS significant genes, 3 (GPNMB, TMEM163, and CTSB) overlapped with the Coloc expression or splicing results (Table 3).
