<div><p>The recent Parkinson Disease GWAS Consortium meta-analysis and replication study reports association at several previously confirmed risk loci <em>SNCA</em>, <em>MAPT</em>, <em>GAK/DGKQ</em>, and <em>HLA</em> and identified a novel risk locus at <em>RIT2</em>. To further explore functional consequences of these associations, we investigated modification of gene expression in prefrontal cortex brain samples of pathologically confirmed PD cases (N = 26) and controls (N = 24) by 67 associated SNPs in these 5 loci. Association between the eSNPs and expression was evaluated using a 2-degrees of freedom test of both association and difference in association between cases and controls, adjusted for relevant covariates. SNPs at each of the 5 loci were tested for <em>cis</em>-acting effects on all probes within 250 kb of each locus. <em>Trans</em>-effects of the SNPs on the 39,122 probes passing all QC on the microarray were also examined. From the analysis of <em>cis</em>-acting SNP effects, several SNPs in the <em>MAPT</em> region show significant association to multiple nearby probes, including two strongly correlated probes targeting the gene <em>LOC644246</em> and the duplicated genes <em>LRRC37A</em> and <em>LRRC37A2</em>, and a third uncorrelated probe targeting the gene <em>DCAKD</em>. Significant <em>cis</em>-associations were also observed between SNPs and two probes targeting genes in the HLA region on chromosome 6. Expanding the association study to examine <em>trans</em> effects revealed an additional 23 SNP-probe associations reaching statistical significance (p<2.8×10<sup>−8</sup>) including SNPs from the <em>SNCA, MAPT</em> and <em>RIT2</em> regions. These findings provide additional context for the interpretation of PD associated SNPs identified in recent GWAS as well as potential insight into the mechanisms underlying the observed SNP associations.</p> </div
