Figure 2. Signals of PD-association within HLA.

A one megabase (MB) region was defined centered on the association peak, rs3129882 in intron 1 of HLA-DRA, spanning from base pair (BP) position 32,017,508 to 33,017,508. The top panel shows all SNPs in this region plotted according to the significance of their association with PD and color-coded according to their linkage disequilibrium (r²) with the most significant SNP, rs3129882. Note that rs3129882 is not strongly correlated (defined as r²≥ 0.8)with any other HLA variant. The LocusZoom software used here calculates r² using the HapMap CEU data. SNPs shown in grey were on the Illumina OMNI chip but not on HAPMAP thus r² was not calculated with this method; however, using the Haploview software and the NGRC data to estimate r², none of the variants was strongly correlated with rs3129882 (r²<0.6, Supplementary Fig. 6). The bottom panel shows the genes in the region, including the closely linked polymorphic HLA-DRB and DQB loci, and DRA, DRB5, and DRQA2 whose expression is correlated with the variation at rs3129882.