Fig. 1
From: Germline variation at 8q24 and prostate cancer risk in men of European ancestry
LocusExplorer plots of the 12 variants at 8q24 significantly associated with PCa risk. ‘Marginal’ and ‘Conditional’ Manhattan plot panels show marginal and conditional association results, respectively. Variant positions (x-axis) and −log10 p-values from the Wald test (y-axis) are shown, with the red line indicating the threshold for genome-wide significant association with PCa risk (p ≤ 5 × 10−8) and blue peaks local estimates of recombination rates. The position of the 12 independent variants is labeled in each plot. Clusters of correlated variants for each independent signal are distinguished using different colors and also depicted on the ‘LD r2 Hits’ track. Stronger shading indicates greater correlation with the lead variant, with variants not correlated at r2 ≥ 0.2 with any lead variant uncolored. Pairwise correlations are based on the European ancestry (EUR) panel from the 1000 Genomes Project (1KGP) Phase 3. The relative position of RefSeq genes and biological annotations are shown in the ‘Genes’ and ‘Biofeatures’ panels, respectively. Genes on the positive strand are denoted in green and those on the negative strand in purple. Annotations displayed are: histone modifications in ENCODE tier 1 cell lines (Histone track), the positions of any variants that were eQTLs with prostate tumor expression in TCGA prostate adenocarcinoma samples and the respective genes for which expression is altered (eQTL track), chromatin state categorizations in the PrEC cell-line by ChromHMM (ChromHMM track), the position of conserved element peaks (Conserved track) and the position of DNaseI hypersensitivity site peaks in ENCODE prostate cell-lines (DNaseI track). The data displayed in this plot may be explored interactively through the LocusExplorer application (http://www.oncogenetics.icr.ac.uk/8q24/)
