Figure 1.

Association results, recombination and LD plots for the region of 2q33 with risk of ESCC. P-values derived from 1 df trend tests across a region of 2q33.1 bounded by rs12693932 and rs3731707, a distance of 473 kb, were plotted. The five colored-line graphs in the upper panel show likelihood ratio statistics (Y-axis on the right) for recombination hotspots from the SequenceLDhot software. The top horizontal line indicates a P-value of 5.0 × 10⁻⁸, and the bottom horizontal line indicates a likelihood ratio statistic cut-off to predict the presence of a hotspot with a false-positive rate of 1 in 3700 independent tests (32). The five different colored lines represent five independent samplings used to estimate the location of the hotspots. The trend P-values from the Chinese, NCI and combined samples were plotted in green triangles, red circles and blue diamonds, respectively. The bottom panel depicts the LD pattern of the region in r², and solid black arrows indicate two flanking recombination hotspots containing five SNPs that exceed genome-wide significance (P-values <5 × 10⁻⁸). The short red vertical lines on the LD heat map indicate the locations of the five genome-wide significant SNPs. The sets of black arrows point to the two recombination hotspots determined in the randomly selected subsets of controls. Since the two panels are on different scales, each has a set of arrows to indicate the hotspots.