Supplementary Figure 6: Association results, recombination and linkage disequilibrium plot for the region at 6p21.32 for the NCI and Henan scans combined (meta), the Henan replication set and the combined estimate from both stages.

The region at 6p21.32: 32,508,399–32,689,013 for the HLA class II locus was plotted. Association results from a trend test in –log₁₀ P values (y axis, left; gray diamonds, stage 1 results including the NCI and Henan scans; purple diamonds, Henan replication results; red diamonds, combined results) of the SNPs are shown according to their chromosomal positions (x axis). Linkage disequilibrium structure based on 1000 Genomes Project CHB data (n = 91) was visualized with snp.plotter software. Owing to the hypervariability of the locus, the number of SNPs was pruned so that no two sites were within the same 500-bp window. The line graph shows the likelihood ratio statistics (y axis, right) for recombination hotspot as determined by SequenceLDhot software on the basis of the background recombination rates inferred by PHASE v2.1 using 100 randomly sampled controls from the NCI scan (red line) and Henan scan (blue line) data from stage 1. Physical locations are based on NCBI human genome Build 37. Gene annotation was based on the NCBI RefSeq genes from the UCSC Genome Browser.