PMC

The dashed and solid lines show the power of the UK-GWA study (Phases 1 and 2 combined) and the UK (Phases 1 and 2)-IARC-Texas-GWA studies meta-analysis to identify susceptibility alleles with different minor allele frequencies respectively. Power to identify 5p15.33 (rs4975616), 6p21.33 (rs3117582), and 15q25.1 (rs12914385), variants in each analysis denoted by squares and diamonds respectively (P= 10⁻⁷).

Each panel shows single-marker association statistics (as −log₁₀P) from the analysis of UK-GWA study Phase 1 (diamonds), UK-GWA study Phase 2 (squares), Phases 1 and 2 combined (triangles), as a function of genomic position (NCBI build 36.1). The recombination rate across each region in HapMap CEU is shown in black (right y axis). Also shown for 15q25.1 (a) and 5p15.33 (b) is the relative position of genes mapping to each region of association, there are a large number of genes mapping to the 6p21.33 (c) region so for clarity only BAT3 and TNXB are illustrated. Exons of genes have been redrawn to show the relative positions in the gene, therefore maps are not to physical scale. LD plot was generated using UK-GWA study Phase 2 controls; values and shading show r² between each pair of SNPs; the darker the shading, the greater extent of LD.