Figure 2.

Regional plot of association results, recombination rates and chromatin state segmentation track for 12q24.13 susceptibility locus. Association results of both genotyped (triangles) and imputed (circles) SNPs in the GWAS samples and recombination rates. −log₁₀ P-values (y axis) of the SNPs are shown according to their chromosomal positions (x axis). rs10735079 is shown as a large diamond and is labelled by its rsID. Colour intensity of each symbol reflects the extent of LD with the top genotyped SNP; white (r²=0) through to dark red (r²=1.0) Genetic recombination rates, estimated using HapMap Utah residents of Western and Northern European ancestry (CEU) samples, are shown with a light blue line. Physical positions are based on NCBI Build 37 of the human genome. Also shown are the relative positions of genes and transcripts mapping to the region of association. Genes have been redrawn to show the relative positions; therefore, maps are not to physical scale. The lower panel shows the chromatin state segmentation track (ChromHMM) for LCL data derived from the ENCODE project and the positions of SNPs of interest (produced using visPIG-Visual Plotting Interface for Genetics).