Figure 2.

Allelic association between SNPs across the 7.5 Mb extended MHC region and HLA types at each gene for the combined population data using the 5,754 SNPs that were typed in all populations and are polymorphic across the combined population samples (see Methods for details). (a) The extent of association between SNPs across the region and HLA types at HLA-A (red), HLA-C (light green), HLA-B (dark green), HLA-DRB (blue), HLA-DQA (violet), HLA-DQB (purple) as measured by relative information in the combined population data. The significant information contained within these SNPs located outside the HLA genes is not surprising given the extensive LD between SNPs and HLA loci. LD extended up to 1 Mb from the centre of a given HLA gene and, as a consequence, a single SNP could be informative for more than a single HLA gene. (b) For HLA-C (the position of which is indicated by the vertical blue line), the position of SNPs across the 7.5 Mb region showing weak (0.2 < r² <0.5; grey), moderate (0.5 < r² < 0.8; blue) and strong (r² > 0.8; red) association to each type that is present in each of the four populations. The size of the adjacent green bar indicates the relative frequency of each type in each population (types not present in a population are not shown).