Figure 5

The main haplotypes in the region for a) Europe), b) Asia and c) Africa. The haplotypes blocks were defined applying the criterion of Gabriel et al. [21] on the CEU data. Haplotypes in different blocks are connected with thick lines if shared more than 10% and with thin lines if shared 1–10%. Numbers between blocks indicate average linkage disequilibrium measured as D' between adjacent blocks The ancestral state of each SNP was inferred from the chimpanzee sequence, using the genome variation server. The haplotype CTCCATTTCGT (block 3) has an increased frequency in CEU and consists mainly of derived alleles. It is an inferred risk variant in the Breast Cancer data set (panel d) and is in strong LD with previously identified susceptibility markers (position of these shown above Figure, and frequency of Rai3'd1 is shown in panel d).