Patterns of LD in African Yoruba (YRI) and Europeans (CEU) from Hapmap show that there are some variants at this locus that are in strong LD in Africans and that this LD spans both sides of a number of putative recombination hotspots. According to Hapmap, MYH9 SNPs rs11912763, rs16996648, rs5756152, rs16996672, and rs16996677 (NCBI36.3 chromosome 22 position 35,014,668, 35,022,698, 35,042,418, 35,055,916, and 35,057,229 respectively) show strong linkage disequilibrium with variants in APOL1 (see Supplementary Figure 1 and 2), have high minor allele frequency, and they are nearly non-existent in European populations. At the same time signals of natural selection in the region have previously been identified in African Yoruba samples and never in European samples within a region containing genes APOL3, APOL4, APOL2, APOL1, and MYH9 (NCBI36.3 coordinates 34800kb-35100kb) in publicly available databases using the long-range haplotype test (LRH) [20], the integrated haplotype score (iHS) [21,22], the rMHH [23], and the composite of multiple signals (CMS) [24]. In this last study, the strongest signal of selection was found for variant rs9622363 (NCBI36.3 position 34,986,501, Genome-wide CMS 14.987, p=1.3×10−5, untyped in
