Figure 2. LD of CUL5 SNPs in AA and EA.

LD of CUL5 SNPs is shown in AA (A) and EA (B). Pairwise D′ plots were generated using Haploview with its standard color scheme. Dark-red squares indicate high D′ values, light-blue squares indicate high D′ values with low LOD scores, and light-red and white squares indicate low D′ values. D′ values were indicated for those not equal to 1.0. A single LD block was defined for both AA and EA under the default confidence interval criteria. A reduced-medium network for the genealogical relationship of CUL5 haplotypes is shown in AA (C) and EA (D). The network was inferred in terms of mutational distance, on the basis of 12 CUL5 SNPs and one chimpanzee (Chimp) sequence. Median vector (mv1), the consensus sequences inferred by parsimony criteria, represents possible unsampled sequences or extinct ancestral sequences. Haplotypes (H1–H11) are represented by circles, whose area reflects the number of alleles observed in each population. The solid branches between haplotypes represent mutational events or SNPs (S1–S12). The circles in green show haplotypes with detrimental effect and those in blue show protective effect on AIDS progression in the Cox model analysis; the protective effect of H3 in light blue was of less certainty (see Results). The haplotypes were separated into two clusters, cluster I and II, carrying ctSNP5 A or G, respectively. Cluster I and II in AA are shaded in blue and green, respectively. SNP2 is omitted in (B) and (D) as it was absent in EA.