HLA, HCP5 and ZNRD1 in HIV Figure 1. Polymorphisms analyzed in this study and their LD patterns in HIV+ subjects from the WHMC cohort. (A) Genomic location of the polymorphisms studied on chromosome 6p21. Green ticks/boxes represent the HCP5, RNF39 and ZNRD1 genes and red ticks denote HLA loci. The relative location of the polymorphisms studied is shown by vertical arrows (along with their respective NCBI rs identifiers). The horizontal arrows under the genes point to the 59R39 orientation of the gene. The predicted size of the two extended haplotypes containing HLA-A10 (,86kb) and B*57 (,157kb) are also shown. (B) Linkage disequilibrium (LD) analysis of the studied alleles. D’ value estimates are denoted by the intensity of the blue color shown on the scale on the top. (C) Estimated frequencies of the haplotypes based on possession of the HLA-B*57, HCP5 and HLA-C59 polymorphisms (top), and separately for HLA-A10 and ZNRD1 (bottom) polymorphisms in HIV+ individuals from the WHMC cohort. Top panel shows the haplotype frequencies for HLA-B*57, HCP5 and HLA-C59 alleles (red and purple colored bars are for EAs and AAs, respectively) while the lower panel is for haplotypes derived based on HLA-A10 and ZNRD1 polymorphisms (red and purple colored bars are for EAs and AAs, respectively). Bars represent the haplotype frequency while the numbers to the right of each bar represents the number of haplotypes found in the WHMC subjects. Numbers in parentheses, total number of haplotypes. As discussed in the text, because of the nearly 100% LD between ZNRD1 and RNF39 SNPs, rs9261129 was used to represent the ZNRD1 SNP in statistical analyses (SNP number 3 in panels B and panel C, bottom). doi:10.1371/journal.pone.0003636.g001 PLoS ONE | www.plosone.org 3 November 2008 | Volume 3 | Issue 11 | e3636