None of the top 10 SNPs identified in our present study map to gene regions that were identified in previous GWAS on HIV-1 control that mainly identified associations between HIV-1 control and SNPs on chromosome 6 [14], [15], [18]–[20]. In a previous study, we were able to confirm SNP rs2395029 in the HCP5 gene region, in complete linkage with HLA-B57, and SNP rs9264942 upstream of the HLA-C gene, that were identified by Fellay et al [15] to be associated with viral load set-point and/or CD4+ T-cell depletion. In our GWAS, however, these associations did not have genome-wide significant P-values [16]. Moreover, HLA-B57 and HLA-B27 were also only associated with time from seroconversion until AIDS-diagnosis but not with time between AIDS-diagnosis and AIDS-related death [6], [16]. Differences in ancestry, gender, transmission route, study design (case-control versus survival analysis), phenotype used for association, or other yet unknown factors may explain the variable outcome of different studies. Indeed, two studies that also used survival time as a phenotype identified signals outside the chromosome 6 HLA-gene region as well [21], [23]. This illustrates that
