Table 3 Top SNPs in or near genes with immunological function or HIV-1 protein interactions
From: A whole genome association study of mother-to-child transmission of HIV in Malawi
CHR | SNPtype | P | Nearest gene | Presumed gene function‡ |
|---|---|---|---|---|
6 | rs3131036a | 2.00E-04 | Discoidin domain receptor family, member 1 (DDR1) | Proximal to HLA genes; interacts w/collagen to up-regulate IL-8 and inflammatory macrophages. |
10 | rs3124199b | 2.00E-04 | Mitogen-activated protein kinase kinase kinase 8 (MAP3K8) | Promotes production of TNF-alpha and IL-2 during T lymphocyte activation; promotes proteolysis of cytokine activator NFKB1 in rats. |
4 | rs1358594b | 3.00E-04 | Interleukin 8 (IL8) | HIV-1 Nef, Tat, and Vpr regulate IL-8 expression. IL-8 protein mediates inflammatory response including CD4+ response to HIV-1 infection. |
7 | rs10254544c | 3.00E-04 | Nucleoporin like 2 (NUPL2) | Interacts with HIV-1 Rev to mediate nuclear import of viral DNA and inhibit nuclear export of HIV-1 mRNA. |
9 | rs302923d | 3.00E-04 | General transcription factor IIIC, polypeptide 4, 90kDa (GTF3C4) | HIV-1 Tat upregulates RNA polymerase III transcription by activating this gene. |
20 | rs6037908b | 3.00E-04 | Prion protein (p27-30) (Creutzfeldt-Jakob disease, Gerstmann-Strausler-Scheinker syndrome, fatal familial insomnia) (PRNP) | HIV-1 Tat binds to a stem-loop structure in the mRNA of PrP, upregulating expression. |
7 | rs6951646b | 4.00E-04 | Sp4 transcription factor (SP4) | Activates the HIV-1 LTR promoter, possibly enhancing HIV-1 Tat-mediated transactivation of the viral promoter. |