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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.
  1. The sources of the presumed gene function are NCBI Entrez Gene and OMIM [88, 94]. CHR, chromosome; SNPtype, SNP and type, where type refers to the position of the SNP relative to the closest gene (aintronic, bintergenic, cupstream, ddownstream); P, adjusted by maternal HIV viral load P-value.