Table 3.

Top SNPs in or near genes with immunological function or HIV-1 protein interactions

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.

The sources of the presumed gene function are NCBI Entrez Gene and OMIM [88,94]. CHR, chromosome; SNP^type, 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.