Table 3

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

CHR

SNP^type

P

Nearest gene

Presumed gene function‡

6

rs3131036^a

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

rs3124199^b

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

rs1358594^b

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

rs10254544^c

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

rs302923^d

3.00E-04

General transcription factor IIIC, polypeptide 4, 90kDa (GTF3C4)

HIV-1 Tat upregulates RNA polymerase III transcription by activating this gene.

20

rs6037908^b

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

rs6951646^b

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.

Joubert et al. Genome Medicine 2010 2:17   doi:10.1186/gm138