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Table 2 Top SNPs in or near genes with roles in pregnancy and development

From: A whole genome association study of mother-to-child transmission of HIV in Malawi

CHR SNPtype P Nearest gene Presumed gene function
17 rs8069770a 3.79E-05 Heparan sulfate (glucosamine) 3-O-sulfotransferase 3A1 (HS3ST3A1) Abundant expression in placenta; HIV-1 requires the gene product heparan sulfate proteoglycans for uptake in trophoblasts (cells forming the placental barrier); involved in biosynthesis of an entry receptor for herpes simplex virus 1
17 rs12306a 3.92E-05 WD repeat and SOCS box-containing 1 (WSB1) Unknown protein function induced by Hedgehog signaling in embryonic structures during chicken development
4 rs1433666a 1.00E-04 Glutamate receptor, ionotropic, delta 2 (GRID2) Homozygosity for this mutation in mice results in death shortly after birth, related to the loss of mid- and hindbrain neurons during late embryogenesis
5 rs6884962b 1.00E-04 NK2 transcription factor related, locus 5 (Drosophila) (NKX2-5) Regulates tissue-specific gene expression essential for tissue differentiation; regulates temporal and spatial patterns of development
7 rs4722999a 1.00E-04 Corticotropin releasing hormone receptor 2 (CRHR2) Detected in placenta, myometrium, decidua, and fetal membranes; expression is down-regulated in uterine tissues during pregnancy, most pronounced in laboring cervix; suggested paracrine role in birth process (for example, effects on macrophages and endothelial cells)
2 rs2677510b 3.00E-04 GLI-Kruppel family member GLI2 (GLI2) Role during embryogenesis, DNA binding, and Sonic hedgehog (Shh) signaling to oncogenes in embryonal carcinoma cells
6 rs2268447a 4.00E-04 Pleiomorphic adenoma gene-like 1 (PLAGL1) Mutations associated with congenital abnormalities, potential role in ovarian and other types of cancer; genetically imprinted in neonatal diabetes
  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); P, adjusted by maternal HIV viral load P-value.