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Table 1 HIV MTCT association results for SNPs, selected by P-value

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

CHR SNPtype A1 A2 MAF Unadjusted OR (95% CI) P Adjusted OR (95% CI) P Nearest gene
17 rs12306a A G 0.23 0.33 (0.20, 0.55) 2.02E-05 0.34 (0.20, 0.57) 3.92E-05 WD repeat and SOCS box-containing 1 (WSB1)
8 rs476321a T C 0.27 2.55 (1.65, 3.92) 2.15E-05 2.50 (1.62, 3.87) 3.42E-05 Protein coding, protein info: transcription factor CP2-like 3, deafness, autosomal dominant 28, grainyhead-like 2 (Drosophila) (GRHL2)
6 rs2268993a C G 0.27 2.71 (1.71, 4.28) 2.20E-05 2.70 (1.70, 4.28) 2.65E-05 Solute carrier family 35 (CMP-sialic acid transporter), member A1 (SLC35A1)
18 rs8084223b T C 0.15 0.26 (0.14, 0.49) 3.41E-05 0.26 (0.14, 0.50) 4.21E-05 AC104961.7
23 rs5934013a G A 0.15 4.18 (2.12, 8.24) 3.61E-05 4.09 (2.08, 8.06) 4.68E-05 FERM and PDZ domain containing 4 (FRMPD4)
8 rs9314565b G C 0.47 0.42 (0.27, 0.63) 4.13E-05 0.41 (0.27, 0.63) 3.64E-05 AC019176.4
3 rs4234621b C T 0.28 0.39 (0.25, 0.61) 5.03E-05 0.38 (0.24, 0.60) 4.58E-05 Pyrin domain containing 2 (PYDC2)
14 rs2287652a C A 0.2 0.32 (0.19, 0.56) 5.15E-05 0.33 (0.19, 0.57) 7.12E-05 aarF domain containing kinase 1 (ADCK1)
9 rs1889055b C N/A 0.24 2.52 (1.61, 3.93) 5.21E-05 2.48 (1.59, 3.87) 6.32E-05 RP11-48L13.1
7 rs216743a A G 0.1 4.22 (2.09, 8.53) 6.16E-05 4.23 (2.08, 8.61) 6.89E-05 cAMP responsive element binding protein 5 (CREB5)
7 rs216744a G G 0.1 4.22 (2.09, 8.53) 6.16E-05 4.23 (2.08, 8.61) 6.89E-05 cAMP responsive element binding protein 5 (CREB5)
22 rs131817a T G 0.23 0.37 (0.22, 0.60) 6.68E-05 0.36 (0.22, 0.59) 6.62E-05 Non-SMC condensin II complex, subunit H2 (NCAPH2)
7 rs4722999a C C 0.32 2.46 (1.58, 3.84) 7.07E-05 2.38 (1.52, 3.72) 1.49E-04 Corticotropin releasing hormone receptor 2 (CRHR2)
17 rs8069770a T G 0.14 0.27 (0.14, 0.51) 7.17E-05 0.25 (0.13, 0.49) 3.79E-05 Heparan sulfate (glucosamine) 3-O-sulfotransferase 3A1 (HS3ST3A1)
5 rs6884962c G A 0.49 2.18 (1.48, 3.21) 7.31E-05 2.15 (1.46, 3.17) 1.07E-04 AC008412.8
12 rs12579934a T A 0.46 2.24 (1.49, 3.36) 9.59E-05 2.48 (1.63, 3.78) 2.45E-05 Branched chain aminotransferase 1, cytosolic (BCAT1)
9 rs12376718b T A 0.15 3.07 (1.75, 5.39) 9.79E-05 2.97 (1.69, 5.20) 1.47E-04 RP11-48L13.1
16 rs6540013b G C 0.39 0.45 (0.30, 0.68) 1.16E-04 0.44 (0.29, 0.66) 8.99E-05 AC010531.8
16 rs12598821a T T 0.48 0.45 (0.30, 0.68) 1.20E-04 0.43 (0.28, 0.65) 6.65E-05 AC010333.7
1 rs3861824b A G 0.11 0.23 (0.11, 0.50) 1.98E-04 0.20 (0.09, 0.44) 6.29E-05 Disabled homolog 1 (Drosophila) (DAB1)
  1. Top 20 most significant SNPs based on P-values from crude and/or adjusted by maternal HIV viral load analyses, sorted by unadjusted P-value. CHR, chromosome; SNPtype, SNP and type, where type refers to the position of the SNP relative to the closest gene (aintronic, bintergenic, cupstream); A1, risk allele designated by PLINK; A2, major allele; MAF, minor allele frequency; OR, odds ratio; 95% CI, 95% confidence interval of the OR; Adjusted OR, OR from analyses adjusted by maternal HIV viral load.