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