Table 2.
Meta-analysis Results of Pharmacokinetic Associations (top 20 SNPs)
| GWAS (genotyped SNPs) | GWAS (imputed SNPs) | Candidate SNPs (30 genotyped SNPs tested) | Candidate SNPs (594 genotyped SNPs tested) | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SNP | chr | gene | Pa | SNP | chr | gene | Pa | SNP | chr | gene | Pb | SNP | chr | gene | Pc |
| rs113162402 | 17 | SEPT4c | 1.40E-07 | rs12662869 | 6 | SLC17A1 | 7.10E-09 | rs3818486 | 13 | ABCC4 | 3.59E-02 | rs3847258 | 9 | AK3 | 2.93E-02 |
| rs359770 | 18 | SMIM21, ZNF516c | 4.00E-06 | rs6926425 | 6 | SLC17A1 | 5.40E-08 | rs2185631 | 6 | ABCC10 | 4.81E-02 | rs16921966 | 9 | AK3 | 3.28E-02 |
| rs359769 | 18 | SMIM21, ZNF516c | 4.10E-06 | rs1179086 | 6 | SLC17A1 | 1.10E-07 | rs6421690 | 11 | SLC22A11 | 7.01E-02 | rs3818486 | 13 | ABCC4 | 3.59E-02 |
| rs438697 | 1 | LPHN2, TTLL7c | 8.20E-06 | chr6:25792711:D | 6 | SLC17A1 | 1.70E-07 | rs4148486 | 13 | ABCC4 | 8.97E-02 | rs10798924 | 1 | AK2 | 3.67E-02 |
| rs1833170 | 16 | C16orf72, GRIN2Ac | 8.40E-06 | rs2586052 | 17 | CUEDC1 | 1.70E-07 | rs2389204 | 13 | ABCC4 | 1.07E-01 | rs12429339 | 13 | ABCC4 | 3.90E-02 |
| re17199679 | 9 | KLF4, IKBKAPc | 9.30E-06 | rs1575535 | 6 | SLC17A1 | 1.70E-07 | rs7924450 | 11 | SLC22A11 | 1.21E-01 | rs11591185 | 1 | AK2 | 4.64E-02 |
| rs6429839 | 1 | LPHN2, TTLL7c | 1.20E-05 | rs1165216 | 6 | SLC17A1 | 3.90E-07 | rs11231803 | 11 | SLC22A11 | 1.24E-01 | rs2185631 | 6 | ABCC10 | 4.81E-02 |
| rs4662167 | 1 | LPHN2, TTLL7c | 1.20E-05 | rs113162402 | 17 | SEPT4 | 4.40E-07 | rs3818493 | 13 | ABCC4 | 1.29E-01 | rs2268691 | 1 | AK2 | 5.29E-02 |
| rs7829911 | 8 | SBSPON, RPL7c | 1.50E-05 | rs1408270 | 6 | SLC17A3 | 5.80E-07 | rs9349256 | 6 | ABCC10 | 1.43E-01 | rs1611822 | 13 | ABCC4 | 5.93E-02 |
| rs1165176 | 6 | SLC17A1 | 2.00E-05 | rs2685506 | 17 | CUEDC1 | 6.20E-07 | rs2274405 | 13 | ABCC4 | 1.71E-01 | rs17268129 | 13 | ABCC4 | 5.98E-02 |
| rs1420040 | 16 | GRIN2A | 2.00E-05 | rs3807044 | 6 | KCNK16 | 6.20E-07 | rs7331142 | 13 | ABCC4 | 1.77E-01 | rs1751033 | 13 | ABCC4 | 7.18E-02 |
| rs765285 | 6 | SLC17A1 | 2.10E-05 | rs390296 | 1 | LPHN2, TTLL7c | 1.90E-06 | rs9524827 | 13 | ABCC4 | 1.82E-01 | rs9561765 | 13 | ABCC4 | 7.94E-02 |
| rs1165177 | 6 | SLC17A1 | 2.10E-05 | rs437749 | 1 | LPHN2, TTLL7c | 1.90E-06 | rs9394952 | 6 | ABCC10 | 2.00E-01 | rs1564351 | 13 | ABCC4 | 8.01E-02 |
| rs1185569 | 6 | SLC17A1 | 2.10E-05 | rs409651 | 1 | LPHN2, TTLL7c | 1.90E-06 | rs1045642 | 7 | ABCB1 | 2.38E-01 | rs7330330 | 13 | ABCC4 | 8.22E-02 |
| rs4319926 | 2 | ST6GAL2, RGPD4-AS1c | 2.20E-05 | rs423768 | 1 | LPHN2, TTLL7c | 1.90E-06 | rs2273697 | 10 | ABCC2 | 2.80E-01 | rs4148487 | 13 | ABCC4 | 8.36E-02 |
| rs4442993 | 2 | ST6GAL2, RGPD4-AS1c | 2.20E-05 | rs6693748 | 1 | LPHN2, TTLL7c | 1.90E-06 | rs717620 | 10 | ABCC2 | 2.87E-01 | rs4148442 | 13 | ABCC4 | 8.68E-02 |
| rs563189 | 1 | LPHN2, TTLL7c | 2.50E-05 | rs7552456 | 1 | LPHN2, TTLL7c | 1.90E-06 | rs2125739 | 6 | ABCC10 | 3.19E-01 | rs4148451 | 13 | ABCC4 | 8.68E-02 |
| rs10503961 | 8 | DUSP26, UNC5Dc | 2.50E-05 | rs10874339 | 1 | LPHN2, TTLL7c | 1.90E-06 | rs4148477 | 13 | ABCC4 | 3.35E-01 | rs1729745 | 13 | ABCC4 | 8.89E-02 |
| rs7144413 | 14 | SCFD1, COCHc | 2.70E-05 | rs12141972 | 1 | LPHN2, TTLL7c | 1.90E-06 | rs4148478 | 13 | ABCC4 | 3.35E-01 | rs4148486 | 13 | ABCC4 | 8.97E-02 |
| rs11844480 | 14 | SCFD1, COCHc | 2.80E-05 | rs10874341 | 1 | LPHN2, TTLL7c | 1.90E-06 | rs17222723 | 10 | ABCC2 | 4.27E-01 | rs9524858 | 13 | ABCC4 | 9.17E-02 |
CHR = Chromosome; SNP = SNP identifier; P = P-value.
a
Significance threshold was 5×10−8 for the genome-wide analyses.
b
Significance threshold was 0.002 for the subset of 30 SNPs.
c
Significance threshold was 8.4×10−5 for the subset of 594 SNPs.
Highlighted: imputed SNP found to be associated with tenofovir clearance