Table 4.
Proportion of explained variation by SNPs and CpG sites associated with the expression of ADME genes
| Gene/Locus | Chr | SNP | CpG site | % of variation in expression explained by | |||
|---|---|---|---|---|---|---|---|
| SNP only | CpG only | SNP and CpG site | SNP and all CpG sites 1 | ||||
| GSTT1 | 22 | rs9612520 | cg05380919 | 50% | 75% | 78% | 84%** |
| CYP3A5 | 7 | CS015290 | cg03133378 | 55% | 7% | 57% | 57% |
| GSTM1 | 1 | rs75953876 | cg18938907 | 11% | 55% | 56% | 61% |
| GPX7 | 1 | rs11810754 | cg11953272 | 48% | 16% | 49% | 52% |
| UGT1A1 | 2 | rs7592624 | cg11811840 | 22% | 41% | 45% | 47% |
| SLC22A18 | 11 | rs413781 | cg24724917 | 30% | 15% | 44% | 49%* |
| FMO4 | 1 | rs2223477 | cg14981176 | 39% | 16% | 39% | 39% |
| GSTM3 | 1 | rs115636764 | cg23645476 | 21% | 20% | 35% | 46%** |
| SLC19A1 | 21 | rs7867 | cg27210852 | 22% | 10% | 30% | 30% |
| GSTO2 | 10 | rs11595547 | cg23659134 | 20% | 24% | 28% | 28% |
| PON1 | 7 | rs854533 | cg07404485 | 13% | 23% | 27% | 30% |
| DHRS2 | 14 | rs57350570 | cg07125017 | 23% | 4% | 26% | 26% |
| GSTA4 | 6 | rs538920 | cg22486834 | 14% | 14% | 20% | 21% |
| CEBPA | 19 | rs80241821 | cg19035908 | 17% | 6% | 20% | 20% |
| MGST3 | 1 | rs10737515 | cg16553119 | 12% | 12% | 13% | 13% |
| DHRS7 | 14 | rs376391 | cg18906360 | 12% | 9% | 13% | 13% |
*F-test p-value < 0.05; **F-test p-value < 0.005.
F-test null hypothesis: model for gene expression with the SNP and CpG site as explanatory variables and model for gene expression with the SNP and all CpG sites1 fit equally well with the differences being due to random chance.
SNP and all CpG sites1 - the CpG sites that have eQTM effects with the expression probe.