Table 1. Summary of associations and allele-specific expression analyses in GenCord.
| Test | Samples | Window size | Phenotype | FDR | Nominal P-value | F | L | T | |
|---|---|---|---|---|---|---|---|---|---|
| eQTLs | genotypes and expression | 183(F) | 1Mb | genes | 10% | 2.2E-05(F); 3.2E-05(L); 1.8E-05(T) | 2433 | 3372 | 2115 |
| 185(L) | |||||||||
| 186(T) | |||||||||
| mQTLs | genotypes and methylation | 107(F) | 5kb | methylation sites | 10% | 4.4E-04(F); 7.9E-04(L); 1.3E-3(T) | 14189 | 22411 | 32318 |
| 111(L) | |||||||||
| 66(T) | |||||||||
| eQTMs | methylation and expression | 110(F) | 50kb | genes | 10% | 7.6E-05(F); 7E-04(L); 6.9E-04(T) | 596 | 3680 | 3838 |
| 118(L) | |||||||||
| 66(T) | |||||||||
| asQTLs | genotypes and alt. splicing | 183(F) | 1Mb | genes | 10% | Permutation per exon-exon link | 382 | 527 | 380 |
| 185(L) | |||||||||
| 186(T) | |||||||||
| asQTMs | methylation and alt. splicing | 110(F) | 50kb | genes | 10% | Permutation per exon-exon link | 4602 | 5663 | 81 |
| 118(L) | |||||||||
| 66(T) | |||||||||
| ASE | allelic imbalance | 178(F) | - | assayable heterozygous sites | 20%* | 0.005 | 7162 | 8211 | 7747 |
| 178(L) | |||||||||
| 180(T) |
Number of significant genes, methylation sites or assayable heterozygous sites in fibroblasts (F), LCLs (L) and T-cells (T). The association analyses on eQTL, mQTLs and eQTMs were previously reported [37].
* FDR calculated as number of expected over number of observed based on the nominal P-value threshold.