Table 2.
Eight trans-eQTLs Affect Hundreds of Transcripts across the Genome
| trans-eQTL | Position | Closest Gene | Distance to Gene | Distance to TSS | CPMAa(pmeta) | Target Overlapb(p) | Effect Directionc(p) | Target Genesd | TF Enrichede | Networkf(p) |
|---|---|---|---|---|---|---|---|---|---|---|
| rs7694213 | chr4: 53,157,184 | SCFD2 | 0 | 108,383 | 1.6 × 10−2 | 1.7 × 10−4 4.0 × 10−2 3.1 × 10−3 | 5.6 × 10−6 2.0 × 10−4 5.6 × 10−6 | 417 | – | 0.18 |
| rs6899963 | chr6: 104,048,696 | NPM1P10 | 21,932 | 21,931 | 1.9 × 10−2 | 3.5 × 10−2 5.1 × 10−3 2.0 × 10−2 | 5.6 × 10−6 1.7 × 10−5 3.9 × 10−5 | 393 | SRF, STAT3 | <10−3 |
| rs9406332 | chr6: 169,317,960 | VTA1P1 | 20,000 | 20,000 | 3.7 × 10−2 | 3.4 × 10−2 2.8 × 10−2 3.9 × 10−2 | 3.4 × 10−5 1.1 × 10−5 5.3 × 10−4 | 77 | – | 0.21 |
| rs10107976 | chr8: 62,689,355 | NKAIN3 | 0 | 167,779 | 7.9 × 10−3 | 1.7 × 10−3 3.4 × 10−2 7.7 × 10−3 | 1.7 × 10−5 5.6 × 10−6 5.6 × 10−6 | 116 | USF1, USF2, MAX, RFX5, ZZZ3 | 0.19 |
| rs4773419 | chr13: 111,658,732 | RP11-65D24.2 | 0 | 62,722 | 2.4 × 10−2 | 5.6 × 10−3 2.6 × 10−2 1.3 × 10−2 | 5.6 × 10−6 1.2 × 10−4 1.2 × 10−4 | 166 | SP1, PBX3, FOS, NRF1, BRCA1 | 0.37 |
| rs11621120 | chr14: 29,324,177 | RP11-562L8.1 | 0 | 54,479 | 1.9 × 10−2 | 8.5 × 10−4 8.2 × 10−3 4.9 × 10−3 | 5.6 × 10−6 5.7 × 10−4 7.8 × 10−5 | 228 | – | 0.19 |
| rs10520643 | chr15: 86,859,175 | AGBL1 | 0 | 55,267 | 2.4 × 10−3 | 4.5 × 10−3 2.3 × 10−2 1.3 × 10−2 | 5.6 × 10−6 5.6 × 10−6 3.9 × 10−5 | 833 | NR2C2 | <10−3 |
| rs7281608 | chr21: 23,675,283 | AP000960.1 | 166,275 | 166,360 | 4.5 × 10−2 | 2.8 × 10−2 4.8 × 10−3 7.1 × 10−3 | 1.5 × 10−2 1.1 × 10−2 4.5 × 10−4 | 97 | – | 1 × 10−2 |
We identified a subset of trans-eQTLs with nominally significant CPMA meta-analysis statistics; pairwise tests of target overlap; and pairwise tests of directionality across three populations. For each trans-eQTL, we defined a consensus set of target transcripts and found significant enrichment of transcription factor binding events at their promoters. These targets also form significant protein-protein interaction subnetworks.
CPMA meta-analysis statistics for the SNP.
Significance for pairwise tests of target overlap across three populations.
Significance for pairwise tests of directionality across three populations.
For each trans-eQTL, we defined a consensus set of target transcripts (FDR < 0.01) by meta-analyzing eQTL statistics for individual probesets across the three populations.
Significant for enrichment of transcription factor binding events at the target promoters.
Significance for protein-protein sub-networks by PINTS.