Table 4.
eQTLs compared to human genome regulatory features.
| Genome regulatory track | Nucleotides per track | Probability* | Expected overlaps | Observed overlaps | Obs:Exp | P-value |
|---|---|---|---|---|---|---|
| ORegAnno | 11,265,267 | 0.00366 | 230 | 744 | 3.24 | 1.73E-159 |
| Functional RNAs | 107,202 | 3.48E-05 | 2.19 | 7 | 3.2 | 0.00725 |
| Gm12892V2.narrowPeak | 80,820,229 | 0.0262 | 1,650 | 4,610 | 2.79 | <1E-308 |
| Gm12891V2.narrowPeak | 84,650,075 | 0.0275 | 1,730 | 4,680 | 2.71 | <1E-308 |
| ENCODE H3k4me3 | 120,458,965 | 0.0391 | 2,460 | 6,500 | 2.64 | <1E-308 |
| Gm12878V3.narrowPeak | 43,937,796 | 0.0143 | 897 | 2,260 | 2.52 | <1E-308 |
| ENCODE H3k27ac | 125,879,335 | 0.0409 | 2,570 | 6,540 | 2.55 | <1E-308 |
| ENCODE H3k4me1 | 242,340,600 | 0.0787 | 4,950 | 11,300 | 2.28 | <1E-308 |
| Patrocles (miRNA database) | 3,375,454 | 0.0011 | 68.9 | 153 | 2.22 | 1.78E-18 |
| ENCODE H3k36me3 | 631,024,019 | 0.205 | 12,900 | 28,200 | 2.19 | <1E-308 |
| ENCODE CTCF | 44,516,245 | 0.0145 | 909 | 1,900 | 2.1 | 1.97E-185 |
| ENCODE 5C interactions † | 10,484,463 | 0.34 | 214 | 510 | 2.38 | 8.80E-130 |
| CpG islands | 21,575,631 | 0.007 | 440 | 817 | 1.86 | 1.84E-58 |
| Conserved TFBS | 1,602,974 | 0.00052 | 32.7 | 54 | 1.65 | 4.00E-04 |
| miRbase (v.13) | 63,451 | 2.06E-05 | 1.3 | 2 | 1.54 | 0.371 |
| TargetScan | 354,030 | 0.000115 | 7.23 | 11 | 1.52 | 0.115 |
| ENCODE H3k27me3 | 1,136,357,520 | 0.369 | 23,200 | 24,700 | 1.07 | 1.02E-37 |
| Vista Enhancers | 1,052,004 | 0.000342 | 21.5 | 16 | 0.745 | 0.906 |
| lincRNAs | 127,119,148 | 0.04 | 2,595 | 1,541 | 0.59 | 1 |
| IHS sites (Z-score > 3) | 2,275,923 | 0.000739 | 46.5 | 24 | 0.52 | 1 |
| F ST sites (Z-score > 3) | 4,088,207 | 0.00133 | 83.4 | 41 | 0.49 | 1 |
| PolymiRTS predicted miRNA binding sites | 11,265,267 | 0.00366 | 230 | 1 | 0.00435 | 1 |
*Probabilities determined based on the fraction of the human genome covered by the feature track (human genome length = 3,080,436,451) and the total unique eSNP positions (n = 62,872). P-values are for binomial tests for enrichment of observed over expected. All ENCODE feature tracks are for lymphoblastoid cell lines and all are for sample GM12878 except where indicated. †ENCODE 5C long range interactions targeted ~1% of the genome this coverage and expectations were derived based on this proportion, and 1% of the unique eSNP positions. TFBS = transcription factor binding sites. miRNA = microRNA. lincRNA = long, intergenic non-coding RNA. IHS = integrated haplotype score. FST = Fixation index.