Synthesis of 53 tissue and cell line expression QTL datasets reveals master eQTLs

BMC Genomics

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. F_ST = Fixation index.

ISSN: 1471-2164