Schema for GTEx Tissue eQTL - Expression QTLs in 44 tissues from GTEx (midpoint release, V6)

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Database: hg19 Primary Table: gtexEqtlTissueBrainCerebelHemi Row Count: 62,462 Data last updated: 2017-10-25
Format description: BED 9+ of expression Quantitative Trait Loci (eQTL). These are variants affecting gene expression
On download server: MariaDB table dump directory

field	example	SQL type	info	description
`bin`	590	`int(10) unsigned`	range	Indexing field to speed chromosome range queries.
`chrom`	chr1	`varchar(255)`	values	Reference sequence chromosome or scaffold
`chromStart`	752565	`int(10) unsigned`	range	Start position in chromosome
`chromEnd`	752566	`int(10) unsigned`	range	End position in chromosome
`name`	rs3094315/LINC00115	`varchar(255)`	values	Variant/gene pair
`score`	48	`int(10) unsigned`	range	Score from 0-1000 (highest probabiliity in cluster * 1000)
`strand`	.	`char(1)`	values	.
`thickStart`	752565	`int(10) unsigned`	range	Start position
`thickEnd`	752566	`int(10) unsigned`	range	End position
`itemRgb`	10526975	`int(10) unsigned`	range	R,G,B color: red +effect, blue -effect. Bright for high, pale for lower (cutoff effectSize 2.0 RPKM).
`variant`	rs3094315	`varchar(255)`	values	Variant (rsID or GTEx identifier if none)
`geneId`	ENSG00000225880.4	`varchar(255)`	values	Target gene identifier
`gene`	LINC00115	`varchar(255)`	values	Target gene symbol
`distance`	-10336	`int(11)`	range	Distance from TSS
`effectSize`	-1.649	`float`	range	Effect size (FPKM)
`pValue`	9.919	`float`	range	Nominal p-value
`causalProb`	0.048	`float`	range	Probability variant is in high confidence causal set

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	itemRgb	variant	geneId	gene	distance	effectSize	pValue	causalProb
590	chr1	752565	752566	rs3094315/LINC00115	48	.	752565	752566	160,160,255	rs3094315	ENSG00000225880.4	LINC00115	-10336	-1.649	9.919	0.048
590	chr1	752720	752721	rs3131972/LINC00115	155	.	752720	752721	160,160,255	rs3131972	ENSG00000225880.4	LINC00115	-10181	-1.505	10.344	0.155
590	chr1	752893	752894	rs3131971/LINC00115	47	.	752893	752894	160,160,255	rs3131971	ENSG00000225880.4	LINC00115	-10008	-1.536	9.918	0.047
590	chr1	753473	753474	rs2073814/LINC00115	315	.	753473	753474	160,160,255	rs2073814	ENSG00000225880.4	LINC00115	-9428	-1.526	10.51	0.315
590	chr1	754502	754503	rs3115859/LINC00115	201	.	754502	754503	160,160,255	rs3115859	ENSG00000225880.4	LINC00115	-8399	-1.518	10.434	0.201
590	chr1	754963	754964	rs3131966/LINC00115	39	.	754963	754964	160,160,255	rs3131966	ENSG00000225880.4	LINC00115	-7938	-1.537	9.887	0.039
590	chr1	760911	760912	rs1048488/LINC00115	73	.	760911	760912	160,160,255	rs1048488	ENSG00000225880.4	LINC00115	-1990	-1.685	10.068	0.073
590	chr1	761146	761147	rs3115850/LINC00115	77	.	761146	761147	160,160,255	rs3115850	ENSG00000225880.4	LINC00115	-1755	-1.686	10.091	0.077
591	chr1	863507	863508	rs7410984/RP11-54O7.3	713	.	863507	863508	160,160,255	rs7410984	ENSG00000223764.2	RP11-54O7.3	8436	-0.127	5.064	0.713
593	chr1	1150180	1150181	rs35659545/B3GALT6	40	.	1150180	1150181	160,160,255	rs35659545	ENSG00000176022.3	B3GALT6	-17448	-1.091	5.981	0.04

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

GTEx Tissue eQTL (gtexEqtlTissue) Track Description

Description

This track shows genetic variants likely affecting proximal gene expression in 44 human tissues from the Genotype-Tissue Expression (GTEx) V6 data release. The data items displayed are gene expression quantitative trait loci within 1MB of gene transcription start sites (cis-eQTLs), significantly associated with gene expression and in the credible set of variants for the gene at a high confidence level (95%). Each eQTL annotation includes the significance of the association, effect size on gene expression, and the probability the eQTL is a member of the 95% credible set (the set containing all causal variants for the gene locus, at 95% confidence level).

Display Conventions

The eQTL item color indicates the effect size attributed to the eQTL:

red	high positive
light red	moderate positive
light blue	moderate negative
blue	high negative
mixed	positive and negative effect in combined eQTL

Effect size is the regression slope, computed from the effect of the alternative allele vs. the reference in FPKM units, based on quantile normalized expression tables. For display purposes, An arbitrary cutoff of +- 2.0 FPKM defines high effect size.

Combined eQTL track

Gene/variant pairs occurring in multiple tissues are combined into a single item in the display. The item label shows the number of tissues where the eQTL was identified, or the tissue name and the GTEx-convention tissue color if the eQTL was identified solely in one tissue. Mouseover lists all tissues affected and the effect size. The item color reflects the largest effect size in any tissue.

Track configuration supports filtering by gene, effect size, or probability. Tissues can be selected via checkboxes or from the UCSC GTEx Body Map graphic.
GTEx Combined eQTL Track Settings: hg19.

Tissue eQTL tracks

This track is a composite track containing 44 subtracks representing the GTEx eQTL tissues. Each subtrack contains all GTEx/CAVIAR eQTLs identified for that tissue.
GTEx 44 Tissues eQTL Track Settings: hg19.

Methods

Laboratory and RNA-seq analysis methods for GTEx V6 are summarized in the GTEx Gene Track description page.

Cis-eQTL's were identified from GTEx RNA-seq and genotype data (variants with minor allele frequency >= 1%) in 44 tissues (those with sample size >=70) using the FastQTL mapper at 5% FDR threshold, by the GTEx Laboratory, Data Analysis and Coordinating Center (LDACC), as part of the GTEx project v6p analysis. These cis-eQTL's were then analyzed together with genome variation information (LD) using the CAVIAR statistical framework to quantify the probability a variant is causal, at the Eskin lab at UCLA, as part of GTEx downstream analysis. The UCSC track was created using the CAVIAR 95% credible set, with significance p-values and effect sizes from the LDACC analysis.

Raw data for these analyses are available from dbGaP (phs000424.v6.p1).

Credits

Thanks to GTEx investigators and analysts -- particularly Farhad Hormozdiari (currently at the Price lab, Harvard), the Eskin lab at UCLA, the GTEx Laboratory, Data Analysis and Coordinating Center and analysts and portal team for providing this data, and to Christopher Brown (U Penn) , for input on design of the track.

References

GTEx Consortium., Laboratory, Data Analysis &Coordinating Center (LDACC)—Analysis Working Group., Statistical Methods groups—Analysis Working Group., Enhancing GTEx (eGTEx) groups., NIH Common Fund., NIH/NCI., NIH/NHGRI., NIH/NIMH., NIH/NIDA., Biospecimen Collection Source Site—NDRI. et al. Genetic effects on gene expression across human tissues. Nature. 2017 Oct 11;550(7675):204-213. PMID: 29022597

Ongen H, Buil A, Brown AA, Dermitzakis ET, Delaneau O. Fast and efficient QTL mapper for thousands of molecular phenotypes. Bioinformatics. 2016 May 15;32(10):1479-85. PMID: 26708335; PMC: PMC4866519

Hormozdiari F, Kostem E, Kang EY, Pasaniuc B, Eskin E. Identifying causal variants at loci with multiple signals of association. Genetics. 2014 Oct;198(2):497-508. PMID: 25104515; PMC: PMC4196608

GTEx Consortium. The Genotype-Tissue Expression (GTEx) project. Nat Genet. 2013 Jun;45(6):580-5. PMID: 23715323; PMC: PMC4010069

GTEx Portal Documentation