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

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Database: hg19 Primary Table: gtexEqtlTissueUterus Row Count: 15,679 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`	591	`int(10) unsigned`	range	Indexing field to speed chromosome range queries.
`chrom`	chr1	`varchar(255)`	values	Reference sequence chromosome or scaffold
`chromStart`	869368	`int(10) unsigned`	range	Start position in chromosome
`chromEnd`	869369	`int(10) unsigned`	range	End position in chromosome
`name`	rs13303328/KLHL17	`varchar(255)`	values	Variant/gene pair
`score`	512	`int(10) unsigned`	range	Score from 0-1000 (highest probabiliity in cluster * 1000)
`strand`	.	`char(1)`	values	.
`thickStart`	869368	`int(10) unsigned`	range	Start position
`thickEnd`	869369	`int(10) unsigned`	range	End position
`itemRgb`	16711680	`int(10) unsigned`	range	R,G,B color: red +effect, blue -effect. Bright for high, pale for lower (cutoff effectSize 2.0 RPKM).
`variant`	rs13303328	`varchar(255)`	values	Variant (rsID or GTEx identifier if none)
`geneId`	ENSG00000187961.9	`varchar(255)`	values	Target gene identifier
`gene`	KLHL17	`varchar(255)`	values	Target gene symbol
`distance`	-26598	`int(11)`	range	Distance from TSS
`effectSize`	2.646	`float`	range	Effect size (FPKM)
`pValue`	5.817	`float`	range	Nominal p-value
`causalProb`	0.512	`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
591	chr1	869368	869369	rs13303328/KLHL17	512	.	869368	869369	255,0,0	rs13303328	ENSG00000187961.9	KLHL17	-26598	2.646	5.817	0.512
591	chr1	912048	912049	rs7367995/PERM1	12	.	912048	912049	255,160,160	rs7367995	ENSG00000187642.5	PERM1	-5448	0.178	5.241	0.012
591	chr1	913888	913889	rs2340596/PERM1	62	.	913888	913889	255,160,160	rs2340596	ENSG00000187642.5	PERM1	-3608	0.172	5.769	0.062
591	chr1	914939	914940	rs13303033/PERM1	19	.	914939	914940	255,160,160	rs13303033	ENSG00000187642.5	PERM1	-2557	0.152	4.927	0.019
592	chr1	918383	918384	rs13303118/PERM1	171	.	918383	918384	255,160,160	rs13303118	ENSG00000187642.5	PERM1	887	0.166	5.047	0.171
592	chr1	921715	921716	rs13303278/RP11-54O7.17	9	.	921715	921716	255,160,160	rs13303278	ENSG00000272512.1	RP11-54O7.17	-11715	0.986	5.035	0.009
592	chr1	924527	924528	rs34712273/RP11-54O7.17	195	.	924527	924528	255,160,160	rs34712273	ENSG00000272512.1	RP11-54O7.17	-8903	0.858	6.278	0.195
592	chr1	930750	930751	rs3128111/RP11-54O7.17	21	.	930750	930751	160,160,255	rs3128111	ENSG00000272512.1	RP11-54O7.17	-2680	-1.404	5.516	0.021
592	chr1	931361	931362	rs2799060/RP11-54O7.17	17	.	931361	931362	160,160,255	rs2799060	ENSG00000272512.1	RP11-54O7.17	-2069	-1.268	5.438	0.017
592	chr1	933789	933790	rs9442392/RP11-54O7.17	25	.	933789	933790	255,160,160	rs9442392	ENSG00000272512.1	RP11-54O7.17	359	0.546	5.454	0.025

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