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

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Database: hg19 Primary Table: gtexEqtlTissueBrainHippocampus Row Count: 20,792 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`	592	`int(10) unsigned`	range	Indexing field to speed chromosome range queries.
`chrom`	chr1	`varchar(255)`	values	Reference sequence chromosome or scaffold
`chromStart`	1027844	`int(10) unsigned`	range	Start position in chromosome
`chromEnd`	1027845	`int(10) unsigned`	range	End position in chromosome
`name`	rs74048006/C1orf159	`varchar(255)`	values	Variant/gene pair
`score`	27	`int(10) unsigned`	range	Score from 0-1000 (highest probabiliity in cluster * 1000)
`strand`	.	`char(1)`	values	.
`thickStart`	1027844	`int(10) unsigned`	range	Start position
`thickEnd`	1027845	`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`	rs74048006	`varchar(255)`	values	Variant (rsID or GTEx identifier if none)
`geneId`	ENSG00000131591.13	`varchar(255)`	values	Target gene identifier
`gene`	C1orf159	`varchar(255)`	values	Target gene symbol
`distance`	-23896	`int(11)`	range	Distance from TSS
`effectSize`	-0.451	`float`	range	Effect size (FPKM)
`pValue`	5.46	`float`	range	Nominal p-value
`causalProb`	0.027	`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
592	chr1	1027844	1027845	rs74048006/C1orf159	27	.	1027844	1027845	160,160,255	rs74048006	ENSG00000131591.13	C1orf159	-23896	-0.451	5.46	0.027
592	chr1	1027845	1027846	rs76994018/C1orf159	27	.	1027845	1027846	160,160,255	rs76994018	ENSG00000131591.13	C1orf159	-23895	-0.451	5.458	0.027
592	chr1	1029804	1029805	rs6689308/C1orf159	19	.	1029804	1029805	160,160,255	rs6689308	ENSG00000131591.13	C1orf159	-21936	-0.445	5.382	0.019
592	chr1	1030564	1030565	rs6687776/C1orf159	10	.	1030564	1030565	160,160,255	rs6687776	ENSG00000131591.13	C1orf159	-21176	-0.429	5.105	0.01
592	chr1	1030632	1030633	rs6678318/C1orf159	10	.	1030632	1030633	160,160,255	rs6678318	ENSG00000131591.13	C1orf159	-21108	-0.429	5.105	0.01
592	chr1	1031972	1031973	rs9651270/C1orf159	13	.	1031972	1031973	160,160,255	rs9651270	ENSG00000131591.13	C1orf159	-19768	-0.437	5.21	0.013
592	chr1	1032953	1032954	rs6699750/C1orf159	15	.	1032953	1032954	160,160,255	rs6699750	ENSG00000131591.13	C1orf159	-18787	-0.44	5.283	0.015
592	chr1	1033595	1033596	rs6604964/C1orf159	14	.	1033595	1033596	160,160,255	rs6604964	ENSG00000131591.13	C1orf159	-18145	-0.447	5.249	0.014
592	chr1	1033625	1033626	rs6604965/C1orf159	97	.	1033625	1033626	160,160,255	rs6604965	ENSG00000131591.13	C1orf159	-18115	-0.468	6.108	0.097
592	chr1	1033669	1033670	rs6604966/C1orf159	23	.	1033669	1033670	160,160,255	rs6604966	ENSG00000131591.13	C1orf159	-18071	-0.451	5.473	0.023

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