Schema for GTEx Combined eQTL - Combined Expression QTLs from 44 Tissues from GTEx (midpoint release, V6) |
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Database: hg19 Primary Table: gtexEqtlCluster Row Count: 1,622,952 Data last updated: 2017-10-25
Format description: BED5+ of eQTLs (variants affecting gene expression) with a target (gene or tissue), and lists of values related to combined factors (e.g. tissues or genes)
On download server: MariaDB table dump directory
| field | example | SQL type | description |
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| bin | 585 | smallint(6) | Indexing field to speed chromosome range queries. |
| chrom | chr1 | varchar(255) | Reference sequence chromosome or scaffold |
| chromStart | 55298 | int(10) unsigned | Start position in chromosome |
| chromEnd | 55299 | int(10) unsigned | End position in chromosome |
| name | rs10399749 | varchar(255) | Name of variant (rsID or GTEx identifier if none) |
| score | 10 | int(10) unsigned | Score from 0-1000 |
| targetId | ENSG00000224956.5 | varchar(255) | Identifier of target (gene or tissue) |
| target | ENSG00000224956.5 | varchar(255) | Name of target (gene or tissue) |
| distance | -608228 | int(11) | Distance from TSS |
| maxEffect | -0.62 | float | Maximum absolute value effect size in cluster |
| effectType | - | char(1) | +, -, 0 (for mixed) |
| maxPvalue | 6.694 | float | Maximum -log10 pValue in cluster |
| expCount | 1 | int(10) unsigned | Number of experiment values |
| expNames | nerveTibial, | longblob | Comma separated list of experiment names (e.g. tissue or gene) |
| expScores | -0.620, | longblob | Comma separated list of effect size values |
| expPvals | 6.694, | longblob | Comma separated list of -log10 transformed p-values |
| expProbs | 0.010, | longblob | Comma separated list of probabilities variant is in high confidence causal set |
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Sample Rows
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| bin | chrom | chromStart | chromEnd | name | score | targetId | target | distance | maxEffect | effectType | maxPvalue | expCount | expNames | expScores | expPvals | expProbs |
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| 585 | chr1 | 55298 | 55299 | rs10399749 | 10 | ENSG00000224956.5 | ENSG00000224956.5 | -608228 | -0.62 | - | 6.694 | 1 | nerveTibial, | -0.620, | 6.694, | 0.010, |
| 585 | chr1 | 55325 | 55326 | rs3107975 | 12 | ENSG00000187583.6 | PLEKHN1 | -846551 | -0.166 | - | 4.585 | 1 | wholeBlood, | -0.166, | 4.585, | 0.012, |
| 585 | chr1 | 58813 | 58814 | rs114420996 | 96 | ENSG00000224956.5 | ENSG00000224956.5 | -604713 | -0.637 | - | 4.5 | 1 | colonTransverse, | -0.637, | 4.500, | 0.096, |
| 585 | chr1 | 63670 | 63671 | rs80011619 | 317 | ENSG00000230021.3 | RP5-857K21.4 | -596259 | 0.04 | + | 5.391 | 1 | lung, | 0.040, | 5.391, | 0.317, |
| 589 | chr1 | 526839 | 526840 | rs60396226 | 12 | ENSG00000224956.5 | ENSG00000224956.5 | -136687 | -0.67 | - | 4.633 | 1 | esophagusMuscular, | -0.670, | 4.633, | 0.012, |
| 589 | chr1 | 529781 | 529782 | rs144425991 | 141 | ENSG00000188157.9 | AGRN | -425721 | -3.579 | - | 4.298 | 1 | xformedfibroblasts, | -3.579, | 4.298, | 0.141, |
| 589 | chr1 | 533169 | 533170 | rs114617477 | 582 | ENSG00000227232.4 | WASH7P | 503617 | -5.049 | - | 5.638 | 1 | skinNotExposed, | -5.049, | 5.638, | 0.582, |
| 590 | chr1 | 676126 | 676127 | rs150820983 | 10 | ENSG00000008128.18 | CDK11A | -979639 | -1.671 | - | 4.906 | 1 | heartLeftVentricl, | -1.671, | 4.906, | 0.010, |
| 590 | chr1 | 691541 | 691542 | rs201999089 | 20 | ENSG00000188976.6 | NOC2L | -203148 | 0.867 | + | 4.623 | 1 | lung, | 0.867, | 4.623, | 0.020, |
| 590 | chr1 | 697411 | 697411 | rs199865571 | 86 | ENSG00000228327.2 | RP11-206L10.2 | -16595 | 1.025 | + | 4.81 | 2 | lung,skinExposed, | 1.025,0.840, | 5.244,4.810, | 0.086,0.012, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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GTEx Combined eQTL (gtexEqtlCluster) Track Description
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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
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US Server