Schema for GTEx Combined eQTL - Combined Expression QTLs from 44 Tissues from GTEx (midpoint release, V6)
  Database: hg19    Primary Table: gtexEqtlCluster    Row Count: 1,622,952   Data last updated: 2017-10-26
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)
fieldexampleSQL type description
bin 585smallint(6) Indexing field to speed chromosome range queries.
chrom chr1varchar(255) Reference sequence chromosome or scaffold
chromStart 55298int(10) unsigned Start position in chromosome
chromEnd 55299int(10) unsigned End position in chromosome
name rs10399749varchar(255) Name of variant (rsID or GTEx identifier if none)
score 10int(10) unsigned Score from 0-1000
targetId ENSG00000224956.5varchar(255) Identifier of target (gene or tissue)
target ENSG00000224956.5varchar(255) Name of target (gene or tissue)
distance -608228int(11) Distance from TSS
maxEffect -0.62float Maximum absolute value effect size in cluster
effectType -char(1) +, -, 0 (for mixed)
maxPvalue 6.694float Maximum -log10 pValue in cluster
expCount 1int(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

Sample Rows
 
binchromchromStartchromEndnamescoretargetIdtargetdistancemaxEffecteffectTypemaxPvalueexpCountexpNamesexpScoresexpPvalsexpProbs
585chr15529855299rs1039974910ENSG00000224956.5ENSG00000224956.5-608228-0.62-6.6941nerveTibial,-0.620,6.694,0.010,
585chr15532555326rs310797512ENSG00000187583.6PLEKHN1-846551-0.166-4.5851wholeBlood,-0.166,4.585,0.012,
585chr15881358814rs11442099696ENSG00000224956.5ENSG00000224956.5-604713-0.637-4.51colonTransverse,-0.637,4.500,0.096,
585chr16367063671rs80011619317ENSG00000230021.3RP5-857K21.4-5962590.04+5.3911lung,0.040,5.391,0.317,
589chr1526839526840rs6039622612ENSG00000224956.5ENSG00000224956.5-136687-0.67-4.6331esophagusMuscular,-0.670,4.633,0.012,
589chr1529781529782rs144425991141ENSG00000188157.9AGRN-425721-3.579-4.2981xformedfibroblasts,-3.579,4.298,0.141,
589chr1533169533170rs114617477582ENSG00000227232.4WASH7P503617-5.049-5.6381skinNotExposed,-5.049,5.638,0.582,
590chr1676126676127rs15082098310ENSG00000008128.18CDK11A-979639-1.671-4.9061heartLeftVentricl,-1.671,4.906,0.010,
590chr1691541691542rs20199908920ENSG00000188976.6NOC2L-2031480.867+4.6231lung,0.867,4.623,0.020,
590chr1697411697411rs19986557186ENSG00000228327.2RP11-206L10.2-165951.025+4.812lung,skinExposed,1.025,0.840,5.244,4.810,0.086,0.012,

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

GTEx Combined eQTL (gtexEqtlCluster) 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