Schema for GTEx Tissue eQTL - Expression QTLs in 44 tissues from GTEx (midpoint release, V6)
  Database: hg19    Primary Table: gtexEqtlTissueBrainNucAccumbens    Row Count: 39,369   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
fieldexampleSQL type info description
bin 590int(10) unsigned range Indexing field to speed chromosome range queries.
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
chromStart 748877int(10) unsigned range Start position in chromosome
chromEnd 748878int(10) unsigned range End position in chromosome
name rs143214544/RP4-669L17.10varchar(255) values Variant/gene pair
score 12int(10) unsigned range Score from 0-1000 (highest probabiliity in cluster * 1000)
strand .char(1) values .
thickStart 748877int(10) unsigned range Start position
thickEnd 748878int(10) unsigned range End position
itemRgb 10526975int(10) unsigned range R,G,B color: red +effect, blue -effect. Bright for high, pale for lower (cutoff effectSize 2.0 RPKM).
variant rs143214544varchar(255) values Variant (rsID or GTEx identifier if none)
geneId ENSG00000237094.7varchar(255) values Target gene identifier
gene RP4-669L17.10varchar(255) values Target gene symbol
distance 431158int(11) range Distance from TSS
effectSize -0.1float range Effect size (FPKM)
pValue 4.965float range Nominal p-value
causalProb 0.012float range Probability variant is in high confidence causal set

Sample Rows
 
binchromchromStartchromEndnamescorestrandthickStartthickEnditemRgbvariantgeneIdgenedistanceeffectSizepValuecausalProb
590chr1748877748878rs143214544/RP4-669L17.1012.748877748878160,160,255rs143214544ENSG00000237094.7RP4-669L17.10431158-0.14.9650.012
592chr1924527924528rs34712273/RP11-54O7.176.924527924528255,160,160rs34712273ENSG00000272512.1RP11-54O7.17-89031.4038.3830.006
592chr1930750930751rs3128111/RP11-54O7.175.930750930751160,160,255rs3128111ENSG00000272512.1RP11-54O7.17-2680-1.3098.7260.005
592chr1931361931362rs2799060/RP11-54O7.17870.931361931362160,160,255rs2799060ENSG00000272512.1RP11-54O7.17-2069-1.27810.3230.87
592chr1933789933790rs9442392/RP11-54O7.1730.933789933790255,160,160rs9442392ENSG00000272512.1RP11-54O7.173591.3559.1180.03
592chr1936110936111rs1936360/RP11-54O7.176.936110936111255,160,160rs1936360ENSG00000272512.1RP11-54O7.1726801.3598.4750.006
592chr1940004940005rs2799056/RP11-54O7.177.940004940005160,160,255rs2799056ENSG00000272512.1RP11-54O7.176574-1.2948.7690.007
592chr1940095940096rs4503294/RP11-54O7.1730.940095940096255,160,160rs4503294ENSG00000272512.1RP11-54O7.1766651.3539.1540.03
592chr110030521003053rs4074992/C1orf15922.10030521003053255,160,160rs4074992ENSG00000131591.13C1orf159-486880.3975.8620.022
592chr110049561004957rs4073176/C1orf15934.10049561004957255,160,160rs4073176ENSG00000131591.13C1orf159-467840.4185.5360.034

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