GTEx Tissue eQTL Track Settings
 
Expression QTLs in 44 tissues from GTEx (midpoint release, V6)   (All Regulation tracks)

Display mode:       Reset to defaults

Effect size (FPKM): to (-9265 to 15363)
Minimum Probability variant is in high confidence causal set: (0 to 1)
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     adiposeSubcut  Expression QTL in Adipose_Subcutaneous from GTEx V6   Schema 
 
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     adiposeVisceral  Expression QTL in Adipose_Visceral_Omentum from GTEx V6   Schema 
 
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     adrenalGland  Expression QTL in Adrenal_Gland from GTEx V6   Schema 
 
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     arteryAorta  Expression QTL in Artery_Aorta from GTEx V6   Schema 
 
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     arteryCoronary  Expression QTL in Artery_Coronary from GTEx V6   Schema 
 
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     arteryTibial  Expression QTL in Artery_Tibial from GTEx V6   Schema 
 
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     brainAnCinCortex  Expression QTL in Brain_Anterior_cingulate_cortex_BA24 from GTEx V6   Schema 
 
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     brainCaudate  Expression QTL in Brain_Caudate_basal_ganglia from GTEx V6   Schema 
 
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     brainCerebelHemi  Expression QTL in Brain_Cerebellar_Hemisphere from GTEx V6   Schema 
 
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     brainCerebellum  Expression QTL in Brain_Cerebellum from GTEx V6   Schema 
 
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     brainCortex  Expression QTL in Brain_Cortex from GTEx V6   Schema 
 
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     brainFrontCortex  Expression QTL in Brain_Frontal_Cortex_BA9 from GTEx V6   Schema 
 
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     brainHippocampus  Expression QTL in Brain_Hippocampus from GTEx V6   Schema 
 
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     brainHypothalamus  Expression QTL in Brain_Hypothalamus from GTEx V6   Schema 
 
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     brainNucAccumbens  Expression QTL in Brain_Nucleus_accumbens_basal_ganglia from GTEx V6   Schema 
 
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     brainPutamen  Expression QTL in Brain_Putamen_basal_ganglia from GTEx V6   Schema 
 
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     breastMamTissue  Expression QTL in Breast_Mammary_Tissue from GTEx V6   Schema 
 
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     colonSigmoid  Expression QTL in Colon_Sigmoid from GTEx V6   Schema 
 
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     colonTransverse  Expression QTL in Colon_Transverse from GTEx V6   Schema 
 
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     esophagusJunction  Expression QTL in Esophagus_Gastroesophageal_Junction from GTEx V6   Schema 
 
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     esophagusMucosa  Expression QTL in Esophagus_Mucosa from GTEx V6   Schema 
 
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     esophagusMuscular  Expression QTL in Esophagus_Muscularis from GTEx V6   Schema 
 
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     heartAtrialAppend  Expression QTL in Heart_Atrial_Appendage from GTEx V6   Schema 
 
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     heartLeftVentricl  Expression QTL in Heart_Left_Ventricle from GTEx V6   Schema 
 
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     liver  Expression QTL in Liver from GTEx V6   Schema 
 
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     lung  Expression QTL in Lung from GTEx V6   Schema 
 
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     muscleSkeletal  Expression QTL in Muscle_Skeletal from GTEx V6   Schema 
 
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     nerveTibial  Expression QTL in Nerve_Tibial from GTEx V6   Schema 
 
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     ovary  Expression QTL in Ovary from GTEx V6   Schema 
 
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     pancreas  Expression QTL in Pancreas from GTEx V6   Schema 
 
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     pituitary  Expression QTL in Pituitary from GTEx V6   Schema 
 
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     prostate  Expression QTL in Prostate from GTEx V6   Schema 
 
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     skinExposed  Expression QTL in Skin_Sun_Exposed_Lower_leg from GTEx V6   Schema 
 
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     skinNotExposed  Expression QTL in Skin_Not_Sun_Exposed_Suprapubic from GTEx V6   Schema 
 
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     smallIntestine  Expression QTL in Small_Intestine_Terminal_Ileum from GTEx V6   Schema 
 
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     spleen  Expression QTL in Spleen from GTEx V6   Schema 
 
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     stomach  Expression QTL in Stomach from GTEx V6   Schema 
 
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     testis  Expression QTL in Testis from GTEx V6   Schema 
 
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     thyroid  Expression QTL in Thyroid from GTEx V6   Schema 
 
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     uterus  Expression QTL in Uterus from GTEx V6   Schema 
 
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     vagina  Expression QTL in Vagina from GTEx V6   Schema 
 
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     wholeBlood  Expression QTL in Whole_Blood from GTEx V6   Schema 
 
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     xformedfibroblasts  Expression QTL in Cells_Transformed_fibroblasts from GTEx V6   Schema 
 
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     xformedlymphocytes  Expression QTL in Cells_EBV-transformed_lymphocytes from GTEx V6   Schema 
    
Data version: GTEx Analysis V6p (https://www.gtexportal.org/home/datasets)

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