GTEx Combined eQTL Track GRCh37/hg19 Combined Expression QTLs from 44 Tissues from GTEx (midpoint release, V6)
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Effect size minimum: +- FPKM (range 0-15362.9)
Probability minimum: (range 0-1.0)      Display tissue color (single tissue eQTL)
Tissues
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N= 350 Adipose - Subcutaneous 153 Esophagus - Gastroesophageal Junction
227 Adipose - Visceral (Omentum) 286 Esophagus - Mucosa
145 Adrenal Gland 247 Esophagus - Muscularis
224 Artery - Aorta 6 Fallopian Tube
133 Artery - Coronary 194 Heart - Atrial Appendage
332 Artery - Tibial 218 Heart - Left Ventricle
11 Bladder 32 Kidney - Cortex
72 Brain - Amygdala 119 Liver
84 Brain - Anterior cingulate cortex (BA24) 320 Lung
117 Brain - Caudate (basal ganglia) 57 Minor Salivary Gland
105 Brain - Cerebellar Hemisphere 430 Muscle - Skeletal
125 Brain - Cerebellum 304 Nerve - Tibial
114 Brain - Cortex 97 Ovary
108 Brain - Frontal Cortex (BA9) 171 Pancreas
94 Brain - Hippocampus 103 Pituitary
96 Brain - Hypothalamus 106 Prostate
113 Brain - Nucleus accumbens (basal ganglia) 250 Skin - Not Sun Exposed (Suprapubic)
97 Brain - Putamen (basal ganglia) 357 Skin - Sun Exposed (Lower leg)
71 Brain - Spinal cord (cervical c-1) 88 Small Intestine - Terminal Ileum
63 Brain - Substantia nigra 104 Spleen
214 Breast - Mammary Tissue 193 Stomach
118 Cells - EBV-transformed lymphocytes 172 Testis
284 Cells - Cultured fibroblasts 323 Thyroid
6 Cervix - Ectocervix 83 Uterus
5 Cervix - Endocervix 96 Vagina
149 Colon - Sigmoid 393 Whole Blood
196 Colon - Transverse
GTEx Body Map illustration not found
Credit: jwestdesign
Data Information
Data last updated: 2017-10-25
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

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