GTEx Combined eQTL Track Settings
 
Combined Expression QTLs from 44 Tissues from GTEx (midpoint release, V6)   (All Regulation tracks)

Display mode:   

Show only items with score at or above:   (range: 0 to 1000)

Filter by gene:
Effect size minimum: +- FPKM (range 0-15362.9)
   Probability minimum: (range 0-1.0)      Display tissue color (single tissue eQTL)

Tissues:  
        Tissue Samples Organ System
 Adipose - Subcutaneous  350  Adipose Tissue  Other
 Adipose - Visceral (Omentum)  227  Adipose Tissue  Other
 Adrenal Gland  145  Adrenal Gland  Endocrine
 Artery - Aorta  224  Blood Vessel  Cardiovascular
 Artery - Coronary  133  Blood Vessel  Cardiovascular
 Artery - Tibial  332  Blood Vessel  Cardiovascular
 Bladder  11  Bladder  Other
 Brain - Amygdala  72  Brain  Brain
 Brain - Anterior cingulate cortex (BA24)  84  Brain  Brain
 Brain - Caudate (basal ganglia)  117  Brain  Brain
 Brain - Cerebellar Hemisphere  105  Brain  Brain
 Brain - Cerebellum  125  Brain  Brain
 Brain - Cortex  114  Brain  Brain
 Brain - Frontal Cortex (BA9)  108  Brain  Brain
 Brain - Hippocampus  94  Brain  Brain
 Brain - Hypothalamus  96  Brain  Brain
 Brain - Nucleus accumbens (basal ganglia)  113  Brain  Brain
 Brain - Putamen (basal ganglia)  97  Brain  Brain
 Brain - Spinal cord (cervical c-1)  71  Brain  Brain
 Brain - Substantia nigra  63  Brain  Brain
 Breast - Mammary Tissue  214  Breast  Reproductive
 Cells - EBV-transformed lymphocytes  118  Blood  Other
 Cells - Transformed fibroblasts  284  Skin  Other
 Cervix - Ectocervix  6  Cervix Uteri  Reproductive
 Cervix - Endocervix  5  Cervix Uteri  Reproductive
 Colon - Sigmoid  149  Colon  Digestive
 Colon - Transverse  196  Colon  Digestive
 Esophagus - Gastroesophageal Junction  153  Esophagus  Digestive
 Esophagus - Mucosa  286  Esophagus  Digestive
 Esophagus - Muscularis  247  Esophagus  Digestive
 Fallopian Tube  6  Fallopian Tube  Reproductive
 Heart - Atrial Appendage  194  Heart  Cardiovascular
 Heart - Left Ventricle  218  Heart  Cardiovascular
 Kidney - Cortex  32  Kidney  Other
 Liver  119  Liver  Digestive
 Lung  320  Lung  Other
 Minor Salivary Gland  57  Salivary Gland  Other
 Muscle - Skeletal  430  Muscle  Other
 Nerve - Tibial  304  Nerve  Other
 Ovary  97  Ovary  Reproductive
 Pancreas  171  Pancreas  Digestive
 Pituitary  103  Pituitary  Endocrine
 Prostate  106  Prostate  Reproductive
 Skin - Not Sun Exposed (Suprapubic)  250  Skin  Other
 Skin - Sun Exposed (Lower leg)  357  Skin  Other
 Small Intestine - Terminal Ileum  88  Small Intestine  Digestive
 Spleen  104  Spleen  Other
 Stomach  193  Stomach  Digestive
 Testis  172  Testis  Reproductive
 Thyroid  323  Thyroid  Endocrine
 Uterus  83  Uterus  Reproductive
 Vagina  96  Vagina  Reproductive
 Whole Blood  393  Blood  Other
View table schema
Data version: GTEx Analysis V6p (https://www.gtexportal.org/home/datasets)
Data last updated: 2017-10-25

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