Description

This track shows genetic variants likely affecting proximal gene expression in 49 human tissues from the Genotype-Tissue Expression (GTEx) V8 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, with a causal posterior probability of >0.1. Each eQTL annotation includes the tissue and causal posterior probability (CPP, described in Hormozdiari et al.)

Display Conventions

The track shows gene/variant pairs for 49 GTEx tissues, following the display conventions for interact tracks where an arc is drawn between the variant and gene. Items in the track are colored according to their tissue, with the color matching those in the GTEx Gene V8 Track. Hovering over the center-point on that arc will display the dbSNP rsID, target gene, tissue, and CPP. Clicking an item will show the details of that interaction as well as link to view more details on the GTEx website.

Track configuration supports filtering by tissue, gene, or CPP.

Methods

Laboratory and RNA-seq analysis methods for GTEx V8 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 49 tissues (those with sample size >=70) using the FastQTL mapper at 5% FDR threshold, as part of the GTEx project v8 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 as part of GTEx downstream analysis. The UCSC track was created using the CAVIAR high-confidence set, which represents the high causal variants that have a (CPP) of > 0.1).

Raw data for these analyses are available from the GTEx Portal.

Data Access

The raw data for this track can be accessed in multiple ways. It can be explored interactively using the Table Browser or Data Integrator. You can also access the data entries in JSON format through our JSON API.

The data in this track are organized in bigInteract file format. The underlying file gtexEqtlsCaviarHighConf.interact.bb can be obtained from our downloads server. Individual regions or the whole set of genome-wide annotations can be obtained using our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system from the utilities directory linked below. For example, to extract only annotations in a given region, you could use the following command:

bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/gtex/eQtl/gtexEqtlsCaviarHighConf.interact.bb -chrom=chr16 -start=34990190 -end=36727467 stdout

Credits

References

GTEx Consortium. The GTEx Consortium atlas of genetic regulatory effects across human tissues. Science. 2020 Sep 11;369(6509):1318-1330. PMID: 32913098; PMC: PMC7737656

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