Schema for GTEx cis-eQTLs - GTEx fine-mapped cis-eQTLs
  Database: hg38    Primary Table: gtexEqtlCaviar Data last updated: 2022-05-05
Big Bed File: /gbdb/hg38/gtex/eQtl/gtexCaviar.bb
Item Count: 1,257,125
Format description: bed12+8 describing interaction between an eQTL and a target gene
fieldexampledescription
chromchr1Chromosome (or contig, scaffold, etc.). For interchromosomal, use 2 records
chromStart165229365Start position of eQTL
chromEnd166166969End position of gene
namers79870753/FAM78B/TestisName of item for display in pattern eQTL name/Gene Symbol/Tissue
score1000Score. Always 1000.
strand++ or - for strand
thickStart165229365eQTL start
thickEnd165229366eQTL end
reserved10921638Item color, based on tissue colors GTEx Gene track
blockCount2Number of blocks
blockSizes1,109544Comma separated list of block sizes
chromStarts0,828060Start positions of blocks relative to chromStart
eqtlPoschr1:165229366-165229366eQTL position
eqtlNamers79870753eQTL name (most often a dbSNP identifier)
genePoschr1:166057426-166166969Gene position
geneNameFAM78BGene symbol of target gene
geneIdENSG00000188859.6ENSG ID of target gene
geneStrand-Strand of target gene
tissueTestisTissue
cpp0.13556Causal Posterior Probability (CPP) that quantifies the probability that a variant is causal

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStartseqtlPoseqtlNamegenePosgeneNamegeneIdgeneStrandtissuecpp
chr1165229365166166969rs79870753/FAM78B/Testis1000+1652293651652293661092163821,1095440,828060chr1:165229366-165229366rs79870753chr1:166057426-166166969FAM78BENSG00000188859.6-Testis0.13556
chr1165293057166166969rs143580740/FAM78B/Brain_Hypothalamus1000+1652930571652930581565849621,1095440,764368chr1:165293058-165293058rs143580740chr1:166057426-166166969FAM78BENSG00000188859.6-Brain_Hypothalamus0.461513
chr1165298240166166969rs138806738/FAM78B/Testis1000+1652982401652982411092163821,1095440,759185chr1:165298241-165298241rs138806738chr1:166057426-166166969FAM78BENSG00000188859.6-Testis0.253557
chr1165400916166249438rs61837974/RXRG/Adipose_Subcutaneous1000-16624943716624943816753999244439,10,848521chr1:166249438-166249438rs61837974chr1:165400917-165445355RXRGENSG00000143171.12-Adipose_Subcutaneous0.589875
chr1165407828166087483rs76408466/RP11-375H19.2/Small_Intestine_Terminal_Ileum1000+1654078281654078291348188621,63010,673354chr1:165407829-165407829rs76408466chr1:166081183-166087483RP11-375H19.2ENSG00000203307.2+Small_Intestine_Terminal_Ileum0.162271
chr1165488910166166969rs190411659/FAM78B/Liver1000+1654889101654889111348188621,1095440,568515chr1:165488911-165488911rs190411659chr1:166057426-166166969FAM78BENSG00000188859.6-Liver0.162762
chr1165488975166166969rs75293841/FAM78B/Liver1000+1654889751654889761348188621,1095440,568450chr1:165488976-165488976rs75293841chr1:166057426-166166969FAM78BENSG00000188859.6-Liver0.162762
chr1165491910166166969rs74118687/FAM78B/Liver1000+1654919101654919111348188621,1095440,565515chr1:165491911-165491911rs74118687chr1:166057426-166166969FAM78BENSG00000188859.6-Liver0.162762
chr1165492337166166969rs74118688/FAM78B/Liver1000+1654923371654923381348188621,1095440,565088chr1:165492338-165492338rs74118688chr1:166057426-166166969FAM78BENSG00000188859.6-Liver0.162762
chr1165497639166166969rs2553640/FAM78B/Brain_Cerebellar_Hemisphere1000+1654976391654976401565849621,1095440,559786chr1:165497640-165497640rs2553640chr1:166057426-166166969FAM78BENSG00000188859.6-Brain_Cerebellar_Hemisphere0.140716

GTEx cis-eQTLs (gtexEqtlHighConf) Track Description
 

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. The data can only be calculated for the autosomes, so no data is shown on chrX.

Display Conventions

Both the CAVIAR and DAP-G tracks show gene/variant pairs for 49 GTEx tissues. Variants are linked to the genes they interact with by a line. Variants are represented by thicker-width, single-base items. Genes are represented as thinner-width items covering the length of the gene. The direction of the chevrons on the line indicate whether the variant is upstream or downstream of the gene with the chevrons always pointing from the variant to the gene. If a variant is internal to the gene, then the variant is shown as a thicker segment than the gene. Items in the track are colored according to their tissue, with the color matching those in the GTEx Gene V8 Track.

Hovering over items in the track display will show the variant ID (often a dbSNP rsID), the target gene, tissue, and posterior probablity (Causal Posterior Probability (CPP) for CAVIAR; SNP Posterior Inclusion Probability (PIP) for DAP-G). Clicking an item will show the details of that interaction with link outs to view more details on the GTEx website.

Track configuration supports filtering by tissue, gene, or posterior probability.

Methods

Details on GTEx v8 analysis, including code, can be found in the GTEx GWAS Analysis Github.

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

CAVIAR

The CAVIAR track at UCSC was created using the CAVIAR high-confidence set, which represents the high causal variants that have a causal posterior probability (CPP) of > 0.1.

DAP-G

The DAP-G track at UCSC was created using the DAP-G 95% credible set, which represents varaints with strong eQTLs signals, which are signal clusters with signal-level posterior inclusion probability (SPIP) > 0.95.

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 bigBed file format. The underlying files 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/gtexCaviar.bb -chrom=chr16 -start=34990190 -end=36727467 stdout

Credits

Thanks to GTEx investigators, analysts, and portal team for providing this data.

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

Lee Y, Luca F, Pique-Regi R, Wen X. Bayesian Multi-SNP Genetic Association Analysis: Control of FDR and Use of Summary Statistics. bioRxiv. 2018 May 8.

Wen X, Lee Y, Luca F, Pique-Regi R. Efficient Integrative Multi-SNP Association Analysis via Deterministic Approximation of Posteriors. Am J Hum Genet. 2016 Jun 2;98(6):1114-1129. PMID: 27236919; PMC: PMC4908152

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