Description
This track contains genetic variants affecting gene expression in genomically
distant genes (trans-eQTLs), identified by GTEx Consortium analysis of 7,051 samples
(44 tissues, 449 donors).
These include interchromosomal effects, and those where the gene transcription start site is
more than 1 Mbp distant from the variant on the same chromosome.
The data presented here are based on analysis of samples from the GTEx midpoint milestone
data release (V6, October 2015), reported in Nature, October 2017 (reference below).
For additional information about the GTEx Consortium and the V6 data analysis, see the
GTEx Analysis hub description.
Display Conventions
This display uses the
interact track format.
Trans-eQTLs on the same chromosome are displayed as arcs connecting the SNP and gene if both
are in the display window, a horizontal line if the interaction crosses the window but neither are
in window, or a vertical and horizontal connector if one is in window.
The height of the arc/horizontal is based on the distance between SNP and gene.
Interchromosomal interactions are indicated by a horizontal line covering the SNP or gene,
a vertical extension, and if space permits, the other chromosome name in blue.
Interactions are colored using GTEx tissue colors. The arc/line style indicates 'direction'
of interaction; solid if SNP precedes gene, otherwise dashed.
Mouse hover or clickthrough to interact details is activated from the interaction ends or peak.
Hover over the peak will show the SNP/gene/tissue. Hover over an end will show the
SNP id or gene name.
Methods
Association mapping was performed using
Matrix eQTL, testing common autosomal variants (MAF > .05) with protein coding
and lincRNA gene transcripts on different chromosomes, or at a distance greater than
1 MB from the transcription start site.
Analyses were performed in each tissue separately.
For all association tests, stringent quality controls were applied to account for
potential false positives due to RNA-seq read mapping errors, repeat elements, and
population stratification.
Full analysis methods are available in
Supplementary Information to the Nature 2017 publication
cited in the References section below.
Intrachromosomal annotations for this track were obtained from the 1MB analysis
included in the GTEx portal
download (gtex_analysis_v6p/single_tissue_eqtl_data/GTEx_Analysis_v6p_intrachromosomal_eQTLs.xlsx).
Interchromosomal data was obtained from the genome-wide analysis posted in
Supplementary file 2 from the Nature publication.
Credits
Thanks to the GTEx LDACC and GTEx Consortium analysts at the Princeton
BEEHIVE (Engelhart Research Group),
and the
Battle Lab at Johns Hopkins
for this data.
For full credits see the bioRxiv manuscript:
Brian Jo, et al.
Distant regulatory effects of genetic variation in multiple human tissues,
https://doi.org/10.1101/074419.
Contacts
For questions about the methods or interpretation of data presented here, contact
Alexis Battle
or
Barbara Engelhart.
For questions about this track hub, the browser display or tools access to this data, contact the
UCSC Genome Browser mailing list.
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
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