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A functional SNP upstream of the ADRB2 gene is associated with COPD
[…] in lymphoblastoid cells, and it is interesting to know whether this variant is correlated with the expression of ADRB2 in lymphoblastoid cells. To address this issue, we utilized eQTL browser (http://eqtl.uchicago.edu/cgi-bin/gbrowse/eqtl/), which collected published eQTL data of lymphoblastoid cell lines (LCL) from four HapMap populations to search for potential association. Interestingly, a sign […]
Pervasive coexpression of spatially proximal genes is buffered at the protein level
[…] RNA‐sequencing data for human lymphoblastoid cell lines (LCLs) have been reported (Pickrell et al, ). Counts per mapped reads were downloaded from http://eqtl.uchicago.edu and converted to log2 “reads per kilobase transcript per million mapped reads” (RPKMs). Genes expressed in < 30 LCLs were removed. In order to make mRNA measurements comparable to pr […]
A genome wide association study identifies six novel risk loci for primary biliary cholangitis
[…] ion 2.2.2 and version 3 of 1000 Genomes Project data as the reference set.We used seeQTL (http://www.bios.unc.edu/research/genomic_software/seeQTL/) and the University of Chicago eQTL browser (http://eqtl.uchicago.edu/cgi-bin/gbrowse/eqtl/) to identify eQTLs amongst significant variants. eQTLs that are in high linkage disequilibrium (r2>0.8) with the most strongly associated SNP at the locus were […]
Prediction of Poly(A) Sites by Poly(A) Read Mapping
[…] ed the raw sequencing data from the Short Read Archive (accession SRP001540) and the high-confidence poly(A) site predictions by Pickrell et al. from the Supplementary website for the article (http://eqtl.uchicago.edu/RNA_Seq_data/results/). […]
Meta Analysis of Genome Wide Association Studies for Abdominal Aortic Aneurysm Identifies Four New Disease Specific Risk Loci
[…] additional eQTL data were integrated from online sources including ScanDB (SNP and CNV Annotation Database), the Broad Institute The Genotype-Tissue Expression browser, and the Pritchard Laboratory (eqtl.uchicago.edu). (2) To search for vascular tissue-specific effects, eQTL data were also obtained from the ASAP (Advanced Study of Aortic Pathology) data set and RNA-seq (whole-genome RNA-sequence […]
Identification of genetic modifiers of age at onset for familial Parkinson’s disease
[…] notations of putative regulatory elements in the regions of our associated signals. We searched eQTL and mQTL databases Genevar (https://www.sanger.ac.uk/resources/software/genevar/) (), eqtl (http://eqtl.uchicago.edu/cgi-bin/gbrowse/eqtl/), SCAN (http://www.scandb.org/newinterface/about.html) () and BRAINEAC (http://www.braineac.org) () for eQTL or mQTL association results for the associated vari […]
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