Genevar protocols

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Genevar specifications

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Unique identifier OMICS_04603
Name Genevar
Alternative name GENe Expression VARiation
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for GENe Expression VARiation

Genevar in pipelines

 (3)
2017
PMCID: 5523649
PMID: 28791018
DOI: 10.3389/fimmu.2017.00860

[…] ≥86% in the probe selection process. additionally, putative transcription factor-binding sites or other regulatory elements containing cis-eqtl polymorphisms (as determined by the web-based software genevar from the wellcome trust sanger institute at p < 0.05 in hapmap ceu samples) adjacent (both upstream and downstream) to those genes were selected (). refinement of targeted regions […]

2016
PMCID: 4804485
PMID: 27005825
DOI: 10.1186/s12881-016-0285-3

[…] mach, http://www.sph.umich.edu/csg/abecasis/mach/index.html, metal, http://www.sph.umich.edu/csg/abecasis/metal/index.html, moose, http://jama.ama-assn.org/cgi/content/full/283/15/2008, genevar, http://www.sanger.ac.uk/science/tools/genevar-gene-expression-variation-archive, hapmap, http://hapmap.ncbi.nlm.nih.gov/, bwa, http://bio-bwa.sourceforge.net/, annovar, […]

2014
PMCID: 4197830
PMID: 24980144
DOI: 10.1186/gb-2014-15-6-r88

[…] in additional file ), taking into account the population to which the highd site was assigned. occurrence of highd and matched sites among expression quantitative trait loci was estimated using the genevar database []., weir and cockerham’s fst[] was calculated using vcftools []. fst values were used to evaluate correlation with δdaf values for the same variants in chosen regions., using cosi […]


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Genevar in publications

 (125)
PMCID: 5906444
PMID: 29670225
DOI: 10.1038/s41598-018-24592-9

[…] data sets, v.3, release 2); (2) the threshold for the minor allele frequency (maf) of the variant was greater than 0.05; and (3) the variant was functional or potentially functional (promoter and genevar). three satisfactory variants (rs1881457, rs2069744 and rs20541) in il13 were selected for this association study (fig. ). rs1881457 is located in the promoter region of il13 […]

PMCID: 5856832
PMID: 29549362
DOI: 10.1038/s41598-018-22552-x

[…] the ld block only contained bnc2 (fig. ). these genome data strongly suggest that bnc2 is the ais susceptibility gene in the locus. rs10738445 in the locus is in high ld (r2 = 0.9) with rs3904778. genevar (gene expression variation) data revealed that the risk allele of the functional snp in this locus, rs10738445, increased bnc2 expression (p = 0.048). our previous in vitro analyses revealed […]

PMCID: 5859892
PMID: 29588580
DOI: 10.2147/COPD.S151153

[…] (data not shown). we further evaluated the effect of this snp on adrb2 expression in lcl from 726 hapmap3 individuals in gene expression variation (http://www.sanger.ac.uk/resources/software/genevar/). the aa genotype of rs12654778 presented a significantly reduced expression of adrb2, compared with the other genotypes ag or gg in most populations (chb, gujarati indians in houston, tx, […]

PMCID: 5611699
PMID: 28979204
DOI: 10.3389/fnagi.2017.00303

[…] patients with lower score of ss-16 had a 4.76-fold risk of suffering from rbd in patients (95% ci: 1.39–16.67; p = 0.013). furthermore, we analyzed snp associated gene expression by eqtl analysis in genevar database and found that gg genotype of rs894278 was associated with higher levels of α-synuclein in nerve tissue (p = 1.5e-8) while tt genotype of rs11931074 was associated with higher levels […]

PMCID: 5395694
PMID: 28469621
DOI: 10.3389/fimmu.2017.00422

[…] (, ). we followed the streis principles in immunogenomic data analysis ()., to further investigate the possibly functional effects of the significant snps, we used gene expression variation (genevar) () database to study the eqtl., a total of 805 sarcoidosis patients and 870 controls were included in this study. the discovery sample set consisted of finnish sarcoidosis patients […]


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Genevar institution(s)
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

Genevar review

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Kathrin Bernt's avatar image No country

Kathrin Bernt

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