SNPnexus protocols

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SNPnexus specifications

Information


Unique identifier OMICS_00188
Name SNPnexus
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Maintainer


  • person_outline Claude Chelala <>

Additional information


http://snp-nexus.org/guide.html

Publications for SNPnexus

SNPnexus in pipelines

 (7)
2016
PMCID: 5037665
PMID: 27589735
DOI: 10.3390/ijms17091385

[…] tested with hapmap; (3) functional consequences; and (4) few or no studies on the role of the snp in mitral valve calcification. the national center for biotechnology information dbsnp, snpinfo, and snpnexus databases were utilized for the snp selection [,]. in total, we selected 50 snps within 24 genes ()., the procedures of dna extraction and genotyping were the same as previously described […]

2015
PMCID: 4350913
PMID: 25745553
DOI: 10.1186/s13229-015-0009-0

[…] the functional roles of genetic variants; the genetic association database [] gives information about genetic studies which previously identified association between the snps we analysed and asc; snpnexus [] is an online database which was used to define regulatory elements and conserved regions; the university of california santa cruz (ucsc) genome browser [] permits to validate functions […]

2015
PMCID: 4503355
PMID: 26176695
DOI: 10.1371/journal.pone.0131202

[…] was performed using plink v1.07 (http://pngu.mgh.harvard.edu/~purcell/plink/) []. functional annotation was performed using haploreg v2 (http://www.broadinstitute.org/mammals/haploreg/) [] and snpnexus (http://www.snp-nexus.org/) []., to assess the accuracy of dna pooling in predicting differences in allele frequency, we individually genotyped 12 random snps in all the participants. […]

2015
PMCID: 4661592
PMID: 26610392
DOI: 10.1038/srep17367

[…] used to retrieve snps in ld with the tagged snp at a relatively low ld threshold of r2 > 0.2., the resulting 96 snps were then subjected to in silico functional predictions and annotations using snpnexus, snpinfo, polyphen 2, the ucsc genome browser, and regulomedb. the results from these searches were organized into a mysql relational database. the complete regulomedb dataset was also […]

2014
PMCID: 4175274
PMID: 25264479
DOI: 10.1186/2040-2392-5-48

[…] through the genetic association database []. manual verification of the loci for functional roles was conducted using the university of california santa cruz (ucsc) genome browser []. finally, snpnexus provided information about structural variants and conservation sites in the loci analyzed []., snp rs2268493 was associated with as (table ). this genetic variation localizes in intron 3 […]


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SNPnexus in publications

 (54)
PMCID: 5900548
PMID: 29686695
DOI: 10.3389/fgene.2018.00112

[…] c to t transition at position 3,222 belongs to a 20 years old female that has a normal bmi (20.7 kg/m2) as well as a normal lipid profile. functional prediction analysis employing sift, targetscan, snpnexus tools revealed that the two novel snp's are simple sequence variants., - chromosomal position is based on chromosome 11 published reference sequence (nc_000011.10) in the ncbi genebank […]

PMCID: 5798519
PMID: 29430509
DOI: 10.3233/BLC-170144

[…] present in the exac database at >0.1% (except those with pathogenic clinvar annotation). the variant classification, gene/protein consequences and effect in protein function were identified using snpnexus (http://www.snp-nexus.org) [], ensembl (http://useast.ensembl.org/index.html) [], uscs genome browser (https://genome.ucsc.edu) [] and refseqncbi reference sequence database […]

PMCID: 5727191
PMID: 29234017
DOI: 10.1038/s41467-017-02182-z

[…] and millions of common variants. for each gene, cis-acting snps were located within ±500 kb of the gene and trans-acting outside this region. functional annotation of snps was performed using snpnexus tool based on ncbi refseq database. we first limited our analysis to snps available on the illumina chip used for genotyping with a minor allele frequency (maf) > 0.05. p values […]

PMCID: 5829525
PMID: 28672053
DOI: 10.1111/bjd.15787

[…] significant variants. the linkage disequilibrium among the top snps was also calculated by plink., in this study we also used multiple related gwas software for different purposes such as snpnexus (barts cancer institute, queen mary university of london, london, u.k.) for snp functional annotation, haploview (broad institute of mit and harvard, cambridge, ma, u.s.a.) for generating […]

PMCID: 5668380
PMID: 29097701
DOI: 10.1038/s41467-017-01429-z

[…] http://www.ncbi.nlm.nih.gov/snp/; exome variant server, http://evs.gs.washington.edu/evs/; 1000 genomes, http://www.1000genomes.org/; exac, http://exac.broadinstitute.org/), were annotated with snpnexus (http://www.snp-nexus.org/). the c.347g>t p.(arg116leu) missense mutation in kcnq1 (mim: 607542), shared between the two genomes, was left in the linkage region after known variants, […]


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SNPnexus institution(s)
Bioinformatics Unit, Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK; Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK; Centre for Computational Biology, Life Sciences Initiative, Queen Mary University of London, London, UK
SNPnexus funding source(s)
Supported by Barts and The London Charity Strategic Research Large Project Grant [MGU0344] and by Pancreatic Cancer Research Fund Tissue Bank Grant.

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