SNPnexus

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Barts Cancer Institute

News

September 2020: Video tutorial released

Our new video tutorial is out today. Check it and share your thoughts.

June 2020: Publication of the SNPnexus paper

We are happy to announce the publication of our latest SNPnexus paper in Nucleic Acids Research
Jorge Oscanoa, Lavanya Sivapalan, Emanuela Gadaleta, Abu Z Dayem Ullah, Nicholas R Lemoine, Claude Chelala, SNPnexus: a web server for functional annotation of human genome sequence variation (2020 update), Nucleic Acids Research, 2020, 48(W1):W185-W192.

December 2019: Fourth release of the SNPnexus tool

SNPnexus has gone through a complete redesign both in its internal architecture as well as its user interface. We've updated all our data sources for the GRCh38/hg38 and GRCh37/hg19 human assemblies and our aim is to keep updating those genome assemblies. The NCBI36/hg18 assembly has been deprecated but it's still available through our legacy page.

We have included two new annotation categories for related biological pathways and potential tumour drivers. Moreover, a novel system of variant filtering based on different features like predicted functionality, global population frequency, predicted deleterious effect, etc. These new features allow users to focus on a set of variants from the original queryset and facilitate the biological interpretation and identification of somatic mutations.

The table below describes all the data sources for this SNPnexus release:

Category GRCh37/hg19 GRCh38/hg38
Source Update time Source Update time
Known SNP information Ensembl Variation 95;dbSNP 151Jan 2019 Ensembl Variation 95;dbSNP 151Jan 2019
Gene Annotation RefSeq UCSC hg19Nov 2018 UCSC hg38Mar 2019
Ensembl Ensembl 95Jan 2019 Ensembl 95Jan 2019
Acembly UCSC hg19May 2011
Vega Vega 43;UCSC hg19Oct 2010
UCSC UCSC hg19Jun 2013 UCSC hg38Nov 2018
CCDS UCSC hg19Nov 2018 UCSC hg38Mar 2019
H-inv UCSC hg19Apr 2010
Protein Effect SIFT SIFT (Ensembl Variation 95) Jan 2019 SIFT (Ensembl Variation 95) Jan 2019
PolyPhen PolyPhen-2 (Ensembl Variation 95) Jan 2019 PolyPhen-2 (Ensembl Variation 95) Jan 2019
Population Data HapMap HapMap (Ensembl Variation 95) Dec 2018 HapMap (Ensembl Variation 95) Nov 2018
1000 Genomes 1000 Genomes (Ensembl Variation 95) Dec 2018 1000 Genomes (Ensembl Variation 95) Nov 2018
gnomAD Exome Data Ensembl Variation Genotype (gnomad v2.1) Jan 2019 Ensembl Variation Genotype (gnomad v2.1) Mar 2019
Regulatory Elements TFBS UCSC hg19May 2011
miRBASE v.20Mar 2014 v.22.1Mar 2018
Vista UCSC hg19Dec 2010
CpG Islands UCSC hg19Apr 2009 UCSC hg38Mar 2019
TargetScan UCSC hg19Dec 2010
TarBase miRNA Ensembl Variation 95Dec 2018 Ensembl Variation 95Dec 2018
Other RNAs UCSC hg19Oct 2010 UCSC hg38Nov 2018
ENCODE regions Ensembl Regulatory Building 95Dec 2018 Ensembl Regulatory Building 95Dec 2018
RoadMap Epigenomics Ensembl Regulatory Building 95Dec 2018 Ensembl Regulatory Building 95Dec 2018
Ensembl Regulatory Build Ensembl Regulatory Building 95Dec 2018 Ensembl Regulatory Building 95Dec 2018
Phenotype/Disease Association GAD UCSC hg19Feb 2014
COSMIC Version 89May 2019 Version 89May 2019
GWAS UCSC hg19Sep 2019 UCSC hg38Sep 2019
ClinVar UCSC hg19Aug 2019 UCSC hg38Aug 2019
Conserved Elements PhastConsElements UCSC hg19Apr 2014 UCSC hg38Sep 2015
GERP++ GERP updateMay 2011
Structural Variations UCSC hg19Sep 2016 UCSC hg38Sep 2016
Non-coding Variation Scoring CADD v1.4
fitCons v1.01
EIGEN v1.1
FATHMM v2.3
GWAVA v1.0
DeepSEA v0.94
FunSeq2 v2.1.6
ReMM v0.3.1
Reactome Pathways Aug 2019 Aug 2019
Cancer Genome Interpreter v1.0.3 v1.0.3 (Using liftOver)

May 2018: Publication of the SNPnexus paper

We are happy to announce the publication of the SNPnexus paper in Nucleic Acids Research
Abu Z Dayem Ullah, Jorge Oscanoa, Jun Wang, Ai Nagano, Nicholas Lemoine, Claude Chelala, SNPnexus: assessing the functional relevance of genetic variation to facilitate the promise of precision medicine, Nucleic Acids Research, 2018, 46(W1):W109-W113.

December 2017: Third release of the SNPnexus tool

We are happy to announce the third release of the SNPnexus. We have substantially improved SNPnexus by including additional categories for the assessment of functional impact, in particular on the non-coding regions of the genome.

In addition to the NCBI36/hg18 and GRCh37/hg19 human genome assembly release, SNPnexus now also supports the latest GRCh38/hg38 release. The data sources for underlying SNPnexus database are described below:

Category hg18 hg19 hg38
Source Update time Source Update time Source Update time
Known SNP information Ensembl Variation 54;dbSNP 129Aug 2009 Ensembl Variation 74;dbSNP 138Dec 2013 Ensembl Variation 90;dbSNP 150Aug 2017
Gene Annotation RefSeq UCSC hg18Apr 2014 UCSC hg19Mar 2014 UCSC hg38Dec 2017
Ensembl Ensembl 54Aug 2009 Ensembl 74Dec 2013 Ensembl 90Aug 2017
Acembly UCSC hg18Sep 2007 UCSC hg19May 2011
Vega Vega 34;UCSC hg18Dec 2007 Vega 43;UCSC hg19Oct 2010
UCSC UCSC hg18May 2009 UCSC hg19Jun 2013 UCSC hg38Jul 2016
CCDS UCSC hg18Apr 2014 UCSC hg19Mar 2014 UCSC hg38Dec 2017
H-inv UCSC hg18 UCSC hg19Apr 2010
Protein Effect SIFT SIFT Human DB (release 63) Aug 2011 Ensembl Variation 90 Aug 2017
PolyPhen PolyPhen-2 (Ensembl Variation 63) Jun 2011 Ensembl Variation 90 Aug 2017
Population Data HapMap UCSC hg18 July 2007 UCSC hg19 Feb 2011
1000 Genomes IGSR GRCh38 April 2017 IGSR GRCh38 April 2017
ExAC ExAC r1 Feb 2017
Regulatory Elements TFBS UCSC hg18Jul 2007 UCSC hg19May 2011
FirstEF UCSC hg18May 2006
miRBASE v.20Mar 2014 v.20Mar 2014 v.21Jun 2014
Vista UCSC hg18Oct 2007 UCSC hg19Dec 2010
CpG Islands UCSC hg18Apr 2006 UCSC hg19Apr 2009 UCSC hg38Mar 2014
miRNA target sites TargetScan: UCSC hg18Nov 2007 TargetScan: UCSC hg19Dec 2010 TarBase: Ensembl Regulation 90Aug 2017
Other RNAs UCSC hg18Sep 2009 UCSC hg19Oct 2010 UCSC hg38Dec 2015
ENCODE regions Ensembl Regulation 74Dec 2013 Ensembl Regulation 90Aug 2017
Roadmap Epigenomics Ensembl Regulation 74Dec 2013 Ensembl Regulation 90Aug 2017
Ensembl Regulatory Build Ensembl Regulation 74Dec 2013 Ensembl Regulation 90Aug 2017
Phenotype/Disease Association GAD UCSC hg18Jan 2008 UCSC hg19Feb 2014
COSMIC version 68Feb 2014 version 68Feb 2014 version 82Aug 2017
GWAS UCSC hg18Apr 2014 UCSC hg19Mar 2014 UCSC hg38Nov 2017
ClinVar UCSC hg38Dec 2017
Conserved Elements PhastConsElements UCSC hg18Feb 2009 UCSC hg19Dec 2009 UCSC hg38Sep 2015
GERP++ GERP update2010 GERP update2010
Structural Variations DGV Build 36Jul 2013 DGV GRCh 37Jul 2013 DGV GRCh 38Sep 2016
Neo-epitope prediction MuPeXI v1.1Apr 2017
MHCflurry v0.9.2Aug 2017
NetTepi v1.0Dec 2016
Non-coding variation scoring CADD v1.3Jul 2015
fitCons v1.01Aug 2014
EIGEN v1.0May 2016
FATHMM v2.3Sep 2014
GWAVA v1.0Apr 2014
DeepSEA v0.94Feb 2016
FunSeq2 v2.1.6May 2015
ReMM v0.3.0Dec 2016

May 2014: Database update

A complete update operation has been performed to the whole underlying database of SNPnexus, as described below:

Category hg18 hg19
Source Update time Source Update time
Known SNP information Ensembl Variation 54;dbSNP 129Aug 2009 Ensembl Variation 74;dbSNP 138Dec 2013
Gene Annotation RefSeq UCSC hg18Apr 2014 UCSC hg19Mar 2014
Ensembl Ensembl 54Aug 2009 Ensembl 74Dec 2013
Acembly UCSC hg18Sep 2007 UCSC hg19May 2011
Vega Vega 34;UCSC hg18Dec 2007 Vega 43;UCSC hg19Oct 2010
UCSC UCSC hg18May 2009 UCSC hg19Jun 2013
CCDS UCSC hg18Apr 2014 UCSC hg19Mar 2014
H-inv UCSC hg18 UCSC hg19Apr 2010
Protein Effect SIFT SIFT Human DB (release 63) Aug 2011
PolyPhen PolyPhen-2 (Ensembl Variation 63) Jun 2011
Regulatory Elements TFBS UCSC hg18Jul 2007 UCSC hg19May 2011
FirstEF UCSC hg18May 2006
miRBASE v.20Mar 2014 v.20Mar 2014
Vista UCSC hg18Oct 2007 UCSC hg19Dec 2010
CpG Islands UCSC hg18Apr 2006 UCSC hg19Apr 2009
TargetScanS UCSC hg18Nov 2007 UCSC hg19Dec 2010
Other RNAs UCSC hg18Sep 2009 UCSC hg19Oct 2010
Phenotype/Disease Association GAD UCSC hg18Jan 2008 UCSC hg19Feb 2014
COSMIC version 68Feb 2014 version 68Feb 2014
GWAS UCSC hg18Apr 2014 UCSC hg19Mar 2014
Conserved Elements PhastConsElements UCSC hg18Feb 2009 UCSC hg19Dec 2009
GERP++ GERP update2010 GERP update2010
Structural Variations DGV Build 36Jul 2013 DGV GRCh 37Jul 2013

January 2014: Database update

Data source for underlying COSMIC annotation category has been updated from COSMIC version 56 to version 67.

October 2013: Database update

Data source for underlying GWAS annotation category has been updated according to UCSC genome annotation database.

March 2013: Database update

Data source for underlying known SNP inforamtion has been changed from Ensembl variation 63 (dbSNP 132) to Ensembl variation 70 (dbSNP 137).

January 2013: Addition of new annotation categories

Two new annotation categories has been added to the SNPnexus tool, as described below:

Category hg18 hg19
Source Update time Source Update time
Protein Effect PolyPhen PolyPhen-2 (Ensembl Variation 63) Jun 2011
Conserved Elements GERP++ GERP update2010 GERP update2010

June 2012: Database update

Data source for underlying miRBase data has been changed from miRBase v.17 to v.18.

April 2012: Publication of the SNPnexus paper

We are happy to announce the publication of the SNPnexus paper in Nucleic Acids Research providing more details about the enhancement in terms of annotation categories and ease of use, updated design and data sources.

Abu Z Dayem Ullah, Nicholas R Lemoine and Claude Chelala, SNPnexus: a web server for functional annotation of novel and publicly known genetic variants (2012 update), Nucleic Acids Research, 2012, 40(W1):W65-W70.

November 2011: Second release of the SNPnexus tool

We are happy to announce the second release of the SNPnexus. We have substantially improved SNPnexus by incorporating a broader range of variations such as insertions/deletions, block substitutions, IUPAC codes submission and region-based analysis, expanding the query size limit, and most importantly including additional categories for the assessment of functional impact.

In addition to the NCBI36/hg18 human genome assembly, SNPnexus now also supports the latest GRCh37/hg19 release. The data sources for underlying SNPnexus database are described below:

Category hg18 hg19
Source Update time Source Update time
Known SNP information Ensembl Variation 54;dbSNP 129Aug 2009 Ensembl Variation 63;dbSNP 132Jun 2011
Gene Annotation RefSeq UCSC hg18Dec 2011 UCSC hg19Dec 2011
Ensembl Ensembl 54Aug 2009 Ensembl 63Jun 2011
Acembly UCSC hg18Sep 2007 UCSC hg19May 2011
Vega Vega 34;UCSC hg18Dec 2007 Vega 43;UCSC hg19Oct 2010
UCSC UCSC hg18May 2009 UCSC hg19Dec 2009
CCDS UCSC hg18Apr 2014 UCSC hg19Dec 2011
H-inv UCSC hg19Apr 2010
Protein Effect SIFT SIFT Human DB (release 63) Aug 2011
Regulatory Elements TFBS UCSC hg18Jul 2007 UCSC hg19May 2011
FirstEF UCSC hg18May 2006
miRBASE v.17Apr 2011 v.17Apr 2011
Vista UCSC hg18Oct 2007 UCSC hg19Dec 2010
CpG Islands UCSC hg18Apr 2006 UCSC hg19Apr 2009
TargetScanS UCSC hg18Nov 2007 UCSC hg19Dec 2010
Other RNAs UCSC hg18Sep 2009 UCSC hg19Oct 2010
Phenotype/Disease Association GAD UCSC hg18Jan 2008 GAD updateOct 2011
COSMIC version 56Nov 2011 version 56Nov 2011
GWAS UCSC hg18Nov 2011 UCSC hg19Nov 2011
Conserved Elements PhastConsElements UCSC hg18Feb 2009 UCSC hg19Jun 2009
HapMap UCSC hg18Jul 2007 UCSC hg19Feb 2011
Structural Variations UCSC hg18Sep 2011 UCSC hg19Sep 2011

December 2008: Publication of the SNPnexus paper

We are happy to announce the publication of the SNPnexus paper in Bioinformatics providing more details about the tool construction, data sources and examples of use.

Claude Chelala, Arshad Khan and Nicholas R Lemoine, SNPnexus: A web database for functional annotation of newly discovered and public domain Single Nucleotide Polymorphisms Bioinformatics, 2009, 25(5):655-61.

November 2008: Release of the SNPnexus tool

We are happy to announce the release of the SNPnexus - a computational tool allowing scientists to functionally annotate newly discovered and public domain single nucleotide polymorphisms in order to help in prioritizing targets in further disease studies and large-scale genotyping projects.

SNPnexus database provides functional annotation for both novel and public SNPs. SNPnexus supports the NCBI36/hg18 human genome assembly.

The underlying SNPnexus database is kept synchronised with the UCSC human genome annotation database. However, data for some annotation categories comes from different sources as described below:

Category Source Update time
Known SNP information Ensembl Variation 54;dbSNP 128 Dec 2007
Gene Annotation RefSeq UCSC hg18 Nov 2008
Ensembl Ensembl 48 Dec 2007
Acembly UCSC hg18 Sep 2007
Vega Vega 34 Dec 2007
UCSC UCSC hg18 Apr 2008
Regulatory Elements TFBS UCSC hg18 Nov 2008
FirstEF UCSC hg18 Nov 2008
miRBase miRBase v.11 Sep 2008
TargetScanS UCSC hg18 Apr 2008
Other RNAs UCSC hg18 Apr 2008
Phenotype/Disease Association GAD UCSC hg18 Apr 2008
HapMap UCSC hg18 Jul 2007
Structural Variations UCSC hg18 Apr 2008