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Treffer: snpXplorer: a web application to explore human SNP-associations and annotate SNP-sets.

Title:
snpXplorer: a web application to explore human SNP-associations and annotate SNP-sets.
Authors:
Tesi N; Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands.; Section Genomics of Neurodegenerative Diseases and Aging, Department of Clinical Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands.; Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands., van der Lee S; Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands.; Section Genomics of Neurodegenerative Diseases and Aging, Department of Clinical Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands., Hulsman M; Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands.; Section Genomics of Neurodegenerative Diseases and Aging, Department of Clinical Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands.; Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands., Holstege H; Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands.; Section Genomics of Neurodegenerative Diseases and Aging, Department of Clinical Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands.; Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands., Reinders MJT; Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands.
Source:
Nucleic acids research [Nucleic Acids Res] 2021 Jul 02; Vol. 49 (W1), pp. W603-W612.
Publication Type:
Journal Article; Research Support, Non-U.S. Gov't
Language:
English
Journal Info:
Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE
Imprint Name(s):
Publication: 1992- : Oxford : Oxford University Press
Original Publication: London, Information Retrieval ltd.
MeSH Terms:
Molecular Sequence Annotation* , Polymorphism, Single Nucleotide* , Software*, Alzheimer Disease/genetics ; Gene Expression ; Genetic Association Studies ; Genomics ; Humans ; Linkage Disequilibrium ; Quantitative Trait Loci
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Entry Date(s):
Date Created: 20210528 Date Completed: 20210719 Latest Revision: 20231107
Update Code:
20250114
PubMed Central ID:
PMC8262737
DOI:
10.1093/nar/gkab410
PMID:
34048563
Database:
MEDLINE

Weitere Informationen

Genetic association studies are frequently used to study the genetic basis of numerous human phenotypes. However, the rapid interrogation of how well a certain genomic region associates across traits as well as the interpretation of genetic associations is often complex and requires the integration of multiple sources of annotation, which involves advanced bioinformatic skills. We developed snpXplorer, an easy-to-use web-server application for exploring Single Nucleotide Polymorphisms (SNP) association statistics and to functionally annotate sets of SNPs. snpXplorer can superimpose association statistics from multiple studies, and displays regional information including SNP associations, structural variations, recombination rates, eQTL, linkage disequilibrium patterns, genes and gene-expressions per tissue. By overlaying multiple GWAS studies, snpXplorer can be used to compare levels of association across different traits, which may help the interpretation of variant consequences. Given a list of SNPs, snpXplorer can also be used to perform variant-to-gene mapping and gene-set enrichment analysis to identify molecular pathways that are overrepresented in the list of input SNPs. snpXplorer is freely available at https://snpxplorer.net. Source code, documentation, example files and tutorial videos are available within the Help section of snpXplorer and at https://github.com/TesiNicco/snpXplorer.
(© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.)