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.
Nucleic Acids Res. 2021 Jul 2;49(W1):W603-W612. doi: 10.1093/nar/gkab410.
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.
遗传关联研究常用于研究众多人类表型的遗传基础。然而，快速探究特定基因组区域在多个性状上的关联程度以及遗传关联的解释往往是复杂的，需要整合多个注释来源，这涉及到高级生物信息学技能。我们开发了 snpXplorer，这是一个易于使用的 Web 服务器应用程序，用于探索单核苷酸多态性 (SNP) 关联统计信息并对 SNP 集进行功能注释。snpXplorer 可以叠加来自多个研究的关联统计信息，并显示包括 SNP 关联、结构变异、重组率、eQTL、连锁不平衡模式、基因和组织中基因表达在内的区域信息。通过叠加多个 GWAS 研究，snpXplorer 可用于比较不同性状之间的关联程度，这有助于解释变异后果。给定 SNP 列表，snpXplorer 还可用于执行变体到基因映射和基因集富集分析，以识别输入 SNP 列表中过表达的分子途径。snpXplorer 可在 https://snpxplorer.net 免费使用。snpXplorer 的帮助部分以及 https://github.com/TesiNicco/snpXplorer 中提供了源代码、文档、示例文件和教程视频。
