The Exploration tab allows you to explore association statistics from published Genome-Wide Association Studies (GWAS). You can search for your favourite SNP or gene, and overlay multiple GWAS statistics on top of each other, allowing comparison between them.
GWAS summary statistics are shown in the context of the closest genes, recombination rates, and structural variations (SV). Gene expression per-tissue from GTEx is shown for the genes in the window. A side panel reports GWAS statistics and SV statistics, and allows to download data as a table.
The Annotation tab allows you to annotate a set of SNPs and/or perform gene-set enrichment analysis. Annotation is performed integrating public QTL datasets (eQTLs, sQTLs), variant pathogenicity (CADD), and genomic position, and reportsa list of likely affected genes.
If gene-set enrichment analysis is requested, the list of genes associated with the SNPs is used in a sampling-based framework to test for the pathways significantly enriched in the list of genes. This procedure allows multiple genes to be associated with each variant.
The About tab gives you more information about snpXplorer. You can check out the publication in Nucleic Acid Research or download the PDF of the paper. Please do not forget to cite us if you find snpXplorer useful for your research.
Here you can also check the references snpXplorer uses and the studies included.
The Help tab guides you through snpXplorer functionalities with vignettes, for both the Exploration and Annotation sections.
snpXplorer was developed by Niccolò Tesi at Amsterdam UMC and TU Delft.
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