SNPSelect - Annotate selected SNPs with TFBS matches

SNPSelect Tools Input Form

Upload a SNP Set (VCF or rsID format)

        from a FILE:            
        or from a URL:        
        or paste a SNP Set:

SNPIntersect - Intersect genomic regions with variants affecting TF-binding

     Upload custom List (in BED format)
            from a FILE:
            or from a URL:
     Select available Data Sets (ChIP-seq peak or TSS genomic coordinates)
              Data Type:   

     Region Range (to extend/set the range of the genomic regions/features)
            5' ext (bp):     3' ext (bp):     

PWMs from Library

Indicate a Gene of interest


Background: SNPSelect is a Web interface to select and visualize user defined variants that affect single or multiple TFBS variability.

SNPSelect may be used in four different ways:

  • Upload a SNP set

    Users may upload the variants in two different formats, i.e either a vcf file or a list of rsIDs. We annotate the user file against our custom database (present at the FTP repository for download) of variants affecting TFBS, and report the matches. The annotated files can be downloaded by the user.

    This resource outputs three plots showing the number of variants affecting different TFs, a TF enrichment graph where users can visualilze the most affected TFs against their variants, and an annotation plot of selected regulatory variants based on their context.

  • SNPIntersect

    User-provided lists can be uploaded in BED format (narrowpeak format is also accepted). Bedtools is used to intersect the user list with our variants selected based on significant effect on TF binding.

    The tool outputs a pie chart showing the percentages of genomic regions overlapping with TF-related variants, a TF enrichment plot as well as a variant annotation plot.

  • PWMs from Library

    Users may select single PWMs representing TFBSs from the JASPAR CORE 2014 vertebrates libray.

    The tool outputs a Venn Diagram showing selected variants affecting the specific TF as well as a variant annotation bar plot. Variant match files in various formats (tab-delimited text, annotated and BED) are also included for download.

  • Gene of Interest

    Users may select single genes by giving the gene name.

    The output includes both the variant annotation and the TF enrichment plots.

Last update November 2019