Welcome to EnigmaVis!

EnigmaVis is a tool for generating interactive plots. To get begin , make a query using the fields below. Hit “Generate plot from query” to generate your plot. Additional documentation of features will be displayed below the plot, after it is generated. EnigmaVis is free to use. If you use the tool, please cite EnigmaVis publication

Contributors: Natalia Shatokhina (developer), Derrek Hibar, Neda Jahanshad, Jason Stein (scientific idea), Nic Novak (initial implementation)

Search by SNP, Position or Gene:

Step 1)

Select phenotypes to plot. You may add up to 8 phenotypes by clicking the checkboxes.

Optional: You can use EnigmaVis to plot your own data alongside the results from the ENIGMA consortium. To do this, upload a comma-delimited CSV file containing the data you would like to plot. An example file demonstrating the correct format is provided here. You can upload files up to 2Mb in size. After you choose your file, press “Upload selected file,” and your data will be uploaded and then appear in the phenotype selection dropdown, above. If your data does not appear immediately, please refresh the page.

Step 2)

Enter your query in the box below. EnigmaVis will interpret what you want to plot. Example queries are provided in blue below to help get you started. You can search by SNP, position, or gene.

Search by SNP (queries by example):

  • rs16869805 – Searches for the SNP designated by rs11956830. Without specifying anything else, EnigmaVis will look 300kb on either side of the SNP.
  • rs10903844:500,000 – Searches for the SNP designated by rs3813916, looking 500,000 bp upstream and downstream of the SNP.
  • rs3813916:100,000-200,000 – Searches for the SNP designated by rs3813916, looking 100,000 bp upstream of the SNP and 200,000 bp downstream.
  • For all SNP searches, a vertical line will indicate the position of the queried SNP.

Search by position (queries by example):

Search by gene (queries by example):

  • F11 – Search for the gene F11. Without specifying anything else, EnigmaVis will look 200kb on either side of the gene.
  • OR4A15:30,000 – Search for OR4A15, looking 30kb on either side.
  • GLE1:0-400,000 – Search for GLE1, looking 400kb downstream.


  • The radius of each SNP circle represents the minor allele frequency.
  • For SNP searches, the “rs” in your query must be lowercase.
  • EnigmaVis does not currently support searches on the X or Y chromosome.
  • Currently EnigmaVis only displays genes and SNP’s that are in Gencode Release 19 gene model (protein coding genes only) and in dbSNP assembly GRCh37/hg19: Common SNP’s (142)
  • NEW!!  Check out a new feature: an isoform view. Click on the “+” sign on the right of the gene track to expand the track and see the isoforms. Check if a SNP of interest hits an exon: hover a mouse over the SNP – the exonic hits will be highlighted.

Chart options and features

Zooming – To zoom in to the plot, simply drag the area you wish to enlarge directly on the plot. A button will appear at the top of the plot, prompting you to zoom.


Summary statistics from our GWAS publications are available for bulk download here

EnigmaVis was programmed by Nic Novak, 2011 and Natalia Shatokhina, 2015. Many thanks to Dmitry Baranovskiy for developing the Raphaël JavaScript Library.

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