EnigmaVis



Welcome to EnigmaVis. EnigmaVis is a tool for generating interactive plots that you can use to visualize and navigate datasets from ENIGMA. To get begin, make a query using the fields below. Hit “submit” 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 the EnigmaVis paper:

Novak, N. et al., EnigmaVis: Online Interactive Visualization of Genome-Wide Association Studies of the Enhancing NeuroImaging Genetics through Meta-Analysis (ENIGMA) Consortium. Twin Res Hum Genet. 2012 Jun;15(3):414-8.

Search by SNP, Position or Gene:

Step 1) Select phenotypes to plot. Select up to three phenotpes from the tree below.

You may add up to 3 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.

You can use the button below to generate a wide (Manhattan) plot. Currently, Manhattan plots cannot be generated for multiple phenotypes. The Manhattan plot is generated from the phenotype chosen in the phenotype selection dropdown box, above.



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.


Notes

  • 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.





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.

Export as Image – Click the image at the left to convert the plot into an image, for printing or for use in presentations. Please note that this currently has limited functionality, and works best in the Google Chrome browser.


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