Joint visualization of association study results and linkage disequilibrium

Back to the description of the algorithm

Instructions for running the visualization

Generating a plot for your own data is simple:

1. Click the file upload button to the left of the example plot.
2. Select a data file to upload and visualize.
3. Select the appropriate HapMap population under "Data Options."
4. Enter the appropriate chromosome number for your data.
5. Choose your data and image options.
6. Click the "Submit" button at the bottom of the menu.

The program will then process your data and generate a plot. To save the generated plot of your own work, either right-click on the plot and select 'Save as...' or simply drag the plot from your browser to your desktop.

Details about each menu option are available in the glossary.

An example Χ2 input file is available that shows the space-delimited format read by the program. The input file contains a list of SNP ids (rs format) and their corresponding Χ2 values from the association study. This input file also serves as the default file to create the initial plot below. If no upload file is specified, this file will automatically be used, allowing you to easily examine the various data and image options available on the menu to the left of the plot. The order of the SNPs in the data file determines the order of the SNPs in the plot. This allows plotting in forward or reverse directions along the chromosome. It is best to restrict the range of SNPs to include no more than ~1,000 SNPs. Beyond ~1,000 SNPs, the calculation takes a long time.

By deault, the off diagonal r2 values were gleaned from from the June 2006 HapMap linkage disequilibrium data (release rel#21 NCBI B35). Since we are concerned with the most significant values, r2 < 0.5 have been ommitted from the database for enhanced speed.

Instead of using the default HapMap r2 values, the user may optionally upload their own LD r2 data. An example LD r2 input file is available that shows the space-delimited format read by the program. The input file contains a list of pairs of SNP ids (rs format) and their corresponding r2 values.

An option is also provided for the user to upload their own image data. An example image input file is available that shows the space-delimited format read by the program. The input file contains a list of pairs of SNP ids (rs format) and their corresponding effective Χ2 values. If an image file is uploaded, the program will ignore any uploaded Χ2 or LD r2 input files.

Data Options Optional image file to upload: Optional LD file to upload: Χ2 file to upload: HapMap population: CEU CHB JPT YRI Chromosome (1-22,X): Starting SNP rs#: Number of SNPs forward:
Image Options Result plotted: Χ2 -log10(p-value) Smoothing: on off SNP annotation position: right left Annotate all SNPs: yes no Annotation threshold: Grid_size: default small medium large Number of colors (2-253): Color Palette: Default Gold Modified_Gold Spectrum Biased_Spectrum

This web application was implemented by Mark Kvale.