Manhattan Plot Chart

This screen will display the association test data in the widely used Manhattan Plot chart. Selecting the Manhattan Plot node in the tree (1) will display this chart (2). It is a static png image containing all the markers of this association test. To zoom-in on a given area, please check above.

Manhattan Plots are drawn using the chromosome blocks, with markers ordered in ascending physical position on the X-axis. The Y-axis shows the inverted, log(10) p-Values of the Markers. A red line will mark the significance threshold as per the WTCCC Genome-wide association study (Nature. 2007 Jun 7;447(7145):645-6).

Clicking on a chromosomes will create a new dynamic Manhattan Plot chart. The window will contain (if enough RAM is available) all the markers for this chromosome. Hovering with the mouse over a marker will pop-up a tool-tip with the marker’s ID, it’s p-Value and it’s position. You can navigate back to the table above by clicking on the button “Back to Table” (4).

Detailed Manhattan Plots are drawn using markers ordered in ascending physical position on the X-axis. The Y-axis shows the inverted, log(10) p-Values of the Markers. A red line will mark the significance threshold as per the WTCCC Genome-wide association study (Nature. 2007 Jun 7;447(7145):645-6).

Note: Generating this graphic may take several seconds depending on the number of markers available in this Allelic Association test.

You can further zoom in on this chart by dragging a rectangle (2) over the desired zone:

Clicking on a given marker or region will open a browser with the selected external resource database, based on the rsID or the chromosome and position info to locate the specified region.

Pressing the “Reset” button will bring you back to the original 1000 markers view, centered on your selected marker.