Association Reports

This screen will display the Allelic Association test data in ascending p-Value order.
Selecting the Allelic Association node in the tree (1) will display this screen.

The screen has a description text area (2) which holds some information realted to the test such as how it has been generated, the QA thresholds that have been applied and how many markers and samples it contains.
Additionally, you can edit this description and append whatever information you see fit, with a limit of 2000 characters.

Specify how many lines you want to see in the report and push the “Get” button (3) to reload the requested rows.

The table containing the Association test data (4) has following columns:

  • Marker ID: The unique ID that your sequencing technology used to name the markers
  • Rs ID: The dbSNP ID
  • Chr: Chromosome
  • Pos: Physical position within chromosome
  • Min. Allele: Minor allele based on provided genotypes
  • Maj. Allele: Major allele based on provided genotypes
  • X²: Chi Square Allelic Association test
  • p-Value: p-Value calculated from the X², based on a distribution with 1 degree of freedom
  • Odds Ratio

View our methods page to learn how these values are calculated.
The next two columns are for accessing further details on each marker:

  • Zoom:

This will create a new dynamic Manhattan Plot chart (2) centered on the marker you have chosen (3). The window will contain (if available) 500 markers to the left and to the right of the chosen marker (1000 markers in all). 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.

  • Querry DB:

This will open a browser window querying the external resource database that you have selected in the drop-down box. It will use, as specified, the rsID or the chromosome and position info to locate the specified region.