HAD Visualizer

Upload custom data

Here you can generate ancestral allele frequency images using custom genotyping data. Upload your data file in tab-delimited plain text format, where data columns for each SNP row are as follows:

chr - chromosome of the SNP
SNP_ID - (RefSeq) ID of the SNP
position - SNP genomic position
ID1,ID2,... - SNP alleles for each individual

Example:

When using the PLINK toolset, you can get the file with the command plink --file data --recode --alleleACGT --tab --transpose. You can omit column headers (headers are used to display individual ID-s). Please upload one chromosome at a time.

Select file:

rs0000 (NCBI 36)
chr0:000 000 000
Additional info from:

BRCA2 (NCBI 36)

Location:	chr 13:317000000.. 318200000
Strand:	reverse
Type:	known protein coding
Description:	Breast Cancer Susceptibility Gene Candidate 2 (Source: some stuff etc.)

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Legend for image colors →

Current dataset →
Click to change dataset.

← Current chromosome. Click to go to specific region.

← Click again to hide instructions.

Click anywhere on the image to zoom to the corresponding region.

Legend for image colors →

Current dataset →
Click to change dataset.

← Current chromosome. Click to go to specific region.

← Click again to hide instructions.

Sample size ↓

↓ A mouse click on the image brings out a tooltip box to access additional options for corresponding SNP.

← Click on the x to close the tooltip.

← Use these links to get additional details about the SNP.

← Click this button to reorder image rows according to the AAF values of this SNP.
Click again to restore the original arrangement.

← Use any of these semi-transparent buttons to move around the image or zoom out for an overview.

Click on a population name on to view geographical map. →
Clicking on any of the revealed population numbers will
(de)select the number also on the map and show(hide) corresponding data image row.
Click on any name on the population list again to hide the map and clear all population selections.

← Click on any number on the map to select it in the population list and reveal corresponding image row. Click the number again to deselect the population.

← Click on this text to hide the map (only leaving map edge shown).
Then click on the edge to reveal the whole map again.

This web page has been tested and confirmed working on all current major web browsers (in Windows XP and Mac OSX 10.6).

However, while most browsers do a decent job excelling the javascript and CSS code on this page (with Safari/Chrome being fastest), using Internet Explorer (incl. IE 8) is not recommended due to its fairly slow javascript and buggy CSS engine.

For any questions, please contact email