Using UCSC's Table Tool

Question

[Sasha]

I have a table of coordinates in BED format, and I'm trying to find any SNPs within the coordinate ranges. I've set the 'Group' to 'Variation' and the Track to 'Common SNPs' but I don't understand how to change UCSC's table tool query from inputting rsIDs and receiving coordinates to inputting coordinates and receiving rsIDs. Is there a box I've just failed to find and check? Or will I need to make a custom track?

Thank you for your help!

Answer 1

[Matthias Zepper]

If you wish to use the coordinates from your .bed file, you need to click the button define regions next to the lookup button, which will lead you to a separate page, where you can either copy + paste or upload your .bed file. This works for up to 1000 regions.

In case you have more than that, I would recommend to download the annotation and do the intersection with e.g. Bedtools.