11 June, 2010

SNPs in high LD

A new section has been added to the variation page in Ensembl 58 that allows you to find other variations in strong linkage disequilibrium with the SNP you are viewing.

Clicking on "Linked variations" from the menu on the left hand side of the variation page takes you to a view like this one for rs1333049. Linkage disequilibrium values are calcuated on the fly and presented in one table for each population.

The table shows both r2 and D' values, along with the distance between the linked and current variations, any overlapping genes and any phenotypes associated with the linked variations. The table can be sorted by any of these columns by clicking on the column header (see previous post). The view is extensively configurable - clicking on Configure this page allows you to select populations to be displayed, change the distance over which linked variations are looked for, and filter the variations returned.

This view is currently only available for Ensembl Human, and is limited to variations with enough associated genotypes to calculate linkage disequilibrium values.


Karina said...

Perfect!! Just what I needed. Please integrate LD information into Biomart!!

Ensembl Helpdesk (Giulietta) said...

Hi Karina,

We're happy you find this view useful! While it would be great to have these data in BioMart, it's not feasible. LD values are calculated on the fly. Storing all potential pairs of variations (and their LD values) would generate an enormous amount of data. Thus, LD values are calculated "on the go" rather than stored.

However, there are ways to obtain these values (besides this view). Look out for a future post describing export from Linkage Data view in the browser, and using Ensembl scripts to generate the LD values for variation pairs.

We're happy to hear your suggestions! Keep them coming!

Bob said...

Hurray ! You made my life so much easier, thanks a lot :)