LD browser

Linkage disequilibrium server, for finding variants in LD with variant of interest. More on ld_server on github.

Example:

• variant= 6:44693011:A:G

• window=1000000

• reference panel: sisu42 and

• ld threshold = 0.9:

http://api.finngen.fi/api/ld?variant=6:44693011:A:G&window=1000000&panel=sisu42&r2_thresh=0.9

http://api.finngen.fi/api/ld?variant=6:44693011:A:G&window=1000000&panel=sisu42&r2_thresh=0.9api.finngen.fi

You can get the variants in LD with the parameters you want by changing the query parameters in the example url. Parameters variant, window and panel are required query parameters. r2_thresh is optional.

Variant needs to be in format chr:pos:ref:alt. Can have chr prefix. X can be X or 23.

Window size is limited to 100000-5000000.

Currently sisu V4.2 (panel parameter value sisu42), sisu V4 (panel parameter value sisu4) and sisu V3 (panel parameter value sisu3) imputation panels are supported. These panels contain the same variants as imputed FinnGen data: sisu3 until data freeze 7, sisu4 in data freezes 8 and 9, sisu4.2 from data freeze 10 onwards.