Importing custom LD information in LocusZoom

[Jaehyun Park]

Hello,

I would like to send a similar inquiry about drawing LD information with custom files.

I tried to use LD information calculated with TOPMED datasets.

When I uploaded the LD information, it was successfully reflected for the SNPs that already had LD information in 1000G.

(ex) 1:109275684, 4:147480038, ...)

However, for the SNPs that did not have LD information in 1000G (so the other variants were all grey), uploading custom LD information did not make any changes.

(ex) 6:160598408, 8:19963722, ...)

The table file was formatted as follows (3 first rows shown):

6       160598408       chr6:160598408:A:C      6       160098447       chr6:160098447:G:T      0.00193236
6       160598408       chr6:160598408:A:C      6       160098455       chr6:160098455:C:T      1.89299e-05
6       160598408       chr6:160598408:A:C      6       160098456       chr6:160098456:G:A      5.68081e-05

Since both working SNPs and not-working SNPs used the same table format, the format issue seems not to be a problem.

I would like to ask the possible reason of the problem and whether there is something I can do to solve it.

Thank you.

Best regards,

Jaehyun Park.

[Andy Boughton]

For format instructions, see these instructions (PLINK 1.9. LD tab).

https://statgen.github.io/localzoom/#instructions

I apologize for this feature being a mite fiddly: we had originally hoped to have some nice server-side harmonization, but got snarled up because no one could agree about whether user-provided LD was sensitive data. The client-side user provided file was a bit of a workaround for human-centered processes.

Generally, LD information can only come from one source in a plot at a time (server OR user provided file).

-Andy Boughton
abo...@umich.edu

Applications Programmer/Analyst, Lead
Center for Statistical Genetics
University of Michigan

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