Question: Where to find information on LD ~ distance?
0
gravatar for moushengxu
3 months ago by
moushengxu310
moushengxu310 wrote:

We want to know how far away Linkage Disequilibrium (LD) can go between SNPs, but I have difficulty locating such information. I checked out SNPsnap from Broad Institute at https://data.broadinstitute.org/mpg/snpsnap/database_download.html, but it actually does not have such information.

Any help would be highly appreciated.

snp genome • 171 views
ADD COMMENTlink written 3 months ago by moushengxu310

Haploreg LD data based on 1000 Genomes Phase 1: http://archive.broadinstitute.org/mammals/haploreg/data/

ADD REPLYlink written 3 months ago by zx87544.8k
2
gravatar for Pierre Lindenbaum
3 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum111k wrote:

ftp://ftp.ncbi.nlm.nih.gov/hapmap/ld_data/latest

?

ADD COMMENTlink written 3 months ago by Pierre Lindenbaum111k

That is it!

Thanks so much!

ADD REPLYlink written 3 months ago by moushengxu310

One more question: it looks like the they limited the distance between SNPs to be under 200kb, while at 200kb, there are still tons of significant LDs as the data can tell. I am not sure why they cut it off at 200kb and do not look beyond 200kb?

ADD REPLYlink written 3 months ago by moushengxu310
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1504 users visited in the last hour