How to get a list of SNPs in LD with another list of SNPs

Question

[kakukeshi]

Hi there,

I have a list of 100 SNPs from one dataset and I would like to map them into another dataset (different array). When I do it directly by the SNP id only 10 are in both datasets, so I was thinking to also include the ones that are in the present in the second dataset and in LD (>0.9) with my subset of 100 SNPs.

Do you know what is the simplest way to do this? I especially interested if there is an R package used for this?

[Nitin Narwade]

Can you please post some sample input and expected output....??