Identify Population Specific SNPs from List of SNPs

Question

[gaiusjaugustus]

I have a list of SNPs (from an array, so a lot of them). I want to pull out those that are informative for a particular population (e.g. YRI vs CEU from HapMap).

I usually use SPSmart to do this, but it can't handle so much information. Is there any other way to do this?

Perhaps an R package or a Python module or something?