I would like to obtain an accurate estimate of the number of SNPs in my SNP set that occupy LD-independent loci.
I am using a SNP set culled from large GWA data set (selection of gene-resident variants was based on an a priori hypothesis) to examine SNP-trait associations -- we feel the the 5E-8 alpha testing level is too stringent in this case, as we are examining association tests on ~13,000 SNPs. We'd like to get an idea of how many and which of these are in nearly complete LD (r2 >= 0.80 in CEU).
- I have access a to list of SNPs from a public source with values for marker ID & p-value.
- I DO NOT have access to genotype values for individuals (cannot compute linkage structure).
Essentially we want to select SNPs representative of LD-independent loci and compute Q-values on the SNP-trait tests. Is there a way to take my SNP set marker ID values and obtain information on LD structure in my sample using a proxy sample? The CEU or CEU+TSI would be appropriate as a reference.