Selecting/estimating control SNPs from genotyping array for enrichment analysis on regulatory regions

Question

[muralinmars]

Hi,

Will try to keep it short. I am currently running enrichment analysis on regulatory regions (chromatin marks). Using this new tool called Epigwas where it estimates the enrichment score of the GW significant variants (testSNPs) for chromatin marks like H3K4me3.

Additionally, we can also see if the enrichment score of the testSNPs is significant from the controlSNP set. For which we would require a controlSNP set from a genome-wide genotyping array (like Affymetrix 660W) matching the following parameters of the testSNPs

- size of the LD block (+/- 5 SNPs), 
- minor allele frequency of the lead SNP (+/- 0.1), 
- distance to the nearest gene (+/- 25 kb if outside gene),
- number of nearby genes within a +/- 500 kb interval (+/- 3 genes).

My question would be, is there a tool that facilitates to estimate the controlSNP set, by providing the testSNP list?

Thanks in advance Murali