To create a bed file using the list of input human SNPs you can download latest dbSNP, our link is for version 147. Follow these steps and using awk create a bed file for your input SNP list.
Follow these steps to perform LD analysis using Broad SNAP tool, and to select SNPs with D'>8. As SNAP doesn't allow to select for D' use r2>0.2 then awk to select D'>0.8.
Download a file I prepared using DNase-Seq open chromatin regions in 125 ENCODE cell lines by combining open chromatin regions form all cell lines.
#get distance column
Remove long distances that originate from other SNPs in the original file that are on the same chromosome:
Plot the number of original SNPs that are not in open chromatin whose LD SNPs can overlap a potentially open chromatin region.
Note these are obtained from a combined ENCODE dataset so this number refers to SNPs in LD that may be in open chromatin, whether or not they will be in the open chromatin it depends on the specific cell type of interest and specific conditions that will determine whether that region will be open or not. However all these regions have a potential to be open regions, meaning they are functional in a certain context.