I want to check linkage disequilibrium between pairs of SNPs that may be more than 500kb away from one another or on different chromosomes (trans-LD).
A paper from 2009 had a tool which did this called GLIDERS. That website is currently down. SNAP and most tools typically limit comparisons between SNPs to cis-LD and 500kb limits. In the absence of downloading genotype data from Hapmap, are there any tools which allow this to be done in batch as was possible with GLIDERS beyond the limits (cis/500k) mentioned above.