Usually for genetic association analysis there are lots of SNPs, but we generally select few tagSNPs based on LD value (r2)? How can we calculate the r2 value to know which SNPs are to be chosen?
I think that using this tool may help you. http://www.broadinstitute.org/mpg/snap/ldsearch.php
You can input the SNPs in that region into haploview and it will calculate the LD and or r square for you
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