Get all SNPs that are high in Linkage Disequilibrium for set of SNPs

Question

[Raju]

Hello, I have calculated LD for a set of SNPs of a specific Gene using the below command:

plink --bfile Obesity --allow-no-sex --extract ADRA2A_SNPs.txt --r2 --out LD_file

Output:

 CHR_A         BP_A           SNP_A  CHR_B         BP_B           SNP_B           R2 
    10    112340060     kgp11784838     10    112349204      kgp7971364     0.268577 
    10    112340060     kgp11784838     10    112349422      kgp5177378            1 
    10    112340060     kgp11784838     10    112349879       rs3737294      0.27927 
    10    112343591      rs11195199     10    112349204      kgp7971364     0.630264 
    10    112343591      rs11195199     10    112349879       rs3737294     0.681088 
    10    112349204      kgp7971364     10    112349422      kgp5177378     0.268577 
    10    112349204      kgp7971364     10    112349879       rs3737294     0.936585 
    10    112349422      kgp5177378     10    112349879       rs3737294      0.27927 
    10    112349602       rs3737293     10    112353346     kgp22819565     0.946159 

Now, I would like to obtain all SNPs that are in high linkage disequilibrium (LD) for a set of all SNPs with threshold LD (r2 > 0.6) for a list of SNPs.