I'm using a proxy-finding script with plink that reports potential proxies with their D' and R^2:
proxy D' R^2 9:12345698:rs12345 1.0 0.000758121 9:12345999:rs87654 1.0 0.039958 9:12346999:rs54321 1.0 0.0399958
However, what cutoffs should be used? From what I've read, D' is ideal when it's about 1, and R^2 is good when it's about 1 as well. However, these results above seem to contradict each other.