I'd like to know if two of my significant GWAS loci (p < 5E-8) independently contribute to my trait. Index SNPs for these loci are approximately 2Mb apart.
According to LDLink, these SNPs are in linkage equilibrium (r^2 = 0.01 in Europeans, my GWAS population).
However, after conditioning for SNP 1 in PLINK, SNP 2 is insignificant (p = 5E-4). If these SNPs are not independent, why would r^2 suggest they are in linkage equilibrium?