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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?

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