LD in heritability estimate

Hi Cheng,

Yes, you can estimate the heritability explained by SNPs after doing the LD pruning. But I usually fit all the SNPs in the model. From the Figure 2 in Yang et al. 2010 Nature Genetics, actually I don't think the estimate will change too much whether fitting all the SNPs or a subset of SNPs, unless a very small proportion of SNPs. Have you check the SD? If the SD is large, probably, it is hard to conclude that the estimate after LD pruning is larger.

PS: I usually fit the first 10 or 20 PCs as covariates to correct for genetic structure and population structure when doing the analysis.

Cheers,
Zhihong