we suggested in Yang et al. (2010) a stringent threshold, i.e. 0.025, to remove cryptic relatedness from the data so that the estimate of can be compared directly to the results from GWAS in response to the “missing heritability” problem [2]. In practice, observing a much smaller SE of using all common SNPs than that predicted from theory is a caveat suggesting substantial cryptic relatedness remaining in the data.
