the GCTA estimate is being driven by the relationship of phenotypic similarity to genetic relatedness among closely-related individuals (i.e., it is essentially biometric). At the lower GRM thresholds, GCTA is estimating the proportion of phenotypic variance accountable by all of the markers genotyped in the GWAS. Consequently, the differences in the GCTA estimates at the differing GRM threshold gives some indication of the extent to which heritability would remain missing even in an infinite GWAS sample.
