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On the observed scale (0-1 disease status), the genetic variance can be greater Vp per definition, i. if the heritability on the underlying scale (h2L) is high and the disease prevalence is low, it is possible that the heritability on the observed scale (h2O) can be greater than 1. By default, GCTA does not allow any estimate of variance component to be negative. However, you need to be cautious that any artefacts between cases and control will be estimated as 'genetic' variance, especially when cases and controls were genotyped separately (e.