because closely related individuals will share SNPs identical by descent on more than one chromosome; 2) systematic difference in allele frequencies between subpopulations (population stratification). We modelled the variance attributed to these two forms of population structure as hC2(sep)−hC2=b0+b1LC+ε, where the slope b1 allows the possibility that longer chromosomes track population structure better than smaller chromosomes. To illustrate the effect of population structure, we also estimated hC2(sep) and hC2 in the entire sample of 14,347 individuals (i.e. without removing close relatives). The intercept b0 appears to be due to cryptic relatedness because when we eliminate relatives with a relationship > 0.025, b0 declines to zero (Fig. 3). We therefore predicted that cryptic relatedness accounted for 1.5%, 0.084%, 0.22% and 0.065% (not significant) of the phenotypic variance for height, BMI, vWF and QTi, respectively, in the entire sample. The variance attributed to cryptic relatedness is irrespective of chromosome length because it does not require many SNPs per chromosome to detect close relatives. Conversely, the regression slope b1 appears to be due to population stratification because longer chromosomes are likely to have more ancestry informative markers (AIMs), assuming that the AIMs are randomly distributed across the genome. We then predicted that population
