Our method is also capable of estimating the total narrow sense heritability attributable to a particular genomic region. This is accomplished by constructing the kinship matrix using just those ancestry segments in the region of interest and applying the variance component model to the phenotype of interest using the region-specific kinship matrix (see Online Methods). We partitioned the heritability for each of the phenotypes from the CARe data set across each of the chromosomes31. We applied weighted linear regression to determine the relationship between heritability and chromosome length (see Online Methods). The results for height are presented in Figure 2 and the full results are provided in Supplementary Table 2. We find a strong correlation between chromosome length and the heritability of height (Pearson correlation = 0.513, weighted p-value = 0.0028). logHDL, BMI, and SBP, also produced significant results (weighted p-value < 0.03, 0.02, 0.02 respectively). Other phenotypes had standard errors too large to produce meaningful results. To address this, we averaged the heritability from each chromosome across all phenotypes (using WBC|FY instead of WBC) and we observed a significant correlation between chromosome length and mean chromosomal heritability (Pearson correlation=0.686, weighted p-value <0.0002).
