To quantify the effect of known associated variants on the results, we included the FTO SNP rs9939609 on chromosome 16 for BMI and the ABO SNP rs612169 on chromosome 9 for vWF as a covariate when estimating hC2 by the joint analysis of all autosomes. FTO was the first locus to be detected through GWAS that is associated with BMI14 and ABO is a major determinant of vWF19. When compared to the result without adjustment, the estimate of variance due to chromosome 16 ( h162) for BMI decreased from 1.19% to 0.61%, in line with an estimate of ~0.34% to ~1% of variance explained by the FTO locus for BMI in previous GWAS12,14,15 and an estimate of ~0.46% from association analysis in the present study; the estimate of h92 for vWF decreased by 11.8%, consistent with an estimate of ~10% of variance for vWF explained by the ABO locus in GWAS16; and the estimates for the other chromosomes remained the same (Supplementary Fig. 8).
