A large fraction of human copy number variation arises from common, diallellic polymorphisms20. Most of these CNPs are in LD with adjacent SNPs, so their contribution to phenotypes can be assessed via these SNPs20. We used these SNP–CNP LD relationships to assess the extent to which this subset of human copy number variation might influence BMI (see Methods). The distribution of BMI association P values in stage 1 samples for CNP-tagging SNPs conforms closely to the distribution expected under the null hypothesis, except for a single SNP (rs2815752, P = 9.3 × 10−6) (Fig. 4a).
