We previously typed 1,350 copy number polymorphisms (CNPs) in the HapMap analysis panels; 360 of these CNPs were found to be common (minor allele frequency >5%) in individuals with European ancestry (HapMap CEU), explaining more than 80% of the copy number differences between any two individuals. 323 common CNPs seemed to be diallelic, and of these 261 were in strong LD with HapMap SNPs that are close to, but do not overlap, the CNPs20. For the current work, for each of these common, diallelic CNPs, we identified (from among the SNPs successfully typed or imputed in the GIANT meta-analysis) the SNP that best captured each CNP via LD in HapMap CEU. This formed the set of 261 ‘CNP-tagging SNPs’ that were used for analysis here; we used the GIANT meta-analysis P values for these SNPs.
