To provide a simple benchmark, we selected an imputation region that contained exactly 10,000 polymorphic sites in the European panel of 1000 haplotypes; this yielded the 1.9-Mb interval [11200000,13096366] on chromosome 17. This region contains a larger number of SNPs in the Cosmopolitan reference panel, but we restricted that panel to the same 10,000 SNPs to simplify the comparison. In practice, GWAS investigators may perform similar filtering on Cosmopolitan reference panels to remove variants that are underpowered in a particular study.
