Of approximately 6.9 million SNPs in dbSNP release 122 approximately 4.7 million were selected for genotyping by Perlegen. 2.5 million SNPs were excluded because no assay could be designed and a further 350,000 were excluded for other reasons (see Methods). Perlegen performed genotyping using custom high-density oligonucleotide arrays as previously described15 (link). Additional genotype submissions are described in the text. QC filters were applied as previously described3 (link). Where multiple submissions met the QC criteria the submission with the lowest missing data rate was chosen for inclusion in the non-redundant filtered data set. Haplotypes were estimated from genotype data as described previously3 (link). Ancestral states at SNPs were inferred by parsimony by comparison to orthologous bases in the chimpanzee (panTro2) and rhesus macaque (rheMac2) assemblies. Recombination rates and the location of recombination hotspots were estimated as described previously3 (link). Additional details can be found in the Methods section and the Supplementary Information. The data described in this paper are in release 21 of the International HapMap Project.