For all 24 candidate genes we inferred tagSNPs from our sequenced variants as well as from data available through the HapMap project. European variants for our candidate gene regions (±10 Kb) and a MAF ≥5% were obtained from the HapMap website (www.hapmap.org). For the gene re-sequencing data, we generally considered variants (SNPs and insertion/deletions) with MAF ≥2%; the 684 re-sequencing variants included 30 variants with a MAF <2%. The Tagger tagSNP selection algorithm implemented in Haploview (version 4.1, http://www.broad.mit.edu/node/443) was used for selecting tagSNPs. 3% of singleton variants (MAF = 1.1%) are exclusively observed in the Southeast Asian sample as opposed to over 30% in the European samples. These specific Southeast Asian variants are included in our report but were excluded from the tagSNP analysis.
