Genotyping data from the lllumina 650Y panel. SNP genotyping was performed on the same set of samples that were genotyped on the Affymetrix 500K panel using the Sentrix humanHap650Y genotyping beadchip from Illumina. The genotyping was carried out at the Illumina genotyping facility in La Jolla, California. This chip consists of 655,352 tag SNP markers derived from the International HapMap Project (http://www.hapmap.org) on a single BeadChip, with ∼100,000 Yoruba-specific tag SNPs to provide more comprehensive coverage in African and African-American populations. Genotyping was attempted on 517 samples. A total of 497 samples were genotyped successfully, and 654,069 SNP assays genotyped successfully. The same genotype quality control measures applied to the Affymetrix 500K dataset were applied to Illumina HumanHap 650Y dataset to determine the analysis set. The sample set for analysis (n = 397) was restricted to those identified or imputed as Caucasian. Of the 397 samples we attempted to genotype, 13 failed the Illumina genotyping assay (overall call rate < 75%), resulting in a set of 384 genotyped samples carried forward for the expression analysis. In total, 652,648 SNPs were
