To explore genetic variation in this combined set of 910 human genes, we created a general purpose genome-wide SNP relational database. The foundation for this database was Build 128 of dbSNP (http://www.ncbi.nlm.nih.gov/projects/SNP), which was our source of physical mapping data and SNP/gene functional properties. We then examined the SNP coverage of these genes as provided by seven commercial microarrays: the Illumina HumanHap300 Duo, HumanHap550, HumanHap650Y and Human1M (http://www.illumina.com), and the Affymetrix Genome-Wide Human SNP Array 5.0 and 6.0 (http://www.affymetrix.com). To assess genomic coverage of common SNPs by these microarrays, we used genotype data for four populations from the International HapMap Project, Public Release 23a (http://www.hapmap.org): African (Yoruba people of Ibidan, Nigeria – YRI), Chinese (Beijing – CHB), European-Americans (CEPH – CEU), and Japanese (Japan – JPT). To estimate LD, we used the program HaploView (version 4.0, http://www.broad.mit.edu/mpg/haploview) [18] to estimate r 2 for all SNPs within 500 kb of each other. The commonly used condition r 2≥0.8 was used to assess whether a SNP is tagged through LD in a given population by a given SNP microarray. General database management was done with a combination of SAS [19] and Perl [20].
