Subjects included in the expression study were genotyped on either the Affymetrix 500k Array Set, the Genome-Wide Human SNP Array 5.0 or the Genome-Wide Human SNP Array 6.0 (as mentioned above, this study is part of a long-term project, during which individuals have been genotyped using the best available platform at the time). Human SNP Array 5.0 and 6.0 genotypes were called using Birdseed (70). SNPs were excluded based on the same quality control filters described above, except that they were calculated for all individuals genotyped on any platform (n = 1418). For eQTL mapping, 246 010 SNPs passed all quality control thresholds and 245 647 SNPs were re-annotated to the human genome (hg18, March 2006 based on dbSNP130 records). 138 206 of those were classified as nearby (within 150 kb) at least one gene.
