A total of 85,508 SNPs were represented in both the Illumina and Affymetrix SNP sets. Therefore, there were 782,476 unique SNPs successfully genotyped in the HLC such that the call rate was greater than 75%, the MAF >4%, and there was not significant deviation from Hardy-Weinberg equilibrium at the 0.0001 significance level. The sample set for analysis was restricted to the 427 HLC samples that had both genotype and gene expression data available, passed the criteria outlined above and those that were identified as Caucasian, or imputed to be Caucasian when data was missing (see below).
