Transcript levels of 8,568 genes (54.5% of the total genes tested) are significantly affected by the somatic copy number changes in the corresponding coding regions (FDR < 0.1). Among the 1,359 targets genes of the cis-acting SNP loci, 880 (64.8%) are also significantly associated with somatic copy number. We also identified 2,529 transcripts (16.1% of the total genes tested) that are affected by the methylation of CpG islands in the promoter region (FDR < 0.1). Among these genes, 210 are also target genes of eQTLs (15.5%, Figure 1A). Of the 15,732 genes tested, the cis-acting SNP loci account for 1.2% of the total variance of the expression. Somatic copy number alterations account for 7.3% and methylation status account for 3.3% of variation in gene expression (Figure 1B).
