In the cis- or local eQTL analysis we evaluated the associations between the genotype at a given SNP locus and transcripts located within a 2-Mb interval (1-Mb range up and down stream). We excluded 90,238 SNP loci with minor allele frequency < 0.05 and 396 genes with low expression levels - absent calls in more than 90% of the samples. The expression profile of each gene was first adjusted for somatic copy number effects and CpG methylation using a multivariate linear model. The p-value corresponds to the regression coefficient based on the residual expression level and germline genotype.
