One should be aware that sequence polymorphisms can cause many false cis-eQTLs [53]. Such false cis-eQTLs do not reflect actual expression differences caused by sequence polymorphisms in cis-acting factors that affect mRNA levels. Instead they indicate hybridization differences caused by sequence polymorphisms in the mRNA region that is targeted by the microarray expression probes. Therefore, SNP-probe combinations were excluded from the cis-eQTL analysis when the 50 bp long expression probe mapped to a genomic location that contained a known SNP that was showing at least some LD (r2>0.1) with the cis-SNP. We used SNP data from the 1000 Genomes Projects, as it contains LD information for 9,633,115 SNPs (April 2009 release, based on 57 CEU samples of European descent).
