Associations involving SNPs located within 1 Mb of either the 5′ or 3′ end of the associated gene were considered cis ( File S1 ) and other associations were considered trans. In accordance with previous results [2]–[6], most of the genetic variability affecting the transcriptome was of cis origin. At study-wise significance, the number of cis and trans eQTLs were 2,477 and 349, respectively, yielding a cis/trans ratio of 7.1 (81 eQTLs were both cis- and trans-modulated). At less stringent levels of significance the number of trans associations considerably increased, as expected by chance, whereas the number of cis eQTLs only modestly increased, indicating that the high stringency used for cis eQTLs identification did not result in an important under-estimation of the true number of cis eQTLs ( Figure 1 ).
