cis-eQTL SNP was in LD (r2 > 0.2) with any SNP in the cis-probe sequence, using the Western European subpopulations of the 1000 genomes project25 (2011-05-21 release, 286 individuals, excluding Finnish individuals) as a reference. If we observed this to be the case the respective cis-eQTLs were removed. Furthermore, for each trans-eQTL we investigated whether portions of the probe sequence could map in the vicinity of the trans-eQTL SNP (which in fact would imply a cis-eQTL, rather than a trans-eQTL effect). Therefore, we tried to map the trans-eQTL probe sequences, using very permissive settings, within a 5 Mb window of the trans-eQTL SNP. SNP-probe combinations where the probe mapped with at least 15 bp within the 5 Mb window, were deemed false-positive and removed from further analysis. After this filtering we recalculated the FDR for both the cis- and trans-eQTL results.
