Detected trans-eQTLs might also reflect false-positives, although we initially had attempted to map the expression probes as accurately as possible, by using the aforementioned three different mapping strategies: it is still well possible that some of the identified, putative trans-eQTLs in fact reflect very subtle cross-hybridization (e.g. pertaining to only a small subsequence of the probe). We therefore tried to falsify each of the putative trans-eQTLs by attempting to map each trans-probe into the vicinity of the SNP probe location, by using a highly relaxed mapping approach. All putative Illumina trans-expression probes were mapped using SHRiMP [54], which uses a global alignment approach, to the human reference genome (NCBI 36.3 build). The mapping settings were chosen very loosely to permit the identification of nearly all potential hybridization locations: match score was 10, the mismatch score was 0, the gap open penalty was −250, the gap extension penalty was −100, Smith and Waterman minimum identical alignment threshold was 30.0%, while other SHRiMP parameters were left at default. Using these settings all mappings with a minimum overlap of 15 bases, or with
