Trans analysis was limited to SNPs located on a different chromosome than the tested transcript. Post-QC analysis of the trans-eQTLs revealed 52 probes with extreme outlier effects which were filtered from further trans analysis. Transcripts associated with a trans-SNP at P<5×10−8 were used for calculations of transcript-wise FDR from the complete list of p values using the qvalue package20 implemented in R2.11 37.
