Anti-sense RNA was synthesized, amplified and purified using the Ambion Illumina TotalPrep Amplification Kit (Ambion, USA) following the manufacturers' protocol. Complementary RNA was either hybridized to Illumina HumanRef-8 v2 arrays (229 samples, further referred to as H8v2) or Illumina HumanHT-12 arrays (1,240 samples, further referred to as HT12) and scanned on the Illumina BeadArray Reader. Raw probe intensities were extracted using Illumina's BeadStudio Gene Expression module v3.2 (No background correction was applied, nor did we remove probes with low expression). The raw expression data of the 1,240 HT12 peripheral blood samples were combined with the raw expression data of 296 replication samples (described in detail in paragraph ‘Trans-eQTL replication dataset’). Both datasets (H8v2 and HT12) were quantile normalized separately to the median distribution and expression values were subsequently log2 transformed. Subsequently, the probes were centered to zero and linearly scaled such that each probe had a standard deviation of one.
