The results were classified by the marker type (SNP or indel), expression type (exon or gene-level) and distance of marker to transcription start site (cis or trans). CNVs were not included as a marker type because an analysis for common CNVs (MAF >5%) of >100 kb associated with gene expression did not identify any significant associations (at 1% FDR). We consider an eQTL signal to be cis-acting if the lead marker (or ‘sentinel’) is located within 1 Mb of the transcription start site of the associated transcript. For each of these eight classification groups in each tissue (plus average-all), we calculated the number of tests conducted and converted the nominal P values into FDRs using the Benjamini-Hochberg procedure57. We defined associations with FDR <1% as significant.
