DNA from 450 donors was genotyped using Illumina Human Omni 2.5M and 5M Beadchips. Genotypes were phased and imputed with SHAPEIT268 and IMPUTE269, respectively, using multi-ethnic panel reference from 1000 Genomes Project Phase 370. Variants were excluded from analysis if they: 1) had a call rate < 95%; 2) had minor allele frequencies < 1%; 3) deviated from Hardy–Weinberg equilibrium (P <1.0×10−6); or 4) had an imputation info score <0.4. The final genotyped and imputed array VCF (file format v4.1) for autosomal variants contains genotype posterior probabilities for each of the three possible genotypes for 11,552,519 variants across 450 GTEx donors. The dosages of the alternative alleles relative to the human reference genome hg19 were used as the genotype measure for subsequent eQTL analysis. In addition to array-based genotyping, 148 and 524 donors were whole-genome and exome sequenced, respectively. Additional details on genotyping, imputation and sequencing can be found in the Supplementary Information.
