Flowchart summarizing the study design. (A) Flowchart describing the quality control (QC) process for the SNP genotype and gene expression data (See Methods for details). The numbers inside the triangles correspond to the numbers of SNPs or probes/genes that are left after the removal of those (numbers given inside parentheses) that fail to meet the QC criteria outlined in the text next to the arrows. 1,492,955 genotyped SNPs passed the QC filters and were imputed. 16,252 gene expression probes corresponding to 12,363 unique genes passed the QC filters and were included in the eQTL analysis. (B) Flowchart summarizing the imputation and post-imputation QC steps for the 1,492,955 genotyped SNPs that passed QC in (A) and were imputed using 1000 Genomes as reference to provide data on 28,156,045 SNPs (see Methods for details). The description of each step along with the numbers of SNPs that were excluded at each is listed next to the arrows. The final dataset consisted of 8,400,922 imputed SNPs in 48 individuals.