Supplemental Data
Document S1. Figures S1–S8 and Table S1
Table S2. Antibody Screen Results
Table S3. Figure S4 Spot IDs
Table S4. Figure S5 Spot IDs
Table S5. Protein Quantifications
Table S6. siRNA Knockdown Results
Table S7. Significant Protein-Covariate Associations
Table S8. Significant RNA-Seq Covariate Associations
Table S9. pQTLs Identified at FDR = 0.20
Table S10. pQTL Validation Cohort Protein Quantifications
Table S11. eQTL and pQTL Genome Annotation Enrichments
Table S12. GWAS pQTL Overlap
Document S2. Article plus Supplemental Data

Web Resources
The URLs for data presented herein are as follows:1000 Genomes, http://browser.1000genomes.org
BIMBAM, http://stephenslab.uchicago.edu/software.html#bimbam
CRAN – Package lme4, http://cran.r-project.org/web/packages/lme4/index.html
CRAN – Package LMERConvenienceFunctions, http://cran.r-project.org/web/packages/LMERConvenienceFunctions/index.html
dbSNP, http://www.ncbi.nlm.nih.gov/projects/SNP/
eqtl.uchicago.edu, http://eqtl.uchicago.edu/cgi-bin/gbrowse/eqtl
Gene Expression Omnibus (GEO), http://www.ncbi.nlm.nih.gov/geo/
GWAS Catalog, http://www.genome.gov/gwastudies/
International HapMap Project, http://hapmap.ncbi.nlm.nih.gov/
Online Mendelian Inheritance in Man (OMIM), http://www.omim.org/
Python, https://www.python.org/
R statistical software, http://www.r-project.org/
RefSeq, http://www.ncbi.nlm.nih.gov/RefSeq
SeattleSeq Annotation 138 (129 used in this study), http://snp.gs.washington.edu/SeattleSeqAnnotation138/
UCSC Genome Browser, http://genome.ucsc.edu

Acknowledgments
Cell lines were provided by the Lymphoblastoid Cell Line Core of the PAAR-Pharmacogenomics of Anticancer Agents Research Group. We would like to acknowledge Shannon Delaney and Claudia Wing for assistance in collecting cell pellets. We also thank Jonathan Pritchard, Joseph Pickrell, and Mark Ciaccio for helpful discussions regarding study design; Jack Degner, Joseph Maranville, Eric Gamazon, and Nancy Cox for helpful discussions regarding data analysis; and Barbara Stranger and Fabiola Rivas for reviewing the manuscript. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/3.0/).