Supplemental Data
Document S1. Figures S1–S30 and Tables S1–S10
Document S2. Article plus Supplemental Data

Web Resources
The URLs for data presented herein are as follows:1000 Genomes Phase 1 Analysis Results, ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/phase1/analysis_results/
Complete Genomics, 69 Genomes Data, http://www.completegenomics.com/public-data/69-Genomes/
Ensembl Genome Browser, http://www.ensembl.org
Ensembl Variant Effect Predictor, http://www.ensembl.org/info/docs/tools/vep/
GeneMANIA, http://www.genemania.org/
Geuvadis Data Browser, http://www.ebi.ac.uk/Tools/geuvadis-das/
Geuvadis RNA sequencing project, http://www.geuvadis.org/web/geuvadis/RNAseq-project
GWAS catalog, http://www.genome.gov/admin/gwascatalog.txt
HaploReg, http://www.broadinstitute.org/mammals/haploreg
Illumina Platinum Genomes, whole-genome sequencing data, http://www.illumina.com/platinumgenomes/
LFR data for family members, ftp://ftp2.completegenomics.com/
PhyloP conservation scoring, http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP100way/
RegulomeDB, http://regulomedb.org/
UCSC Genome Browser, http://genome.ucsc.edu

Accession Numbers
The Gene Expression Omnibus accession number for the RNA-seq data of all 17 individuals reported in this paper is GSE56961.

Acknowledgments
We would like to thank Tomas Babak, Christopher Brown, Hunter Fraser, Arend Sidow, and members of the S.B.M. lab for critical review of this work and manuscript. This work was supported by the Edward Mallinckrodt, Jr. Foundation and the Li Ka Shing Foundation. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/3.0/).