1 Spencer, C.C., Su, Z., Donnelly, P. & Marchini, J. Designing genome-wide association studies: sample size, power, imputation, and the choice of genotyping chip. PLoS Genet. 5, e1000477 (2009).

2 Speliotes, E.K. et al. Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index. Nat. Genet. 42, 937–948 (2010).

3 Manolio, T.A. et al. Finding the missing heritability of complex diseases. Nature 461, 747–753 (2009).

4 Perera, M.A. et al. The missing association: sequencing-based discovery of novel SNPs in VKORC1 and CYP2C9 that affect warfarin dose in African Americans. Clin. Pharmacol. Ther. 89, 408–415 (2011).

5 Ritchie, M.D. The success of pharmacogenomics in moving genetic association studies from bench to bedside: study design and implementation of precision medicine in the post-GWAS era. Hum. Genet. 131, 1615–1626 (2012).

6 Smemo, S. et al. Obesity-associated variants within FTO form long-range functional connections with IRX3. Nature 507, 371–375 (2014).

7 Nicolae, D.L. et al. Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS. PLoS Genet. 6, e1000888 (2010).

8 Gamazon, E.R., Huang, R.S., Cox, N.J. & Dolan, M.E. Chemotherapeutic drug susceptibility associated SNPs are enriched in expression quantitative trait loci. Proc. Natl. Acad. Sci. USA 107, 9287–9292 (2010).

9 Davis, L.K. et al. Partitioning the heritability of Tourette syndrome and obsessive compulsive disorder reveals differences in genetic architecture. PLoS Genet. 9, e1003864 (2013).

10 Gamazon, E.R. et al. The convergence of eQTL mapping, heritability estimation and polygenic modeling: emerging spectrum of risk variation in bipolar disorder. arXiv 1303.6227 (2013).

11 Gusev, A. et al. Regulatory variants explain much more heritability than coding variants across 11 common diseases. bioRxiv 004309 (21 April 2014).

12 ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74 (2012).

13 GTEx Consortium. The Genotype-Tissue Expression (GTEx) project. Nat. Genet. 45, 580–585 (2013).

14 GTEx Consortium. The Genotype-Tissue Expression (GTEx) pilot analysis: multi-tissue gene regulation in humans. Science 348, 648–660 (2015).

15 Lappalainen, T. et al. Transcriptome and genome sequencing uncovers functional variation in humans. Nature 501, 506–511 (2013).

16 Battle, A. et al. Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals. Genome Res. 24, 14–24 (2014).

17 Ramasamy, A. et al. Genetic variability in the regulation of gene expression in ten regions of the human brain. Nat. Neurosci. 17, 1418–1428 (2014).

18 Tibshirani, R. Regression shrinkage and selection via the Lasso. J. R. Stat. Soc., B 58, 267–288 (1996).

19 Zou, H. & Hastie, T. Regularization and variable selection via the elastic net. J. R. Stat. Soc. Series B Stat. Methodol. 67, 301–320 (2005).

20 Yang, J., Lee, S.H., Goddard, M.E. & Visscher, P.M. GCTA: a tool for genome-wide complex trait analysis. Am. J. Hum. Genet. 88, 76–82 (2011).

21 Hammer, G.E., Kanaseki, T. & Shastri, N. The final touches make perfect the peptide–MHC class I repertoire. Immunity 26, 397–406 (2007).

22 Wellcome Trust Case Control Consortium. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447, 661–678 (2007).

23 Cotsapas, C. et al. Pervasive sharing of genetic effects in autoimmune disease. PLoS Genet. 7, e1002254 (2011).

24 Jostins, L. et al. Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature 491, 119–124 (2012).

25 Hindorff, L.A. et al. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc. Natl. Acad. Sci. USA 106, 9362–9367 (2009).

26 Noble, J.A. & Valdes, A.M. Genetics of the HLA region in the prediction of type 1 diabetes. Curr. Diab. Rep. 11, 533–542 (2011).

27 Hakonarson, H. et al. A novel susceptibility locus for type 1 diabetes on Chr12q13 identified by a genome-wide association study. Diabetes 57, 1143–1146 (2008).

28 Wang, H. et al. Genetically dependent ERBB3 expression modulates antigen presenting cell function and type 1 diabetes risk. PLoS ONE 5, e11789 (2010).

29 Hart, A.B. et al. Genome-wide association study of d-amphetamine response in healthy volunteers identifies putative associations, including cadherin 13 (CDH13). PLoS ONE 7, e42646 (2012).

30 Hart, A.B. et al. Genetic variation associated with euphorigenic effects of d-amphetamine is associated with diminished risk for schizophrenia and attention deficit hyperactivity disorder. Proc. Natl. Acad. Sci. USA 111, 5968–5973 (2014).

31 Psychiatric GWAS Consortium Bipolar Disorder Working Group. Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4. Nat. Genet. 43, 977–983 (2011).

32 Morley, M. et al. Genetic analysis of genome-wide variation in human gene expression. Nature 430, 743–747 (2004).

33 Price, A.L. et al. Single-tissue and cross-tissue heritability of gene expression via identity-by-descent in related or unrelated individuals. PLoS Genet. 7, e1001317 (2011).

34 Gilad, Y., Rifkin, S.A. & Pritchard, J.K. Revealing the architecture of gene regulation: the promise of eQTL studies. Trends Genet. 24, 408–415 (2008).

35 Cookson, W., Liang, L., Abecasis, G., Moffatt, M. & Lathrop, M. Mapping complex disease traits with global gene expression. Nat. Rev. Genet. 10, 184–194 (2009).

36 Manor, O. & Segal, E. Robust prediction of expression differences among human individuals using only genotype information. PLoS Genet. 9, e1003396 (2013).

37 Torres, J.M. et al. Cross-tissue and tissue-specific eQTLs: partitioning the heritability of a complex trait. Am. J. Hum. Genet. 95, 521–534 (2014).

38 Wang, Z., Gerstein, M. & Snyder, M. RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 10, 57–63 (2009).

39 Howie, B., Fuchsberger, C., Stephens, M., Marchini, J. & Abecasis, G.R. Fast and accurate genotype imputation in genome-wide association studies through pre-phasing. Nat. Genet. 44, 955–959 (2012).

40 Fuchsberger, C., Abecasis, G.R. & Hinds, D.A. minimac2: faster genotype imputation. Bioinformatics 31, 782–784 (2015).

41 Stegle, O., Parts, L., Piipari, M., Winn, J. & Durbin, R. Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses. Nat. Protoc. 7, 500–507 (2012).

42 Hastie, T., Tibshirani, R. & Friedman, J.H. The Elements of Statistical Learning: Data Mining, Inference, and Prediction (Springer, 2009).

43 Breiman, L. Random Forests. Mach. Learn. 45, 5–32 (2001).

44 Wheeler, H.E. et al. Poly-omic prediction of complex traits: OmicKriging. Genet. Epidemiol. 38, 402–415 (2014).

45 Harrow, J. et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 22, 1760–1774 (2012).

46 Shabalin, A.A. Matrix eQTL: ultra fast eQTL analysis via large matrix operations. Bioinformatics 28, 1353–1358 (2012).

47 Franke, A. et al. Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. Nat. Genet. 42, 1118–1125 (2010).

48 Okada, Y. et al. Genetics of rheumatoid arthritis contributes to biology and drug discovery. Nature 506, 376–381 (2014).

49 Liu, J.Z. et al. A versatile gene-based test for genome-wide association studies. Am. J. Hum. Genet. 87, 139–145 (2010).

50 Wu, M.C. et al. Powerful SNP-set analysis for case-control genome-wide association studies. Am. J. Hum. Genet. 86, 929–942 (2010).

51 Wu, M.C. et al. Rare-variant association testing for sequencing data with the sequence kernel association test. Am. J. Hum. Genet. 89, 82–93 (2011).