Cindy Boer

90 | Chapter 2.1 nome-wide association studies in celiac disease and rheumatoid arthritis identifies fourteen non- HLA shared loci. PLoS Genet. 2011;7: e1002004 doi: 10.1371/journal.pgen.1002004 18. Han J-W, Zheng H-F, Cui Y, Sun L-D, Ye D-Q, Hu Z, et al. Genome-wide association study in a Chinese Han population identifies nine new susceptibility loci for systemic lupus erythematosus. Nat Gen- et. 2009;41: 1234–7. doi: 10.1038/ng.472 19. Ramos YFM, den Hollander W, Bovée JVMG, Bomer N, van der Breggen R, Lakenberg N, et al. Genes involved in the osteoarthritis process identified through genome wide expression analysis in ar- ticular cartilage; the RAAK study. PLoS One. 2014;9: e103056 doi: 10.1371/journal.pone.0103056 20. Westra H-J, Peters MJ, Esko T, Yaghootkar H, Schurmann C, Kettunen J, et al. Systematic identifica- tion of trans eQTLs as putative drivers of known disease associations. Nat Genet. Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.; 2013;45: 1238–1243. doi: 10.1038/ng.2756 21. Pers TH, Karjalainen JM, Chan Y, Westra J, Wood AR, Yang J, et al. Biological interpretation of ge- nome-wide association studies using predicted gene functions. Nat Commun. Nature Publishing Group; 2015;6: 5890 doi: 10.1038/ncomms6890 22. Raychaudhuri S. VIZ-GRAIL: Visualizing functional connections across disease loci. Bioinformatics. 2011;27: 1589–1590. doi: 10.1093/bioinformatics/btr185 23. Wu MC, Lee S, Cai T, Li Y, Boehnke M, Lin X. Rare-variant association testing for sequencing data with the sequence kernel association test. Am J Hum Genet. 2011;89: 82–93. doi: 10.1016/j. ajhg.2011.05.029 24. Maurano MT, Humbert R, Rynes E, Thurman RE, Haugen E, Wang H, et al. Systematic localiza- tion of common disease-associated variation in regulatory DNA. Science. 2012;337: 1190–5. doi: 10.1126/science.1222794 25. Trynka G, Sandor C, Han B, Xu H, Stranger BE, Liu XS, et al. Chromatin marks identify critical cell types for fine mapping complex trait variants. Nat Genet. 2013;45: 124–30. doi: 10.1038/ng.2504 26. Rosenbloom KR, Sloan C a, Malladi VS, Dreszer TR, Learned K, Kirkup VM, et al. ENCODE data in the UCSC Genome Browser: year 5 update. Nucleic Acids Res. 2013;41: D56–63. doi: 10.1093/nar/ gks1172 27. Consortium RE, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, et al. Integrative analysis of 111 reference human epigenomes. doi: 10.1038/nature14248 [PMC free article] [PubMed] 28. Bernstein BE, Stamatoyannopoulos J a, Costello JF, Ren B, Milosavljevic A, Meissner A, et al. The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol. Nature Publishing Group; 2010;28: 1045–8. doi: 10.1038/nbt1010-1045 29. Appleton CTG, Usmani SE, Bernier SM, Aigner T, Beier F. Transforming growth factor alpha sup- pression of articular chondrocyte phenotype and Sox9 expression in a rat model of osteoarthritis. Arthritis Rheum. 2007;56: 3693–705. doi: 10.1002/art.22968 30. Usmani SE, Pest M a, Kim G, Ohora SN, Qin L, Beier F. Transforming growth factor alpha controls the transition from hypertrophic cartilage to bone during endochondral bone growth. Bone. Elsevier Inc.; 2012;51: 131–41. doi: 10.1016/j.bone.2012.04.012 31. Fairfax BP, Humburg P, Makino S, Naranbhai V, Wong D, Lau E, et al. Innate immune activity con- ditions the effect of regulatory variants upon monocyte gene expression. Science. 2014;343: 1246949 doi: 10.1126/science.1246949 32. Enomoto H, Enomoto-Iwamoto M, Iwamoto M, Nomura S, Himeno M, Kitamura Y, et al. Cbfa1 is a positive regulatory factor in chondrocyte maturation. J Biol Chem. 2000;275: 8695–702. Available: http://www.ncbi.nlm.nih.gov/pubmed/10722711 33. Dyment D a, Smith AC, Alcantara D, Schwartzentruber J a, Basel-Vanagaite L, Curry CJ, et al. Mu- tations in PIK3R1 Cause SHORT Syndrome. Am J Hum Genet. 2013; 158–166. doi: 10.1016/j. ajhg.2013.06.005 34. Volders P-J, Verheggen K, Menschaert G, Vandepoele K, Martens L, Vandesompele J, et al. An update on LNCipedia: a database for annotated human lncRNA sequences. Nucleic Acids Res.