[1] |
Ahmadiyeh, N., Pomerantz, M.M., Grisanzio, C. et al. 8q24 prostate, breast, and colon cancer risk loci show tissue-specific long-range interaction with MYC Proc. Natl. Acad. Sci. USA, 107 (2010),pp. 9742-9746
|
[2] |
Aran, D., Sabato, S., Hellman, A. DNA methylation of distal regulatory sites characterizes dysregulation of cancer genes Genome Biol., 14 (2013),p. R21
|
[3] |
Bauer, D.E., Kamran, S.C., Lessard, S. et al. Science, 342 (2013),pp. 253-257
|
[4] |
Bell, C.G., Finer, S., Lindgren, C.M. et al. Integrated genetic and epigenetic analysis identifies haplotype-specific methylation in the FTO type 2 diabetes and obesity susceptibility locus PLoS One, 5 (2010),p. e14040
|
[5] |
Bergholdt, R., Brorsson, C., Palleja, A. et al. Identification of novel type 1 diabetes candidate genes by integrating genome-wide association data, protein–protein interactions, and human pancreatic islet gene expression Diabetes, 61 (2012),pp. 954-962
|
[6] |
Bojesen, S.E., Pooley, K.A., Johnatty, S.E. et al. Multiple independent variants at the TERT locus are associated with telomere length and risks of breast and ovarian cancer Nat. Genet., 45 (2013),pp. 371-384
|
[7] |
Bruno, A.E., Li, L., Kalabus, J.L. et al. miRdSNP: a database of disease-associated SNPs and microRNA target sites on 3′ UTRs of human genes BMC Genomics, 13 (2012),p. 44
|
[8] |
Burkhardt, R., Kenny, E.E., Lowe, J.K. et al. Common SNPs in HMGCR in Micronesians and Caucasians associated with LDL-Cholesterol levels affect alternative splicing of exon13 Arterioscler. Thromb. Vasc. Biol., 28 (2008),pp. 2078-2084
|
[9] |
Caussy, C., Charrière, S., Marçais, C. et al. Am. J. Hum. Genet., 94 (2014),pp. 129-134
|
[10] |
Civelek, M., Lusis, A.J. Systems genetics approaches to understand complex traits Nat. Rev. Genet., 15 (2014),pp. 34-48
|
[11] |
Claussnitzer, M., Dankel, S.N., Klocke, B. et al. Leveraging cross-species transcription factor binding site patterns: from diabetes risk loci to disease mechanisms Cell, 156 (2014),pp. 343-358
|
[12] |
Cowper-Sal lari, R., Zhang, X., Wright, J.B. et al. Breast cancer risk-associated SNPs modulate the affinity of chromatin for FOXA1 and alter gene expression Nat. Genet., 44 (2012),pp. 1191-1198
|
[13] |
Dayeh, T.A., Olsson, A.H., Volkov, P. et al. Identification of CpG-SNPs associated with type 2 diabetes and differential DNA methylation in human pancreatic islets Diabetologia, 56 (2013),pp. 1036-1046
|
[14] |
De Gobbi, M., Viprakasit, V., Hughes, J.R. et al. A regulatory SNP causes a human genetic disease by creating a new transcriptional promoter Science, 312 (2006),pp. 1215-1217
|
[15] |
Deveci, M., Catalyürek, U.V., Toland, A.E. mrSNP: software to detect SNP effects on microRNA binding BMC Bioinformatics, 15 (2014),p. 73
|
[16] |
Edwards, S.L., Beesley, J., French, J.D. et al. Beyond GWASs: illuminating the dark road from association to function Am. J. Hum. Genet., 93 (2013),pp. 779-797
|
[17] |
ENCODE Project Consortium, Bernstein, B.E., Birney, E., Dunham, I. et al. An integrated encyclopedia of DNA elements in the human genome Nature, 489 (2012),pp. 57-74
|
[18] |
Farber, C.R., Bennett, B.J., Orozco, L. et al. PLoS Genet., 7 (2011),p. e1002038
|
[19] |
Fogarty, M.P., Cannon, M.E., Vadlamudi, S. et al. Identification of a regulatory variant that binds FOXA1 and FOXA2 at the CDC123/CAMK1D type 2 diabetes GWAS locus PLoS Genet., 10 (2014),p. e1004633
|
[20] |
French, J.D., Ghoussaini, M., Edwards, S.L. et al. Functional variants at the 11q13 risk locus for breast cancer regulate cyclin D1 expression through long-range enhancers Am. J. Hum. Genet., 92 (2013),pp. 489-503
|
[21] |
Furlong, L.I. Human diseases through the lens of network biology Trends Genet., 29 (2013),pp. 150-159
|
[22] |
Ghoussaini, M., Edwards, S.L., Michailidou, K. et al. Evidence that breast cancer risk at the 2q35 locus is mediated through IGFBP5 regulation Nat. Commun., 23 (2014),p. 4999
|
[23] |
Gong, J., Tong, Y., Zhang, H.M. et al. Genome-wide identification of SNPs in microRNA genes and the SNP effects on microRNA target binding and biogenesis Hum. Mutat., 33 (2012),pp. 254-263
|
[24] |
Gregory, A.P., Dendrou, C.A., Attfield, K.E. et al. TNF receptor 1 genetic risk mirrors outcome of anti-TNF therapy in multiple sclerosis Nature, 488 (2012),pp. 508-511
|
[25] |
Harismendy, O., Notani, D., Song, X. et al. 9p21 DNA variants associated with coronary artery disease impair interferon-gamma signalling response Nature, 470 (2011),pp. 264-268
|
[26] |
Hausser, J., Zavolan, M. Identification and consequences of miRNA-target interactions-beyond repression of gene expression Nat. Rev. Genet., 15 (2014),pp. 599-612
|
[27] |
Hindorff, L.A., Sethupathy, P., Junkins, H.A. et al. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits Proc. Natl. Acad. Sci. USA, 106 (2009),pp. 9362-9367
|
[28] |
Hitchins, M.P., Rapkins, R.W., Kwok, C.T. et al. Cancer Cell, 20 (2011),pp. 200-213
|
[29] |
Huan, T., Zhang, B., Wang, Z. et al. A systems biology framework identifies molecular underpinnings of coronary heart disease Arterioscler. Thromb. Vasc. Biol., 33 (2013),pp. 1427-1434
|
[30] |
Huang, Q., Whitington, T., Gao, P. et al. Nat. Genet., 46 (2014),pp. 126-135
|
[31] |
Hutchinson, J.N., Raj, T., Fagerness, J. et al. Allele-specific methylation occurs at genetic variants associated with complex disease PLoS One, 9 (2014),p. e98464
|
[32] |
Ishii, N., Ozaki, K., Sato, H. et al. Identification of a novel non-coding RNA, MIAT, that confers risk of myocardial infarction J. Hum. Genet., 51 (2006),pp. 1087-1099
|
[33] |
Jendrzejewski, J., He, H., Radomska, H.S. et al. The polymorphism rs944289 predisposes to papillary thyroid carcinoma through a large intergenic noncoding RNA gene of tumor suppressor type Proc. Natl. Acad. Sci. USA, 109 (2012),pp. 8646-8651
|
[34] |
Jia, L., Landan, G., Pomerantz, M. et al. Functional enhancers at the gene-poor 8q24 cancer-linked locus PLoS Genet., 5 (2009),p. e1000597
|
[35] |
Kapeller, J., Houghton, L.A., Mönnikes, H. et al. Evidence for an association of a functional variant in the microRNA-510 target site of the serotonin receptor-type 3E gene with diarrhea predominant irritable bowel syndrome Hum. Mol. Genet., 17 (2008),pp. 2967-2977
|
[36] |
Kulkarni, S., Savan, R., Qi, Y. et al. Differential microRNA regulation of HLA-C expression and its association with HIV control Nature, 472 (2011),pp. 495-498
|
[37] |
Kulzer, J.R., Stitzel, M.L., Morken, M.A. et al. Am. J. Hum. Genet., 94 (2014),pp. 186-197
|
[38] |
Kumar, V., Westra, H.J., Karjalainen, J. et al. Human disease-associated genetic variation impacts large intergenic non-coding RNA expression PLoS Genet., 9 (2013),p. e1003201
|
[39] |
Liu, C., Zhang, F., Li, T. et al. MirSNP, a database of polymorphisms altering miRNA target sites, identifies miRNA-related SNPs in GWAS SNPs and eQTLs BMC Genomics, 13 (2012),p. 661
|
[40] |
López-Bigas, N., Audit, B., Ouzounis, C. et al. Are splicing mutations the most frequent cause of hereditary disease? FEBS Lett., 579 (2005),pp. 1900-1903
|
[41] |
Macintyre, G., Bailey, J., Haviv, I. et al. is-rSNP: a novel technique for in silico regulatory SNP detection Bioinformatics, 26 (2010),pp. i524-530
|
[42] |
Mäkinen, V.P., Civelek, M., Meng, Q. et al. Integrative genomics reveals novel molecular pathways and gene networks for coronary artery disease PLoS Genet., 10 (2014),p. e1004502
|
[43] |
Malik, M., Simpson, J.F., Parikh, I. et al. CD33 Alzheimer's risk-altering polymorphism, CD33 expression, and exon 2 splicing J. Neurosci., 33 (2013),pp. 13320-13325
|
[44] |
Matys, V., Fricke, E., Geffers, R. et al. TRANSFAC: transcriptional regulation, from patterns to profiles Nucleic Acids Res., 31 (2003),pp. 374-378
|
[45] |
Maurano, M.T., Humbert, R., Rynes, E. et al. Systematic localization of common disease-associated variation in regulatory DNA Science, 337 (2012),pp. 1190-1195
|
[46] |
Meyer, K.B., O'Reilly, M., Michailidou, K. et al. Am. J. Hum. Genet., 93 (2013),pp. 1046-1060
|
[47] |
Meyer, K.B., Maia, A.T., O'Reilly, M. et al. PLoS Biol., 6 (2008),p. e108
|
[48] |
Miller, C.L., Haas, U., Diaz, R. et al. PLoS Genet., 10 (2014),p. e1004263
|
[49] |
Musunuru, K., Strong, A., Frank-Kamenetsky, M. et al. Nature, 466 (2010),pp. 714-719
|
[50] |
Nakata, K., Lipska, B.K., Hyde, T.M. et al. DISC1 splice variants are upregulated in schizophrenia and associated with risk polymorphisms Proc. Natl. Acad. Sci. USA, 106 (2009),pp. 15873-15878
|
[51] |
Nguyen, H.H., Takata, R., Akamatsu, S. et al. Hum. Mol. Genet., 21 (2012),pp. 2076-2085
|
[52] |
Nicolae, D.L., Gamazon, E., Zhang, W. et al. Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS PLoS Genet., 6 (2010),p. e1000888
|
[53] |
Nicoloso, M.S., Sun, H., Spizzo, R. et al. Single-nucleotide polymorphisms inside microRNA target sites influence tumor susceptibility Cancer Res., 70 (2010),pp. 2789-2798
|
[54] |
Ning, S., Zhao, Z., Ye, J. et al. LincSNP: a database of linking disease-associated SNPs to human large intergenic non-coding RNAs BMC Bioinformatics, 15 (2014),p. 152
|
[55] |
Paraboschi, E.M., Rimoldi, V., Soldà, G. et al. Functional variations modulating PRKCA expression and alternative splicing predispose to multiple sclerosis Hum. Mol. Genet., 20 (2014),pp. 6746-6761
|
[56] |
Pasmant, E., Sabbagh, A., Vidaud, M. et al. FASEB J., 25 (2011),pp. 444-448
|
[57] |
Pittman, A.M., Naranjo, S., Jalava, S.E. et al. PLoS Genet., 6 (2010),p. e1001126
|
[58] |
Pomerantz, M.M., Ahmadiyeh, N., Jia, L. et al. The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in colorectal cancer Nat. Genet., 41 (2009),pp. 882-884
|
[59] |
Praetorius, C., Grill, C., Stacey, S.N. et al. Cell, 155 (2013),pp. 1022-1033
|
[60] |
Rademakers, R., Eriksen, J.L., Baker, M. et al. Hum. Mol. Genet., 17 (2008),pp. 3631-3642
|
[61] |
Raval, A., Tanner, S.M., Byrd, J.C. et al. Downregulation of death-associated protein kinase 1 (DAPK1) in chronic lymphocytic leukemia Cell, 129 (2007),pp. 879-890
|
[62] |
Reynard, L.N., Bui, C., Canty-Laird, E.G. et al. Hum. Mol. Genet., 20 (2011),pp. 3450-3460
|
[63] |
Reynard, L.N., Bui, C., Syddall, C.M. et al. Hum. Genet., 133 (2014),pp. 1059-1073
|
[64] |
Richardson, K., Louie-Gao, Q., Arnett, D.K. et al. PLoS One, 6 (2011),p. e17944
|
[65] |
Richardson, K., Nettleton, J.A., Rotllan, N. et al. Gain-of-function lipoprotein lipase variant rs13702 modulates lipid traits through disruption of a microRNA-410 seed site Am. J. Hum. Genet., 92 (2013),pp. 5-14
|
[66] |
Robertson, K.D. DNA methylation and human disease Nat. Rev. Genet., 6 (2005),pp. 597-610
|
[67] |
Sandelin, A., Alkema, W., Engstrom, P. et al. JASPAR: an open-access database for eukaryotic transcription factor binding profiles Nucleic Acids Res., 32 (2004),pp. D91-D94
|
[68] |
Schödel, J., Bardella, C., Sciesielski, L.K. et al. Common genetic variants at the 11q13.3 renal cancer susceptibility locus influence binding of HIF to an enhancer of cyclin D1 expression Nat. Genet., 44 (2012),pp. 420-425
|
[69] |
Seo, S., Takayama, K., Uno, K. et al. Functional analysis of deep intronic SNP rs13438494 in intron 24 of PCLO gene PLoS One, 8 (2013),p. e76960
|
[70] |
Shen, H., Fridley, B.L., Song, H. et al. Epigenetic analysis leads to identification of HNF1B as a subtype-specific susceptibility gene for ovarian cancer Nat. Commun., 4 (2013),p. 1628
|
[71] |
Small, K.S., Hedman, A.K., Grundberg, E. et al. Nat. Genet., 43 (2011),pp. 561-564
|
[72] |
Smemo, S., Tena, J.J., Kim, K.H. et al. Obesity-associated variants within FTO form long-range functional connections with IRX3 Nature, 507 (2014),pp. 371-375
|
[73] |
Sotelo, J., Esposito, D., Duhagon, M.A. et al. Long-range enhancers on 8q24 regulate c-Myc Proc. Natl. Acad. Sci. USA, 107 (2010),pp. 3001-3005
|
[74] |
Syddall, C.M., Reynard, L.N., Young, D.A. et al. PLoS Genet., 9 (2013),p. e1003557
|
[75] |
Szymanski, M., Wang, R., Bassett, S.S. et al. Alzheimer's risk variants in the clusterin gene are associated with alternative splicing Transl. Psychiatry, 1 (2011),p. e18
|
[76] |
Quigley, D., Balmain, A. Systems genetics analysis of cancer susceptibility: from mouse models to humans Nat. Rev. Genet., 10 (2009),pp. 651-657
|
[77] |
The CARDIoGRAMplusC4D Consortium Large-scale association analysis identifies new risk loci for coronary artery disease Nat. Genet., 45 (2013),pp. 25-33
|
[78] |
Thomas-Chollier, M., Hufton, A., Heinig, M. et al. Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs Nat. Protoc., 6 (2011),pp. 1860-1869
|
[79] |
Thomson, D.W., Bracken, C.P., Goodall, G.J. Experimental strategies for microRNA target identification Nucleic Acids Res., 39 (2011),pp. 6845-6853
|
[80] |
Tuupanen, S., Turunen, M., Lehtonen, R. et al. The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling Nat. Genet., 41 (2009),pp. 885-890
|
[81] |
Verlaan, D.J., Berlivet, S., Hunninghake, G.M. et al. Allele-specific chromatin remodeling in the ZPBP2/GSDMB/ORMDL3 locus associated with the risk of asthma and autoimmune disease Am. J. Hum. Genet., 85 (2009),pp. 377-393
|
[82] |
Visser, M., Kayser, M., Palstra, R.J. Genome Res., 22 (2012),pp. 446-455
|
[83] |
Voight, B.F., Scott, L.J., Steinthorsdottir, V. et al. Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis Nat. Genet., 42 (2010),pp. 579-589
|
[84] |
Wasserman, N.F., Aneas, I., Nobrega, M.A. Genome Res., 20 (2010),pp. 1191-1197
|
[85] |
Welter, D., MacArthur, J., Morales, J. et al. The NHGRI GWAS Catalog, a curated resource of SNP-trait associations Nucleic Acids Res., 42 (2014),pp. D1001-D1006
|
[86] |
Wright, J.B., Brown, S.J., Cole, M.D. Mol. Cell Biol., 30 (2010),pp. 1411-1420
|
[87] |
Xu, Z., Taylor, J.A. SNPinfo: integrating GWAS and candidate gene information into functional SNP selection for genetic association studies Nucleic Acids Res., 37 (2009),pp. W600-W605
|
[88] |
Yu, C.Y., Theusch, E., Lo, K. et al. Hum. Mol. Genet., 23 (2014),pp. 319-332
|
[89] |
Zhang, B., Gaiteri, C., Bodea, L.G. et al. Integrated systems approach identifies genetic nodes and networks in late-onset Alzheimer's disease Cell, 153 (2013),pp. 707-720
|
[90] |
Zhang, X., Cowper-Sal lari, R., Bailey, S.D. et al. Genome Res., 22 (2012),pp. 1437-1446
|
[91] |
Zhou, B., Wei, F.Y., Kanai, N. et al. Identification of a splicing variant that regulates type 2 diabetes risk factor CDKAL1 level by a coding-independent mechanism in human Hum. Mol. Genet., 23 (2014),pp. 4639-4650
|
[92] |
Zhou, X., Baron, R.M., Hardin, M. et al. Hum. Mol. Genet., 21 (2012),pp. 1325-1335
|