Genetic variation within transcriptional regulatory elements and its implications for human disease

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

Hindorff, L. A., Sethupathy, P., Junkins, H. A., Ramos, E. M., Mehta, J. P., Collins, F. S., & Manolio, T. A. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0903103106 · Cited by 4,013 · see citing works

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

Maurano, M. T., Humbert, R., Rynes, E., Thurman, R. E., Haugen, E., Wang, H., Reynolds, A. P., Sandstrom, R., Qu, H., Brody, J., et al. (2012) · Science · doi:10.1126/science.1222794 · Cited by 3,716 · see citing works

Genome-wide association studies for complex traits: consensus, uncertainty and challenges

McCarthy, M. I., Abecasis, G. R., Cardon, L. R., Goldstein, D. B., Little, J., Ioannidis, J. P. A., & Hirschhorn, J. N. (2008) · Nature Reviews Genetics · doi:10.1038/nrg2344 · Cited by 2,891 · see citing works

An atlas of active enhancers across human cell types and tissues

The FANTOM Consortium, Andersson, R., Gebhard, C., Miguel-Escalada, I., Hoof, I., Bornholdt, J., Boyd, M., Chen, Y., Zhao, X., Schmidl, C., et al. (2014) · Nature · doi:10.1038/nature12787 · Cited by 2,550 · see citing works

Widespread transcription at neuronal activity-regulated enhancers

Kim, T.-K., Hemberg, M., Gray, J. M., Costa, A. M., Bear, D. M., Wu, J., Harmin, D. A., Laptewicz, M., Barbara-Haley, K., Kuersten, S., et al. (2010) · Nature · doi:10.1038/nature09033 · Cited by 2,450 · see citing works

Five Years of GWAS Discovery

Visscher, P. M., Brown, M. A., McCarthy, M. I., & Yang, J. (2012) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2011.11.029 · Cited by 2,425 · see citing works

A unique chromatin signature uncovers early developmental enhancers in humans

Rada-Iglesias, A., Bajpai, R., Swigut, T., Brugmann, S. A., Flynn, R. A., & Wysocka, J. (2011) · Nature · doi:10.1038/nature09692 · Cited by 2,233 · see citing works

Transcription factors: from enhancer binding to developmental control

Spitz, F., & Furlong, E. E. M. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3207 · Cited by 2,227 · see citing works

Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis

The MAGIC investigators, Voight, B. F., The GIANT Consortium, Scott, L. J., Steinthorsdottir, V., Morris, A. P., Dina, C., Welch, R. P., Zeggini, E., Huth, C., et al. (2010) · Nature Genetics · doi:10.1038/ng.609 · Cited by 1,761 · see citing works

Long Noncoding RNAs with Enhancer-like Function in Human Cells

Ørom, U. A., Derrien, T., Beringer, M., Gumireddy, K., Gardini, A., Bussotti, G., Lai, F., Zytnicki, M., Notredame, C., Huang, Q., et al. (2010) · Cell · doi:10.1016/j.cell.2010.09.001 · Cited by 1,721 · see citing works

Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease

Botstein, D., & Risch, N. (2003) · Nature Genetics · doi:10.1038/ng1090 · Cited by 1,503 · see citing works

The long-range interaction landscape of gene promoters

Sanyal, A., Lajoie, B. R., Jain, G., & Dekker, J. (2012) · Nature · doi:10.1038/nature11279 · Cited by 1,489 · see citing works

A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly

Lettice, L. A. (2003) · Human Molecular Genetics · doi:10.1093/hmg/ddg180 · Cited by 1,164 · see citing works

Large-scale genotyping identifies 41 new loci associated with breast cancer risk

Michailidou, K., kConFab Investigators, Australian Ovarian Cancer Study Group, The GENICA (Gene Environment Interaction and Breast Cancer in Germany) Network, Hall, P. N., González‐Neira, A., Ghoussaini, M., Dennis, J., Milne, R. L., Schmidt, M. K., et al. (2013) · Nature Genetics · doi:10.1038/ng.2563 · Cited by 1,066 · see citing works

Activating RNAs associate with Mediator to enhance chromatin architecture and transcription

Lai, F., Ørom, U. A., Cesaroni, M., Beringer, M., Taatjes, D. J., Blobel, G. A., & Shiekhattar, R. (2013) · Nature · doi:10.1038/nature11884 · Cited by 857 · see citing works

Linking disease associations with regulatory information in the human genomePreprint

Schaub, M. A., Boyle, A. P., Kundaje, A. B., Batzoglou, S., & Snyder, M. P. (2012) · Genome Research · doi:10.1101/gr.136127.111 · Cited by 715 · see citing works

Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture

Berndt, S. I., Gustafsson, S., Mägi, R., Ganna, A., Wheeler, E., Feitosa, M. F., Justice, A. E., Monda, K. L., Croteau-Chonka, D. C., Day, F. R., et al. (2013) · Nature Genetics · doi:10.1038/ng.2606 · Cited by 646 · see citing works

Chromatin marks identify critical cell types for fine mapping complex trait variants

Trynka, G., Sandor, C., Han, B., Xu, H., Stranger, B. E., Liu, X. S., & Raychaudhuri, S. (2013) · Nature Genetics · doi:10.1038/ng.2504 · Cited by 580 · see citing works

Tissue-specific transcriptional regulation has diverged significantly between human and mouse

Odom, D. T., Dowell, R. D., Jacobsen, E. S., Gordon, W., Danford, T. W., MacIsaac, K. D., Rolfe, P. A., Conboy, C. M., Gifford, D. K., & Fraenkel, E. (2007) · Nature Genetics · doi:10.1038/ng2047 · Cited by 506 · see citing works

Extensive Variation in Chromatin States Across Humans

Kasowski, M., Kyriazopoulou-Panagiotopoulou, S., Grubert, F., Zaugg, J. B., Kundaje, A., Liu, Y., Boyle, A. P., Zhang, Q. C., Zakharia, F., Spacek, D. V., et al. (2013) · Science · doi:10.1126/science.1242510 · Cited by 339 · see citing works

Effect of natural genetic variation on enhancer selection and function

Heinz, S., Romanoski, C. E., Benner, C., Allison, K. A., Kaikkonen, M. U., Orozco, L. D., & Glass, C. K. (2013) · Nature · doi:10.1038/nature12615 · Cited by 298 · see citing works

Large-scale discovery of enhancers from human heart tissue

May, D., Blow, M. J., Kaplan, T., McCulley, D. J., Jensen, B. C., Akiyama, J. A., Holt, A., Plajzer-Frick, I., Shoukry, M. I., Wright, C., et al. (2011) · Nature Genetics · doi:10.1038/ng.1006 · Cited by 256 · see citing works

Deciphering the transcriptional cis-regulatory code

Yáñez-Cuna, J. O., Kvon, E. Z., & Stark, A. (2012) · Trends in Genetics · doi:10.1016/j.tig.2012.09.007 · Cited by 124 · see citing works

Epigenomics of human embryonic stem cells and induced pluripotent stem cells: insights into pluripotency and implications for disease

Rada-Iglesias, Á., & Wysocka, J. (2011) · Genome Medicine · doi:10.1186/gm252 · Cited by 54 · see citing works

Human genetic variation within neural crest enhancers: molecular and phenotypic implications

Rada-Iglesias, A., Prescott, S. L., & Wysocka, J. (2013) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2012.0360 · Cited by 24 · see citing works

Interpreting noncoding genetic variation in complex traits and human disease

Ward, L. D., & Kellis, M. (2012) · Nature Biotechnology · doi:10.1038/nbt.2422 · Cited by 6 · cited 3× · see citing works

Enhancers, enhancers – from their discovery to today’s universe of transcription enhancers

Schaffner, W. (2015) · Biological Chemistry · doi:10.1515/hsz-2014-0303 · Cited by 105 · see citing works

Neuronal and glial 3D chromatin architecture informs the cellular etiology of brain disorders

Hu, B., Won, H., Mah, W., Park, R. B., Kassim, B., Spiess, K., Kozlenkov, A., Crowley, C. A., Pochareddy, S., The PsychENCODE Consortium, et al. (2021) · Nature Communications · doi:10.1038/s41467-021-24243-0 · Cited by 103 · see citing works

Towards a map of cis-regulatory sequences in the human genome

Niu, M., Tabari, E. S., Ni, P., & Su, Z. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky338 · Cited by 19 · see citing works

Neuronal and glial 3D chromatin architecture illustrates cellular etiology of brain disordersPreprint

Hu, B., Won, H., Mah, W., Park, R., Kassim, B. S., Spiess, K., Kozlenkov, A., Crowley, C., Pochareddy, S., Li, Y., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.05.14.096917 · Cited by 11 · see citing works

GARLIC: a bioinformatic toolkit for aetiologically connecting diseases and cell type-specific regulatory maps

Nikolić, M., Papantonis, A., & Rada-Iglesias, Á. (2016) · Human Molecular Genetics · doi:10.1093/hmg/ddw423 · Cited by 2 · see citing works

The interaction between enhancer variants and environmental factors as an overlooked aetiological paradigm in human complex disease

Robert, S. M., & Rada-Iglesias, Á. (2023) · BioEssays · doi:10.1002/bies.202300038 · Cited by 1 · see citing works

Genetic Variants Associated with DNA methylation

Wang, F., Zhang, M., Wen, Y. H., & Zhang, S. J. (2015) · Cancer Genetics and Epigenetics · doi:10.5376/cge.2015.03.0007

Decoding the role of regulatory element polymorphisms in complex disease

Vockley, C. M., Barrera, A., & Reddy, T. E. (2016) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2016.10.007 · Cited by 43 · see citing works

Cis-regulatory mutations in human disease

Epstein, D. J. (2009) · Briefings in Functional Genomics and Proteomics · doi:10.1093/bfgp/elp021 · Cited by 113 · see citing works

Probing the dark matter of the human genome with big DNA

Laurent, J. M., Pinglay, S., MITCHELL, L. A., & Brosh, R. (2019) · The Biochemist · doi:10.1042/bio04103046 · Cited by 3 · see citing works

Disease-associated genetic variants in the regulatory regions of human genes: mechanisms of action on transcription and genomic resources for dissecting these mechanisms

Ignatieva, E. V., & Matrosova, E. A. (2021) · Vavilov Journal of Genetics and Breeding · doi:10.18699/vj21.003 · Cited by 12 · see citing works

Genomic approaches for understanding the genetics of complex diseasePreprint

Lowe, W. L., & Reddy, T. E. (2015) · Genome Research · doi:10.1101/gr.190603.115 · Cited by 84 · see citing works