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Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

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Integrative analysis of 111 reference human epigenomes

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The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

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Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

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

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Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

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The NHGRI GWAS Catalog, a curated resource of SNP-trait associations

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Open Targets Genetics: systematic identification of trait-associated genes using large-scale genetics and functional genomics

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Multi-omics single-cell data integration and regulatory inference with graph-linked embedding

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An open approach to systematically prioritize causal variants and genes at all published human GWAS trait-associated loci

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A single-cell atlas of chromatin accessibility in the human genome

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Functionally informed fine-mapping and polygenic localization of complex trait heritability

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Leveraging polygenic enrichments of gene features to predict genes underlying complex traits and diseases

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Single-Cell Transcriptome Analysis Reveals Dynamic Cell Populations and Differential Gene Expression Patterns in Control and Aneurysmal Human Aortic Tissue

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Cohesin and CTCF control the dynamics of chromosome folding

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Cell-type specialization is encoded by specific chromatin topologies

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Transcriptional coupling of distant regulatory genes in living embryos

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Combining SNP-to-gene linking strategies to identify disease genes and assess disease omnigenicity

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Robust Hi-C Maps of Enhancer-Promoter Interactions Reveal the Function of Non-coding Genome in Neural Development and Diseases

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Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes

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A compendium and comparative epigenomics analysis of cis-regulatory elements in the pig genome

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Common variants contribute to intrinsic human brain functional networks

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Non-coding driver mutations in human cancer

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G-quadruplex DNA structures in human stem cells and differentiation

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Promoter-interacting expression quantitative trait loci are enriched for functional genetic variants

Chandra, V., Bhattacharyya, S., Schmiedel, B. J., Madrigal, A., Gonzalez-Colin, C., Fotsing, S., Crinklaw, A., Seumois, G., Mohammadi, P., Kronenberg, M., et al. (2021) · Nature Genetics · doi:10.1038/s41588-020-00745-3 · Cited by 122

Super enhancer regulation of cytokine-induced chemokine production in alcoholic hepatitis

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Massively parallel discovery of human-specific substitutions that alter enhancer activity

Uebbing, S., Gockley, J., Reilly, S. K., Kocher, A. A., Geller, E. T., Gandotra, N., Scharfe, C., Cotney, J. L., & Noonan, J. P. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2007049118 · Cited by 113

Microglial efferocytosis: Diving into the Alzheimer’s disease gene pool

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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

A pan-tissue DNA methylation atlas enables in silico decomposition of human tissue methylomes at cell-type resolution

Zhu, T., Liu, J., Beck, S., Pan, S., Capper, D., Lechner, M., Thirlwell, C., Breeze, C. E., & Teschendorff, A. E. (2022) · Nature Methods · doi:10.1038/s41592-022-01412-7 · Cited by 103

Enhancer Domains Predict Gene Pathogenicity and Inform Gene Discovery in Complex Disease

Wang, X., & Goldstein, D. B. (2020) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2020.01.012 · Cited by 106

Genetic and biological insights into spontaneous coronary artery dissection

Adlam, D., Berrandou, T.-E., Georges, A. B., Nelson, C. P., Giannoulatou, E., Henry, J., Ma, L., Blencowe, M., Turley, T. N., Yang, M., et al. (2023) · Nature Genetics · doi:10.1038/s41588-023-01410-1 · Cited by 105

Enhancers with tissue-specific activity are enriched in intronic regionsPreprint

Borsari, B., Villegas-Mirón, P., Pérez-Lluch, S., Turpín, I., Laayouni, H., Segarra‐Casas, A., Bertranpetit, J., Guigó, R., & Acosta, S. (2021) · Genome Research · doi:10.1101/gr.270371.120 · Cited by 86

Characterization of altered molecular mechanisms in Parkinson’s disease through cell type–resolved multiomics analyses

Lee, A., Kim, C., Park, S.-W., Joo, J., Choi, B., Yang, D., Jun, K., Eom, J., Lee, S., Chung, S. J., et al. (2023) · Science Advances · doi:10.1126/sciadv.abo2467 · Cited by 90

From genetic associations to genes: methods, applications, and challenges

Qi, T., Song, L., Guo, Y., Chen, C., & Yang, J. (2024) · Trends in Genetics · doi:10.1016/j.tig.2024.04.008 · Cited by 85

Global discovery of lupus genetic risk variant allelic enhancer activity

Lu, X., Chen, X., Forney, C. R., Donmez, O. A., Miller, D., Parameswaran, S., Hong, T., Huang, Y., Pujato, M. A., Cazares, T. A., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-21854-5 · Cited by 77

Multi-ancestry and multi-trait genome-wide association meta-analyses inform clinical risk prediction for systemic lupus erythematosus

Khunsriraksakul, C., Li, Q., Markus, H., Patrick, M. T., Sauteraud, R., McGuire, D., Wang, X., Wang, C., Wang, L., Chen, S., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-36306-5 · Cited by 79

LINE retrotransposons characterize mammalian tissue-specific and evolutionarily dynamic regulatory regions

Roller, M., Stamper, E. L., Villar, D., Izuogu, O. G., Martin, F. J., Redmond, A. M., Ramachanderan, R., Harewood, L., Odom, D. T., & Flicek, P. (2021) · Genome biology · doi:10.1186/s13059-021-02260-y · Cited by 72

An effector index to predict target genes at GWAS loci

Forgetta, V., Jiang, L., Vulpescu, N. A., Hogan, M. S., Chen, S., Morris, J. A., Grinek, S., Benner, C., Jang, D., Hoang, Q., et al. (2022) · Human Genetics · doi:10.1007/s00439-022-02434-z · Cited by 76

The cis-regulatory effects of modern human-specific variants

Weiss, C. V., Harshman, L., Inoue, F., Fraser, H. B., Petrov, D. A., Ahituv, N., & Gokhman, D. (2021) · eLife · doi:10.7554/elife.63713 · Cited by 70

A noncoding single-nucleotide polymorphism at 8q24 drives IDH1 -mutant glioma formation

Yanchus, C., Drucker, K. L., Kollmeyer, T. M., Tsai, R., Winick‐Ng, W., Liang, M., Malik, A., Pawling, J., Lorenzo, S. B. D., Ali, A., et al. (2022) · Science · doi:10.1126/science.abj2890 · Cited by 77

DeepLoop robustly maps chromatin interactions from sparse allele-resolved or single-cell Hi-C data at kilobase resolution

Zhang, S., Plummer, D., Lu, L., Cui, J., Xu, W., Wang, M., Liu, X., Prabhakar, N., Shrinet, J., Srinivasan, D., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01116-w · Cited by 63

Genetic effects on liver chromatin accessibility identify disease regulatory variants

Currin, K. W., Erdos, M. R., Narisu, N., Rai, V., Vadlamudi, S., Perrin, H. J., Idol, J. R., Yan, T., Albanus, R. D., Broadaway, K. A., et al. (2021) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2021.05.001 · Cited by 59

Identifying Novel Susceptibility Genes for Colorectal Cancer Risk From a Transcriptome-Wide Association Study of 125,478 Subjects

Guo, X., Lin, W., Wen, W., Huyghe, J. R., Bien, S. A., Cai, Q., Harrison, T. A., Chen, Z., Qu, C., Bao, J., et al. (2020) · Gastroenterology · doi:10.1053/j.gastro.2020.08.062 · Cited by 58

The genome-wide impact of trisomy 21 on DNA methylation and its implications for hematopoiesis

Muskens, I. S., Li, S., Jackson, T., Elliott, N., Hansen, H. M., Myint, S. S., Pandey, P., Schraw, J. M., Roy, R., Anguiano, J., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-21064-z · Cited by 62

Regulatory variants in TCF7L2 are associated with thoracic aortic aneurysm

Roychowdhury, T., Lu, H., Hornsby, W., Crone, B., Wang, G. T., Guo, D., Sendamarai, A. K., Devineni, P., Lin, M., Zhou, W., et al. (2021) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2021.06.016 · Cited by 54

Enhancer–silencer transitions in the human genomePreprint

Huang, D., & Ovcharenko, I. (2022) · Genome Research · doi:10.1101/gr.275992.121 · Cited by 57

Genetic analyses of the electrocardiographic QT interval and its components identify additional loci and pathways

Young, W. J., Lahrouchi, N., Isaacs, A., Duong, T., Foco, L., Ahmed, F., Brody, J. A., Salman, R., Noordam, R., Benjamins, J.-W., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-32821-z · Cited by 49

Deregulated Regulators: Disease-Causing cis Variants in Transcription Factor Genes

van der Lee, R., Correard, S., & Wasserman, W. W. (2020) · Trends in Genetics · doi:10.1016/j.tig.2020.04.006 · Cited by 53

Genetic risk factors for ME/CFS identified using combinatorial analysis

Das, S., Taylor, K., Kozubek, J. A., Sardell, J., & Gardner, S. (2022) · Journal of Translational Medicine · doi:10.1186/s12967-022-03815-8 · Cited by 55

Viewing Nuclear Architecture through the Eyes of Nocturnal Mammals

Feodorova, Y. N., Falk, M. J., Mirny, L. A., & Solovei, I. V. (2020) · Trends in Cell Biology · doi:10.1016/j.tcb.2019.12.008 · Cited by 52

Demystifying non-coding GWAS variants: an overview of computational tools and methods

Schipper, M., & Posthuma, D. (2022) · Human Molecular Genetics · doi:10.1093/hmg/ddac198 · Cited by 57

Integrated methylome and phenome study of the circulating proteome reveals markers pertinent to brain health

Gadd, D. A., Hillary, R. F., McCartney, D. L., Shi, L., Stolicyn, A., Robertson, N., Walker, R. M., McGeachan, R. I., Campbell, A., Shen, X., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-32319-8 · Cited by 45

GWAS meta-analysis of intrahepatic cholestasis of pregnancy implicates multiple hepatic genes and regulatory elements

Dixon, P. H., Levine, A. P., Cebola, I., Chan, M., Amin, A. S., Aich, A., Mozere, M., Maude, H., Mitchell, A., Zhang, J., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-29931-z · Cited by 47

Detection of Neanderthal Adaptively Introgressed Genetic Variants That Modulate Reporter Gene Expression in Human Immune Cells

Jagoda, E., Xue, J. R., Reilly, S. K., Dannemann, M., Racimo, F., Huerta-Sanchez, E., Sankararaman, S., Kelso, J., Pagani, L., Sabeti, P. C., et al. (2022) · Molecular Biology and Evolution · doi:10.1093/molbev/msab304 · Cited by 47

Random allelic expression in the adult human body

Kravitz, S. N., Ferris, E., Love, M. I., Thomas, A., Quinlan, A. R., & Gregg, C. J. (2023) · Cell Reports · doi:10.1016/j.celrep.2022.111945 · Cited by 46

Cell Type-Specific Intralocus Interactions Reveal Oligodendrocyte Mechanisms in MS

Factor, D. C., Barbeau, A. M., Allan, K. C., Hu, L. R., Madhavan, M., Hoang, A. T., Hazel, K. E. A., Hall, P. A., Nisraiyya, S., Najm, F. J., et al. (2020) · Cell · doi:10.1016/j.cell.2020.03.002 · Cited by 48

Cis-regulatory architecture of human ESC-derived hypothalamic neuron differentiation aids in variant-to-gene mapping of relevant complex traits

Pahl, M. C., Doege, C. A., Hodge, K. M., Littleton, S. H., Leonard, M. E., Lu, S., Rausch, R., Pippin, J. A., Rosa, M. C. D., Basak, A., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-27001-4 · Cited by 46

KSHV episome tethering sites on host chromosomes and regulation of latency-lytic switch by CHD4

Kumar, A., Lyu, Y., Yanagihashi, Y., Chantarasrivong, C., Majerciak, V., Salemi, M., Wang, K.-H., Inagaki, T., Chuang, F. Y. S., Davis, R., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.110788 · Cited by 42

The Pol II preinitiation complex (PIC) influences Mediator binding but not promoter–enhancer loopingPreprint

Sun, F., Sun, T., Kronenberg, M., Tan, X., Huang, C., & Carey, M. (2021) · Genes & Development · doi:10.1101/gad.348471.121 · Cited by 46

Progesterone receptor mediates ovulatory transcription through RUNX transcription factor interactions and chromatin remodelling

Dinh, D. T., Breen, J., Nicol, B., Foot, N. J., Bersten, D. C., Emery, A., Smith, K. M., Wong, Y. Y., Barry, S. C., Yao, H. H., et al. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad271 · Cited by 42

Prioritizing effector genes at trait-associated loci using multimodal evidence

Schipper, M., de Leeuw, C., Maciel, B. D. A. P. C., Wightman, D. P., Hubers, N., Boomsma, D. I., O’Donovan, M. C., & Posthuma, D. (2025) · Nature Genetics · doi:10.1038/s41588-025-02084-7 · Cited by 51

Functional dissection of complex trait variants at single-nucleotide resolution

Siraj, L., Castro, R. I., Dewey, H. B., Kales, S., Butts, J. C., Nguyen, T. T. L., Kanai, M., Berenzy, D., Mouri, K., Wang, Q. S., et al. (2026) · Nature · doi:10.1038/s41586-026-10121-6 · Cited by 56

3DIV update for 2021: a comprehensive resource of 3D genome and 3D cancer genome

Kim, K., Jang, I., Kim, M., Choi, J., Kim, M.-S., Lee, B.-W., & Jung, I. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa1078 · Cited by 39

Assigning function to SNPs: Considerations when interpreting genetic variation

Fadason, T., Farrow, S. L., Gokuladhas, S., Golovina, E., Nyaga, D. M., O'Sullivan, J. M., & Schierding, W. S. (2021) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2021.08.008 · Cited by 44

Integrating 3D genomic and epigenomic data to enhance target gene discovery and drug repurposing in transcriptome-wide association studies

Khunsriraksakul, C., McGuire, D., Sauteraud, R., Chen, F., Yang, L., Wang, L., Hughey, J. M., Eckert, S., Weissenkampen, J. D., Shenoy, G., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-30956-7 · Cited by 40

FIREcaller: Detecting frequently interacting regions from Hi-C data

Crowley, C., Yang, Y., Qiu, Y., Hu, B., Abnousi, A., Lipiński, J., Plewczyński, D., Wu, D., Won, H., Ren, B., et al. (2021) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2020.12.026 · Cited by 37

The landscape of long noncoding RNA-involved and tumor-specific fusions across various cancers

Guo, M., Xiao, Z., Dai, Z., Zhu, L., Lei, H., Diao, L., & Xiong, Y. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa1119 · Cited by 40

Epromoters function as a hub to recruit key transcription factors required for the inflammatory response

Santiago‐Algarra, D., Souaid, C., Singh, H. N., Dao, L. T. M., Hussain, S., Medina-Rivera, A., Ramirez-Navarro, L., Castro-Mondragon, J. A., Sadouni, N., Charbonnier, G., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-26861-0 · Cited by 40

An intronic transposon insertion associates with a trans-species color polymorphism in Midas cichlid fishes

Kratochwil, C. F., Kautt, A. F., Nater, A., Härer, A., Liang, Y., Henning, F., & Meyer, A. (2022) · Nature Communications · doi:10.1038/s41467-021-27685-8 · Cited by 40

An expansion of the non-coding genome and its regulatory potential underlies vertebrate neuronal diversity

Closser, M., Guo, Y., Wang, P., Patel, T., Jang, S., Hammelman, J., de Nooij, J. C., Kopunova, R., Mazzoni, E. O., Ruan, Y., et al. (2021) · Neuron · doi:10.1016/j.neuron.2021.10.014 · Cited by 41

Learning the histone codes with large genomic windows and three-dimensional chromatin interactions using transformer

Lee, D., Yang, J., & Kim, S. (2022) · Nature Communications · doi:10.1038/s41467-022-34152-5 · Cited by 40

Systematic discovery and functional dissection of enhancers needed for cancer cell fitness and proliferation

Chen, P. B., Fiaux, P. C., Zhang, K., Li, B., Kubo, N., Jiang, S., Hu, R., Rooholfada, E., Wu, S., Wang, M., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.111630 · Cited by 41

Revisiting 3D chromatin architecture in cancer development and progression

Feng, Y., & Pauklin, S. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa747 · Cited by 36

Antimicrobial resistance in fish pathogens and alternative risk mitigation strategies

Deekshit, V. K., Maiti, B., Kumar, B. K., Kotian, A., Pinto, G. V., Bondad‐Reantaso, M. G., Karunasagar, I., & Karunasagar, I. (2022) · Reviews in Aquaculture · doi:10.1111/raq.12715 · Cited by 35

Prion-like domain mediated phase separation of ARID1A promotes oncogenic potential of Ewing’s sarcoma

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Genomic Evidence Supports the Recognition of Endometriosis as an Inflammatory Systemic Disease and Reveals Disease-Specific Therapeutic Potentials of Targeting Neutrophil Degranulation

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