An Osteoporosis Risk SNP at 1p36.12 Acts as an Allele-Specific Enhancer to Modulate LINC00339 Expression via Long-Range Loop Formation.

[1]  Jacqueline K. White,et al.  Identification of 153 new loci associated with heel bone mineral density and functional involvement of GPC6 in osteoporosis , 2017, Nature Genetics.

[2]  Jesse M. Engreitz,et al.  A Genetic Variant Associated with Five Vascular Diseases Is a Distal Regulator of Endothelin-1 Gene Expression , 2017, Cell.

[3]  Tie-Lin Yang,et al.  A functional SNP regulated by miR‐196a‐3p in the 3′UTR of FGF2 is associated with bone mineral density in the Chinese population , 2017, Human mutation.

[4]  Olena O Yavorska,et al.  MendelianRandomization: an R package for performing Mendelian randomization analyses using summarized data , 2017, International journal of epidemiology.

[5]  Jordan A. Ramilowski,et al.  An atlas of human long non-coding RNAs with accurate 5′ ends , 2017, Nature.

[6]  Emmanouil T. Dermitzakis,et al.  The non-coding variant rs1800734 enhances DCLK3 expression through long-range interaction and promotes colorectal cancer progression , 2017, Nature Communications.

[7]  Nikolaos A Patsopoulos,et al.  Limited statistical evidence for shared genetic effects of eQTLs and autoimmune disease-associated loci in three major immune cell types , 2017, Nature Genetics.

[8]  Judith A. Blake,et al.  Mouse Genome Database (MGD)-2017: community knowledge resource for the laboratory mouse , 2016, Nucleic Acids Res..

[9]  Jonathan M. Cairns,et al.  Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters , 2016, Cell.

[10]  P. Visscher,et al.  Endometriosis risk alleles at 1p36.12 act through inverse regulation of CDC42 and LINC00339. , 2016, Human molecular genetics.

[11]  Fredrick R. Schumacher,et al.  Modeling disease risk through analysis of physical interactions between genetic variants within chromatin regulatory circuitry , 2016, Nature Genetics.

[12]  Dorota H. Sendorek,et al.  Modulation of long noncoding RNAs by risk SNPs underlying genetic predispositions to prostate cancer , 2016, Nature Genetics.

[13]  P. Visscher,et al.  Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets , 2016, Nature Genetics.

[14]  M. Seldin,et al.  A Common Variant in CLDN14 is Associated with Primary Biliary Cirrhosis and Bone Mineral Density , 2016, Scientific Reports.

[15]  Dariusz M Plewczynski,et al.  CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription , 2015, Cell.

[16]  Manolis Kellis,et al.  HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease , 2015, Nucleic Acids Res..

[17]  Vladimir B. Bajic,et al.  HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models , 2015, Nucleic Acids Res..

[18]  David J. Arenillas,et al.  JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles , 2015, Nucleic Acids Res..

[19]  Andrew C. Wood,et al.  Genetic predisposition to neuroblastoma mediated by a LMO1 super-enhancer polymorphism , 2015, Nature.

[20]  Ji-Gang Zhang,et al.  Genome‐Wide Survey of Runs of Homozygosity Identifies Recessive Loci for Bone Mineral Density in Caucasian and Chinese Populations , 2015, Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research.

[21]  Gabor T. Marth,et al.  An integrated map of structural variation in 2,504 human genomes , 2015, Nature.

[22]  Beth Wilmot,et al.  Edinburgh Explorer Whole-genome sequencing identifies EN1 as a determinant of bone density and fracture , 2022 .

[23]  Philip A. Ewels,et al.  Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C , 2015, Nature Genetics.

[24]  Yurii B. Shvetsov,et al.  Identification of six new susceptibility loci for invasive epithelial ovarian cancer , 2015, Nature Genetics.

[25]  Neva C. Durand,et al.  A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping , 2014, Cell.

[26]  William Stafford Noble,et al.  Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes , 2014, Nature Methods.

[27]  Junhui Ge,et al.  Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus , 2014, Cell Research.

[28]  P. Spanheimer,et al.  Sumoylation pathway is required to maintain the basal breast cancer subtype. , 2014, Cancer cell.

[29]  Matthew A. Hibbs,et al.  Phenotypic Dissection of Bone Mineral Density Reveals Skeletal Site Specificity and Facilitates the Identification of Novel Loci in the Genetic Regulation of Bone Mass Attainment , 2014, PLoS genetics.

[30]  D. Graves,et al.  Non-canonical Wnt4 prevents skeletal aging and inflammation by inhibiting NF-κB , 2014, Nature Medicine.

[31]  H. Deng,et al.  Genome-wide Association Studies for Osteoporosis: A 2013 Update , 2014, Journal of bone metabolism.

[32]  A. Uitterlinden,et al.  Multistage genome-wide association meta-analyses identified two new loci for bone mineral density. , 2014, Human molecular genetics.

[33]  Junhui Ge,et al.  Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus , 2014, Cell Research.

[34]  Jesse R. Dixon,et al.  Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells , 2013, Proceedings of the National Academy of Sciences.

[35]  Peggy Hall,et al.  The NHGRI GWAS Catalog, a curated resource of SNP-trait associations , 2013, Nucleic Acids Res..

[36]  Yan Li,et al.  A high-resolution map of three-dimensional chromatin interactome in human cells , 2013, Nature.

[37]  M. Greenblatt,et al.  Mitogen-activated protein kinase pathways in osteoblasts. , 2013, Annual review of cell and developmental biology.

[38]  Pedro G. Ferreira,et al.  Transcriptome and genome sequencing uncovers functional variation in humans , 2013, Nature.

[39]  D. Koller,et al.  Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals , 2013, Genome research.

[40]  Ellen T. Gelfand,et al.  The Genotype-Tissue Expression (GTEx) project , 2013, Nature Genetics.

[41]  J. Wysocka,et al.  Modification of enhancer chromatin: what, how, and why? , 2013, Molecular cell.

[42]  R. Chettier,et al.  Genome-Wide Association Study Link Novel Loci to Endometriosis , 2013, PloS one.

[43]  Y. J. Kim,et al.  Meta-analysis identifies a MECOM gene as a novel predisposing factor of osteoporotic fracture , 2013, Journal of Medical Genetics.

[44]  J. Kocher,et al.  CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model , 2013, Nucleic acids research.

[45]  Mikhail Pachkov,et al.  SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates , 2012, Nucleic Acids Res..

[46]  Bronwen L. Aken,et al.  GENCODE: The reference human genome annotation for The ENCODE Project , 2012, Genome research.

[47]  E. Furlong,et al.  Transcription factors: from enhancer binding to developmental control , 2012, Nature Reviews Genetics.

[48]  Tim D. Spector,et al.  Genetics of osteoporosis from genome-wide association studies: advances and challenges , 2012, Nature Reviews Genetics.

[49]  Raymond K. Auerbach,et al.  An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.

[50]  A. Aszódi,et al.  Deletion of cdc42 in osteoblast progenitors leads to increased adipocyte differentiation and decreased bone formation , 2012 .

[51]  Jesse R. Dixon,et al.  Topological Domains in Mammalian Genomes Identified by Analysis of Chromatin Interactions , 2012, Nature.

[52]  A. Aiba,et al.  Cdc42 is required for chondrogenesis and interdigital programmed cell death during limb development , 2012, Mechanisms of Development.

[53]  Jun Yu Li,et al.  Genetic variants in the SOX6 gene are associated with bone mineral density in both Caucasian and Chinese populations , 2012, Osteoporosis International.

[54]  M. Esteller Non-coding RNAs in human disease , 2011, Nature Reviews Genetics.

[55]  Chee Seng Chan,et al.  CTCF-Mediated Functional Chromatin Interactome in Pluripotent Cells , 2011, Nature Genetics.

[56]  P. Majumder,et al.  CTCF Controls Expression and Chromatin Architecture of the Human Major Histocompatibility Complex Class II Locus , 2010, Molecular and Cellular Biology.

[57]  W. Zou,et al.  Cdc42 regulates bone modeling and remodeling in mice by modulating RANKL/M-CSF signaling and osteoclast polarization. , 2010, The Journal of clinical investigation.

[58]  Nicole Soranzo,et al.  An Integration of Genome-Wide Association Study and Gene Expression Profiling to Prioritize the Discovery of Novel Susceptibility Loci for Osteoporosis-Related Traits , 2010, PLoS genetics.

[59]  E. Dermitzakis,et al.  Candidate Causal Regulatory Effects by Integration of Expression QTLs with Complex Trait Genetic Associations , 2010, PLoS genetics.

[60]  Yurii S. Aulchenko,et al.  Twenty bone mineral density loci identified by large-scale meta-analysis of genome-wide association studies , 2009, Nature Genetics.

[61]  A. Uitterlinden,et al.  Tissue Effect on Genetic Control of Transcript Isoform Variation , 2009, PLoS genetics.

[62]  Mikael Bodén,et al.  MEME Suite: tools for motif discovery and searching , 2009, Nucleic Acids Res..

[63]  K. Frazer,et al.  Human genetic variation and its contribution to complex traits , 2009, Nature Reviews Genetics.

[64]  Kari Stefansson,et al.  Multiple genetic loci for bone mineral density and fractures. , 2008, The New England journal of medicine.

[65]  A Hofman,et al.  Bone mineral density, osteoporosis, and osteoporotic fractures: a genome-wide association study , 2008, The Lancet.

[66]  B. Chadwick,et al.  The insulator factor CTCF controls MHC class II gene expression and is required for the formation of long-distance chromatin interactions , 2008, The Journal of experimental medicine.

[67]  Manuel A. R. Ferreira,et al.  PLINK: a tool set for whole-genome association and population-based linkage analyses. , 2007, American journal of human genetics.

[68]  Wouter de Laat,et al.  CTCF mediates long-range chromatin looping and local histone modification in the beta-globin locus. , 2006, Genes & development.

[69]  A. Silman,et al.  Predictive Value of BMD for Hip and Other Fractures , 2005, Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research.

[70]  P. Donnelly,et al.  The Fine-Scale Structure of Recombination Rate Variation in the Human Genome , 2004, Science.

[71]  S. Ortolani,et al.  Genetics of osteoporosis , 1994, Calcified Tissue International.

[72]  R. Tjian,et al.  Analysis of the DNA-binding and activation properties of the human transcription factor AP-2. , 1991, Genes & development.

[73]  R. Tjian,et al.  Positive and negative regulation of transcription in vitro: Enhancer-binding protein AP-2 is inhibited by SV40 T antigen , 1987, Cell.

[74]  Edward Klorman,et al.  Web Resources , 2019, Istanbul.

[75]  Li Teng,et al.  4DGenome: a comprehensive database of chromatin interactions , 2015, Bioinform..

[76]  Daniel L. Koller,et al.  Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture , 2012, Nature Genetics.

[77]  Ira M. Hall,et al.  BEDTools: a flexible suite of utilities for comparing genomic features , 2010, Bioinform..

[78]  Bjarni V. Halldórsson,et al.  New sequence variants associated with bone mineral density , 2009, Nature Genetics.

[79]  C. Cooper,et al.  Guidelines for diagnosis and management of osteoporosis , 2005, Osteoporosis International.