Making sense of GWAS: using epigenomics and genome engineering to understand the functional relevance of SNPs in non-coding regions of the human genome

Leveraging Functional-Annotation Data in Trans-ethnic Fine-Mapping Studies

(2015) Gleb Kichaev et al.   AMERICAN JOURNAL OF HUMAN GENETICS

GREGOR: evaluating global enrichment of trait-associated variants in epigenomic features using a systematic, data-driven approach

(2015) Ellen M. Schmidt et al.   BIOINFORMATICS

Association of seven thrombotic pathway gene CpG-SNPs with coronary heart disease

(2015) Huadan Ye et al.   BIOMEDICINE & PHARMACOTHERAPY

Engineering Complex Synthetic Transcriptional Programs with CRISPR RNA Scaffolds

(2015) Jesse G. Zalatan et al.   CELL

A CTCF Code for 3D Genome Architecture

(2015) Michael H. Nichols et al.   CELL

CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function

(2015) Ya Guo et al.   CELL

The Role of Chromosome Domains in Shaping the Functional Genome

(2015) Tom Sexton et al.   CELL

Unraveling determinants of transcription factor binding outside the core binding site

(2015) Michal Levo et al.   GENOME RESEARCH

Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators

(2015) Lauren R. Polstein et al.   GENOME RESEARCH

A widespread role of the motif environment in transcription factor binding across diverse protein families

(2015) Iris Dror et al.   GENOME RESEARCH

Integration of multiethnic fine-mapping and genomic annotation to prioritize candidate functional SNPs at prostate cancer susceptibility regions

(2015) Ying Han et al.   HUMAN MOLECULAR GENETICS

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

(2015) Ali Amin Al Olama et al.   HUMAN MOLECULAR GENETICS

Strategies for fine-mapping complex traits

(2015) Sarah L. Spain et al.   HUMAN MOLECULAR GENETICS

Selective Distal Enhancer Control of theMmp13Gene Identified through Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) Genomic Deletions

(2015) Mark B. Meyer et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

15 TFBSshape: a motif database for DNA shape features of transcription factor binding sites

(2015) Lin Yang et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Choosing the Right Tool for the Job: RNAi, TALEN, or CRISPR

(2015) Michael Boettcher et al.   MOLECULAR CELL

Convergence of Developmental and Oncogenic Signaling Pathways at Transcriptional Super-Enhancers

(2015) Denes Hnisz et al.   MOLECULAR CELL

BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis

(2015) Matthew C. Canver et al.   NATURE

Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex

(2015) Silvana Konermann et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers

(2015) Isaac B Hilton et al.   NATURE BIOTECHNOLOGY

Fine mapping of type 1 diabetes susceptibility loci and evidence for colocalization of causal variants with lymphoid gene enhancers

(2015) Suna Onengut-Gumuscu et al.   NATURE GENETICS

Partitioning heritability by functional annotation using genome-wide association summary statistics

(2015) Hilary K Finucane et al.   NATURE GENETICS

Functional annotation of native enhancers with a Cas9–histone demethylase fusion

(2015) Nicola A Kearns et al.   NATURE METHODS

Functional footprinting of regulatory DNA

(2015) Jeff Vierstra et al.   NATURE METHODS

The role of regulatory variation in complex traits and disease

(2015) Frank W. Albert et al.   NATURE REVIEWS GENETICS

FTO Obesity Variant Circuitry and Adipocyte Browning in Humans

(2015) Melina Claussnitzer et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

(2015) et al.   SCIENCE

Generation of Isogenic Human iPS Cell Line Precisely Corrected by Genome Editing Using the CRISPR/Cas9 System

(2015) Benjamin Grobarczyk et al.   Stem Cell Reviews and Reports

A unified architecture of transcriptional regulatory elements

(2015) Robin Andersson et al.   TRENDS IN GENETICS

Efficient inversions and duplications of mammalian regulatory DNA elements and gene clusters by CRISPR/Cas9

(2015) Jinhuan Li et al.   Journal of Molecular Cell Biology

Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci

(2015) Roland Jäger et al.   Nature Communications

Functional annotation of HOT regions in the human genome: implications for human disease and cancer

(2015) Hao Li et al.   Scientific Reports

Deletions, Inversions, Duplications: Engineering of Structural Variants using CRISPR/Cas in Mice

(2015) Katerina Kraft et al.   Cell Reports

Expression quantitative trait locus analysis for translational medicine

(2015) Greg Gibson et al.   Genome Medicine

The Genetic and Mechanistic Basis for Variation in Gene Regulation

(2015) Athma A. Pai et al.   PLoS Genetics

Inferring regulatory element landscapes and transcription factor networks from cancer methylomes

(2015) Lijing Yao et al.   GENOME BIOLOGY

Generation of Isogenic Human iPS Cell Line Precisely Corrected by Genome Editing Using the CRISPR/Cas9 System

(2015) Benjamin Grobarczyk et al.   Stem Cell Reviews and Reports

Enlight: web-based integration of GWAS results with biological annotations

(2014) Y. Guo et al.   BIOINFORMATICS

Development and Applications of CRISPR-Cas9 for Genome Engineering

(2014) Patrick D. Hsu et al.   CELL

Enhancer-targeted genome editing selectively blocks innate resistance to oncokinase inhibition

(2014) D. E. Webster et al.   GENOME RESEARCH

Characterization of Genomic Deletion Efficiency Mediated by Clustered Regularly Interspaced Palindromic Repeats (CRISPR)/Cas9 Nuclease System in Mammalian Cells

(2014) Matthew C. Canver et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Engineering synthetic TALE and CRISPR/Cas9 transcription factors for regulating gene expression

(2014) Ami M. Kabadi et al.   METHODS

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

CRISPR-mediated direct mutation of cancer genes in the mouse liver

(2014) Wen Xue et al.   NATURE

Obesity-associated variants within FTO form long-range functional connections with IRX3

(2014) Scott Smemo et al.   NATURE

Genetic and epigenetic fine mapping of causal autoimmune disease variants

(2014) Kyle Kai-How Farh et al.   NATURE

CRISPR-Cas systems for editing, regulating and targeting genomes

(2014) Jeffry D Sander et al.   NATURE BIOTECHNOLOGY

Genome editing with Cas9 in adult mice corrects a disease mutation and phenotype

(2014) Hao Yin et al.   NATURE BIOTECHNOLOGY

Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment

(2014) Jim R Hughes et al.   NATURE GENETICS

Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility

(2014) Anubha Mahajan et al.   NATURE GENETICS

Genetic variability in the regulation of gene expression in ten regions of the human brain

(2014) Adaikalavan Ramasamy et al.   NATURE NEUROSCIENCE

A guide to genome engineering with programmable nucleases

(2014) Hyongbum Kim et al.   NATURE REVIEWS GENETICS

CTCF: an architectural protein bridging genome topology and function

(2014) Chin-Tong Ong et al.   NATURE REVIEWS GENETICS

Comparison of TALE designer transcription factors and the CRISPR/dCas9 in regulation of gene expression by targeting enhancers

(2014) Xuefei Gao et al.   NUCLEIC ACIDS RESEARCH

CRISPR Reveals a Distal Super-Enhancer Required for Sox2 Expression in Mouse Embryonic Stem Cells

(2014) Yan Li et al.   PLoS One

Multiple Functional Risk Variants in a SMAD7 Enhancer Implicate a Colorectal Cancer Risk Haplotype

(2014) Barbara K. Fortini et al.   PLoS One

Impact of regulatory variation from RNA to protein

(2014) A. Battle et al.   SCIENCE

Cas9 Targeting and the CRISPR Revolution

(2014) R. Barrangou   SCIENCE

Prevention of muscular dystrophy in mice by CRISPR/Cas9-mediated editing of germline DNA

(2014) C. Long et al.   SCIENCE

Common Genetic Variants Modulate Pathogen-Sensing Responses in Human Dendritic Cells

(2014) M. N. Lee et al.   SCIENCE

Innate Immune Activity Conditions the Effect of Regulatory Variants upon Monocyte Gene Expression

(2014) B. P. Fairfax et al.   SCIENCE

Functional annotation of colon cancer risk SNPs

(2014) Lijing Yao et al.   Nature Communications

Linkage of DNA Methylation Quantitative Trait Loci to Human Cancer Risk

(2014) Holger Heyn et al.   Cell Reports

Enhancer variants: evaluating functions in common disease

(2014) Olivia Corradin et al.   Genome Medicine

Comprehensive Functional Annotation of 77 Prostate Cancer Risk Loci

(2014) Dennis J. Hazelett et al.   PLoS Genetics

Quantitative Genetics of CTCF Binding Reveal Local Sequence Effects and Different Modes of X-Chromosome Association

(2014) Zhihao Ding et al.   PLoS Genetics

Methylation QTLs Are Associated with Coordinated Changes in Transcription Factor Binding, Histone Modifications, and Gene Expression Levels

(2014) Nicholas E. Banovich et al.   PLoS Genetics

Beyond GWASs: Illuminating the Dark Road from Association to Function

(2013) Stacey L. Edwards et al.   AMERICAN JOURNAL OF HUMAN GENETICS

One-Step Generation of Mice Carrying Mutations in Multiple Genes by CRISPR/Cas-Mediated Genome Engineering

(2013) Haoyi Wang et al.   CELL

One-Step Generation of Mice Carrying Reporter and Conditional Alleles by CRISPR/Cas-Mediated Genome Engineering

(2013) Hui Yang et al.   CELL

Mapping Human Epigenomes

(2013) Chloe M. Rivera et al.   CELL

Multiplexed activation of endogenous genes by CRISPR-on, an RNA-guided transcriptional activator system

(2013) Albert W Cheng et al.   CELL RESEARCH

Functional Repair of CFTR by CRISPR/Cas9 in Intestinal Stem Cell Organoids of Cystic Fibrosis Patients

(2013) Gerald Schwank et al.   Cell Stem Cell

Identification of CpG-SNPs associated with type 2 diabetes and differential DNA methylation in human pancreatic islets

(2013) T. A. Dayeh et al.   DIABETOLOGIA

Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits

(2013) O. Corradin et al.   GENOME RESEARCH

Genetic associations with expression for genes implicated in GWAS studies for atherosclerotic cardiovascular disease and blood phenotypes

(2013) Xiaoling Zhang et al.   HUMAN MOLECULAR GENETICS

Cross-talk between Site-specific Transcription Factors and DNA Methylation States

(2013) Adam Blattler et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Effect of natural genetic variation on enhancer selection and function

(2013) S. Heinz et al.   NATURE

Charting a dynamic DNA methylation landscape of the human genome

(2013) Michael J. Ziller et al.   NATURE

DNA targeting specificity of RNA-guided Cas9 nucleases

(2013) Patrick D Hsu et al.   NATURE BIOTECHNOLOGY

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

(2013) Kyriaki Michailidou et al.   NATURE GENETICS

Systematic identification of trans eQTLs as putative drivers of known disease associations

(2013) Harm-Jan Westra et al.   NATURE GENETICS

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

TFBSshape: a motif database for DNA shape features of transcription factor binding sites

(2013) Lin Yang et al.   NUCLEIC ACIDS RESEARCH

GWAS3D: detecting human regulatory variants by integrative analysis of genome-wide associations, chromosome interactions and histone modifications

(2013) Mulin Jun Li et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Danielle Welter et al.   NUCLEIC ACIDS RESEARCH

CTCF: the protein, the binding partners, the binding sites and their chromatin loops

(2013) S. J. B. Holwerda et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Coordinated Effects of Sequence Variation on DNA Binding, Chromatin Structure, and Transcription

(2013) H. Kilpinen et al.   SCIENCE

Identification of Genetic Variants That Affect Histone Modifications in Human Cells

(2013) G. McVicker et al.   SCIENCE

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

Efficiency of trans-ethnic genome-wide meta-analysis and fine-mapping

(2012) Rick Twee-Hee Ong et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Gene Overexpression: Uses, Mechanisms, and Interpretation

(2012) G. Prelich   GENETICS

Linking disease associations with regulatory information in the human genome

(2012) M. A. Schaub et al.   GENOME RESEARCH

Annotation of functional variation in personal genomes using RegulomeDB

(2012) A. P. Boyle et al.   GENOME RESEARCH

Integrative functional genomics identifies an enhancer looping to the SOX9 gene disrupted by the 17q24.3 prostate cancer risk locus

(2012) X. Zhang et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

(2012) Alexandre Melnikov et al.   NATURE BIOTECHNOLOGY

A bioinformatics method identifies prominent off-targeted transcripts in RNAi screens

(2012) Frederic D Sigoillot et al.   NATURE METHODS

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

Functions of DNA methylation: islands, start sites, gene bodies and beyond

(2012) Peter A. Jones   NATURE REVIEWS GENETICS

FunciSNP: an R/bioconductor tool integrating functional non-coding data sets with genetic association studies to identify candidate regulatory SNPs

(2012) Simon G. Coetzee et al.   NUCLEIC ACIDS RESEARCH

Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium

(2012) J. Wang et al.   NUCLEIC ACIDS RESEARCH

Mice Lacking a Myc Enhancer That Includes Human SNP rs6983267 Are Resistant to Intestinal Tumors

(2012) I. K. Sur et al.   SCIENCE

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

The Metabochip, a Custom Genotyping Array for Genetic Studies of Metabolic, Cardiovascular, and Anthropometric Traits

(2012) Benjamin F. Voight et al.   PLoS Genetics

Dominantly Inherited Constitutional Epigenetic Silencing of MLH1 in a Cancer-Affected Family Is Linked to a Single Nucleotide Variant within the 5′UTR

(2011) Megan P. Hitchins et al.   CANCER CELL

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease

(2011) Gosia Trynka et al.   NATURE GENETICS

Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina–associated domains

(2011) Benjamin P Berman et al.   NATURE GENETICS

Principles for the post-GWAS functional characterization of cancer risk loci

(2011) Matthew L Freedman et al.   NATURE GENETICS

Enhancer function: new insights into the regulation of tissue-specific gene expression

(2011) Chin-Tong Ong et al.   NATURE REVIEWS GENETICS

HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants

(2011) L. D. Ward et al.   NUCLEIC ACIDS RESEARCH

Comparative Analysis of Proteome and Transcriptome Variation in Mouse

(2011) Anatole Ghazalpour et al.   PLoS Genetics

DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines

(2011) Jordana T Bell et al.   GENOME BIOLOGY

MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes

(2010) Yun Li et al.   GENETIC EPIDEMIOLOGY

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells

(2010) A. P. Boyle et al.   GENOME RESEARCH

From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus

(2010) Kiran Musunuru et al.   NATURE

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

Heritable Individual-Specific and Allele-Specific Chromatin Signatures in Humans

(2010) R. McDaniell et al.   SCIENCE

Liver and Adipose Expression Associated SNPs Are Enriched for Association to Type 2 Diabetes

(2010) Hua Zhong et al.   PLoS Genetics

Trait-Associated SNPs Are More Likely to Be eQTLs: Annotation to Enhance Discovery from GWAS

(2010) Dan L. Nicolae et al.   PLoS Genetics

Genotype Imputation

(2009) Yun Li et al.   Annual Review of Genomics and Human Genetics

Common Regulatory Variation Impacts Gene Expression in a Cell Type-Dependent Manner

(2009) A. S. Dimas et al.   SCIENCE

A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies

(2009) Bryan N. Howie et al.   PLoS Genetics

Genetics of gene expression and its effect on disease

(2008) Valur Emilsson et al.   NATURE