Approaches for establishing the function of regulatory genetic variants involved in disease

GWAS and drug targets

(2014) Chen Cao et al.   BMC GENOMICS

Functional annotation signatures of disease susceptibility loci improve SNP association analysis

(2014) Edwin S Iversen et al.   BMC GENOMICS

Leveraging Cross-Species Transcription Factor Binding Site Patterns: From Diabetes Risk Loci to Disease Mechanisms

(2014) Melina Claussnitzer et al.   CELL

Determining causality and consequence of expression quantitative trait loci

(2014) A. Battle et al.   HUMAN GENETICS

Detection and replication of epistasis influencing transcription in humans

(2014) Gibran Hemani et al.   NATURE

Genetics of single-cell protein abundance variation in large yeast populations

(2014) Frank W. Albert et al.   NATURE

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

A promoter-level mammalian expression atlas

(2014)   NATURE

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

(2014) Scott Smemo et al.   NATURE

A general framework for estimating the relative pathogenicity of human genetic variants

(2014) Martin Kircher et al.   NATURE GENETICS

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

(2014) Jim R Hughes et al.   NATURE GENETICS

An atlas of genetic influences on human blood metabolites

(2014) So-Youn Shin et al.   NATURE GENETICS

Heritability and genomics of gene expression in peripheral blood

(2014) Fred A Wright et al.   NATURE GENETICS

Efficient genome modification by CRISPR-Cas9 nickase with minimal off-target effects

(2014) Bin Shen et al.   NATURE METHODS

Defining functional DNA elements in the human genome

(2014) M. Kellis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Protein Quantitative Trait Loci Identify Novel Candidates Modulating Cellular Response to Chemotherapy

(2014) Amy L. Stark 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

8.2% of the Human Genome Is Constrained: Variation in Rates of Turnover across Functional Element Classes in the Human Lineage

(2014) Chris M. Rands et al.   PLoS Genetics

A Polymorphic p53 Response Element in KIT Ligand Influences Cancer Risk and Has Undergone Natural Selection

(2013) Jorge Zeron-Medina et al.   CELL

Mapping Human Epigenomes

(2013) Chloe M. Rivera et al.   CELL

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

Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals

(2013) A. Battle et al.   GENOME RESEARCH

BLUEPRINT: mapping human blood cell epigenomes

(2013) J. H. A. Martens et al.   HAEMATOLOGICA

Sex- and age-interacting eQTLs in human complex diseases

(2013) Chen Yao et al.   HUMAN MOLECULAR GENETICS

Impacts of Variation in the Human Genome on Gene Regulation

(2013) Rajini R. Haraksingh et al.   JOURNAL OF MOLECULAR BIOLOGY

Proteomic Studies Related to Genetic Determinants of Variability in Protein Concentrations

(2013) Péter Horvatovich et al.   JOURNAL OF PROTEOME RESEARCH

Genetics of rheumatoid arthritis contributes to biology and drug discovery

(2013) Yukinori Okada et al.   NATURE

Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen et al.   NATURE

DNase I–hypersensitive exons colocalize with promoters and distal regulatory elements

(2013) Tim R Mercer et al.   NATURE GENETICS

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

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

Genome engineering using the CRISPR-Cas9 system

(2013) F Ann Ran et al.   Nature Protocols

The UCSC Genome Browser database: 2014 update

(2013) Donna Karolchik et al.   NUCLEIC ACIDS RESEARCH

Extensive Variation in Chromatin States Across Humans

(2013) M. Kasowski et al.   SCIENCE

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

(2013) H. Kilpinen et al.   SCIENCE

Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution

(2013) A. B. Stergachis et al.   SCIENCE

Identification of Genetic Variants That Affect Histone Modifications in Human Cells

(2013) G. McVicker et al.   SCIENCE

An Erythroid Enhancer of BCL11A Subject to Genetic Variation Determines Fetal Hemoglobin Level

(2013) D. E. Bauer et al.   SCIENCE

RNA-Guided Human Genome Engineering via Cas9

(2013) P. Mali et al.   SCIENCE

Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells

(2013) Ophir Shalem et al.   SCIENCE

Genetic Screens in Human Cells Using the CRISPR-Cas9 System

(2013) Tim Wang et al.   SCIENCE

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

Interpreting the Epstein-Barr Virus (EBV) Epigenome Using High-Throughput Data

(2013) Aaron Arvey et al.   Viruses-Basel

Epigenetic analysis leads to identification of HNF1B as a subtype-specific susceptibility gene for ovarian cancer

(2013) Hui Shen et al.   Nature Communications

The Next Generation of Transcription Factor Binding Site Prediction

(2013) Anthony Mathelier et al.   PLoS Computational Biology

Disentangling the Many Layers of Eukaryotic Transcriptional Regulation

(2012) Katherine M. Lelli et al.   Annual Review of 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

Identification of cis-regulatory variation influencing protein abundance levels in human plasma

(2012) Anbarasu Lourdusamy et al.   HUMAN MOLECULAR GENETICS

Resolving the variable genome and epigenome in human disease

(2012) J. C. Knight   JOURNAL OF INTERNAL MEDICINE

TNF receptor 1 genetic risk mirrors outcome of anti-TNF therapy in multiple sclerosis

(2012) Adam P. Gregory et al.   NATURE

DNase I sensitivity QTLs are a major determinant of human expression variation

(2012) Jacob F. Degner et al.   NATURE

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Interpreting noncoding genetic variation in complex traits and human disease

(2012) Lucas D Ward et al.   NATURE BIOTECHNOLOGY

Use of genome-wide association studies for drug repositioning

(2012) Philippe Sanseau et al.   NATURE BIOTECHNOLOGY

Common genetic variants at the 11q13.3 renal cancer susceptibility locus influence binding of HIF to an enhancer of cyclin D1 expression

(2012) Johannes Schödel et al.   NATURE GENETICS

Genetics of gene expression in primary immune cells identifies cell type–specific master regulators and roles of HLA alleles

(2012) Benjamin P Fairfax et al.   NATURE GENETICS

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

(2012) Gosia Trynka et al.   NATURE GENETICS

ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions

(2012) Terrence S. Furey   NATURE REVIEWS GENETICS

Genomewide Association Studies and Common Disease — Realizing Clinical Utility

(2012) Lars Fugger et al.   NEW ENGLAND JOURNAL OF MEDICINE

Evidence for additive and interaction effects of host genotype and infection in malaria

(2012) Y. Idaghdour et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

(2012) M. Jinek et al.   SCIENCE

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Genomic modulators of the immune response

(2012) Julian C. Knight   TRENDS IN GENETICS

Patterns of Cis Regulatory Variation in Diverse Human Populations

(2012) Barbara E. Stranger et al.   PLoS Genetics

The effects of EBV transformation on gene expression levels and methylation profiles

(2011) Minal Çalışkan et al.   HUMAN MOLECULAR GENETICS

A synonymous variant in IRGM alters a binding site for miR-196 and causes deregulation of IRGM-dependent xenophagy in Crohn's disease

(2011) Patrick Brest et al.   NATURE GENETICS

Identification of an imprinted master trans regulator at the KLF14 locus related to multiple metabolic phenotypes

(2011) Kerrin S Small et al.   NATURE GENETICS

The Architecture of Gene Regulatory Variation across Multiple Human Tissues: The MuTHER Study

(2011) Alexandra C. Nica et al.   PLoS Genetics

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor

(2010) William McLaren et al.   BIOINFORMATICS

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

(2010) Kiran Musunuru et al.   NATURE

Biological, clinical and population relevance of 95 loci for blood lipids

(2010) Tanya M. Teslovich et al.   NATURE

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

Overexpression of Fto leads to increased food intake and results in obesity

(2010) Chris Church et al.   NATURE GENETICS

Variation in Transcription Factor Binding Among Humans

(2010) M. Kasowski et al.   SCIENCE

Abundant Quantitative Trait Loci Exist for DNA Methylation and Gene Expression in Human Brain

(2010) J. Raphael Gibbs 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

Genetic analysis of radiation-induced changes in human gene expression

(2009) Denis A. Smirnov et al.   NATURE

Inactivation of the Fto gene protects from obesity

(2009) Julia Fischer et al.   NATURE

Geographical genomics of human leukocyte gene expression variation in southern Morocco

(2009) Youssef Idaghdour et al.   NATURE GENETICS

The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in colorectal cancer

(2009) Mark M Pomerantz et al.   NATURE GENETICS

Global patterns of cis variation in human cells revealed by high-density allelic expression analysis

(2009) Bing Ge et al.   NATURE GENETICS

A Simple Cipher Governs DNA Recognition by TAL Effectors

(2009) M. J. Moscou et al.   SCIENCE

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

(2009) A. S. Dimas et al.   SCIENCE

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

(2009) E. Lieberman-Aiden et al.   SCIENCE

Genome-wide analysis of transcript isoform variation in humans

(2008) Tony Kwan et al.   NATURE GENETICS