DNA methylation QTL mapping across diverse human tissues provides molecular links between genetic variation and complex traits

Genetic variation influencing DNA methylation provides insights into molecular mechanisms regulating genomic function

(2022) Johann S. Hawe et al.   NATURE GENETICS

Identification of rare and common regulatory variants in pluripotent cells using population-scale transcriptomics

(2021) Marc Jan Bonder et al.   NATURE GENETICS

A fast and efficient colocalization algorithm for identifying shared genetic risk factors across multiple traits

(2021) Christopher N. Foley et al.   Nature Communications

Bisulfite-free epigenomics and genomics of single cells through methylation-sensitive restriction

(2021) Christoph Niemöller et al.   Communications Biology

Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing

(2021) James K. Nuñez et al.   CELL

Genome-wide enhancer maps link risk variants to disease genes

(2021) Joseph Nasser et al.   NATURE

Uncovering genetic mechanisms of hypertension through multi-omic analysis of the kidney

(2021) James M. Eales et al.   NATURE GENETICS

A compendium of uniformly processed human gene expression and splicing quantitative trait loci

(2021) Nurlan Kerimov et al.   NATURE GENETICS

Genomic and phenotypic insights from an atlas of genetic effects on DNA methylation

(2021) Josine L. Min et al.   NATURE GENETICS

Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression

(2021) Urmo Võsa et al.   NATURE GENETICS

Multi-omics integration analysis identifies novel genes for alcoholism with potential overlap with neurodegenerative diseases

(2021) Manav Kapoor et al.   Nature Communications

Genome-wide sequencing-based identification of methylation quantitative trait loci and their role in schizophrenia risk

(2021) Kira A. Perzel Mandell et al.   Nature Communications

Multi-omics colocalization with genome-wide association studies reveals a context-specific genetic mechanism at a childhood onset asthma risk locus

(2021) Marcus M. Soliai et al.   Genome Medicine

From GWAS to Function: Using Functional Genomics to Identify the Mechanisms Underlying Complex Diseases

(2020) Eddie Cano-Gamez et al.   Frontiers in Genetics

Expression Quantitative Trait Methylation Analysis Reveals Methylomic Associations With Gene Expression in Childhood Asthma

(2020) Soyeon Kim et al.   CHEST

A Quantitative Proteome Map of the Human Body

(2020) Lihua Jiang et al.   CELL

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

(2020) Maya Ghoussaini et al.   NUCLEIC ACIDS RESEARCH

The GTEx Consortium atlas of genetic regulatory effects across human tissues

(2020)   SCIENCE

Where Are the Disease-Associated eQTLs?

(2020) Benjamin D. Umans et al.   TRENDS IN GENETICS

PhenomeXcan: Mapping the genome to the phenome through the transcriptome

(2020) Milton Pividori et al.   Science Advances

Probabilistic colocalization of genetic variants from complex and molecular traits: promise and limitations

(2020) Abhay Hukku et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Integrative analysis of gene expression, DNA methylation, physiological traits, and genetic variation in human skeletal muscle

(2019) D. Leland Taylor et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of DNA motifs that regulate DNA methylation

(2019) Mengchi Wang et al.   NUCLEIC ACIDS RESEARCH

QTLbase: an integrative resource for quantitative trait loci across multiple human molecular phenotypes

(2019) Zhanye Zheng et al.   NUCLEIC ACIDS RESEARCH

Genome-wide identification of DNA methylation QTLs in whole blood highlights pathways for cardiovascular disease

(2019) Tianxiao Huan et al.   Nature Communications

Integrate GWAS, eQTL, and mQTL Data to Identify Alzheimer’s Disease-Related Genes

(2019) Tianyi Zhao et al.   Frontiers in Genetics

Human Lung DNA Methylation Quantitative Trait Loci Colocalize with Chronic Obstructive Pulmonary Disease Genome-Wide Association Loci

(2018) Jarrett D. Morrow et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

A Bayesian framework for multiple trait colocalization from summary association statistics

(2018) Claudia Giambartolomei et al.   BIOINFORMATICS

Consent to a Postmortem Tissue Procurement Study: Distinguishing Family Decision Makers' Knowledge of the Genotype-Tissue Expression Project

(2018) Laura A. Siminoff et al.   BIOPRESERVATION AND BIOBANKING

Evaluating the potential role of pleiotropy in Mendelian randomization studies

(2018) Gibran Hemani et al.   HUMAN MOLECULAR GENETICS

Using an atlas of gene regulation across 44 human tissues to inform complex disease- and trait-associated variation

(2018) Eric R. Gamazon et al.   NATURE GENETICS

Co-occurring expression and methylation QTLs allow detection of common causal variants and shared biological mechanisms

(2018) Brandon L. Pierce et al.   Nature Communications

Integrative analysis of omics summary data reveals putative mechanisms underlying complex traits

(2018) Yang Wu et al.   Nature Communications

Identifying gene targets for brain-related traits using transcriptomic and methylomic data from blood

(2018) Ting Qi et al.   Nature Communications

Consent to a Postmortem Tissue Procurement Study: Distinguishing Family Decision Makers' Knowledge of the Genotype-Tissue Expression Project

(2018) Laura A. Siminoff et al.   Biopreservation and Biobanking

Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions

(2018) Sarah M. Urbut et al.   NATURE GENETICS

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

Predicting causal variants affecting expression by using whole-genome sequencing and RNA-seq from multiple human tissues

(2017) Andrew Anand Brown et al.   NATURE GENETICS

Estimating the causal tissues for complex traits and diseases

(2017) Halit Ongen et al.   NATURE GENETICS

Enhancing GTEx by bridging the gaps between genotype, gene expression, and disease

(2017) Barbara E Stranger et al.   NATURE GENETICS

Identification of 12 new susceptibility loci for different histotypes of epithelial ovarian cancer

(2017) Catherine M Phelan et al.   NATURE GENETICS

An xQTL map integrates the genetic architecture of the human brain's transcriptome and epigenome

(2017) Bernard Ng et al.   NATURE NEUROSCIENCE

The Epigenomic Analysis of Human Obesity

(2017) Christopher G. Bell   Obesity

Genome-wide mapping of genetic determinants influencing DNA methylation and gene expression in human hippocampus

(2017) Herbert Schulz et al.   Nature Communications

Cross-tissue integration of genetic and epigenetic data offers insight into autism spectrum disorder

(2017) Shan V. Andrews et al.   Nature Communications

GeneHancer: genome-wide integration of enhancers and target genes in GeneCards

(2017) Simon Fishilevich et al.   Database-The Journal of Biological Databases and Curation

Integrating molecular QTL data into genome-wide genetic association analysis: Probabilistic assessment of enrichment and colocalization

(2017) Xiaoquan Wen et al.   PLoS Genetics

Mechanisms and Disease Associations of Haplotype-Dependent Allele-Specific DNA Methylation

(2016) Catherine Do et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Efficient Integrative Multi-SNP Association Analysis via Deterministic Approximation of Posteriors

(2016) Xiaoquan Wen et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Molecular QTL discovery incorporating genomic annotations using Bayesian false discovery rate control

(2016) Xiaoquan Wen   Annals of Applied Statistics

Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells

(2016) Lu Chen et al.   CELL

Insulators and domains of gene expression

(2016) Tamer Ali et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Disease variants alter transcription factor levels and methylation of their binding sites

(2016) Marc Jan Bonder et al.   NATURE GENETICS

Genetic and environmental influences interact with age and sex in shaping the human methylome

(2016) Jenny van Dongen et al.   Nature Communications

A Genome-Wide mQTL Analysis in Human Adipose Tissue Identifies Genetic Variants Associated with DNA Methylation, Gene Expression and Metabolic Traits

(2016) Petr Volkov et al.   PLoS One

Fast and efficient QTL mapper for thousands of molecular phenotypes

(2015) Halit Ongen et al.   BIOINFORMATICS

Network-Based Integration of GWAS and Gene Expression Identifies a HOX-Centric Network Associated with Serous Ovarian Cancer Risk

(2015) S. P. Kar et al.   CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION

Human body epigenome maps reveal noncanonical DNA methylation variation

(2015) Matthew D. Schultz et al.   NATURE

Function and information content of DNA methylation

(2015) Dirk Schübeler   NATURE

Methylation QTLs in the developing brain and their enrichment in schizophrenia risk loci

(2015) Eilis Hannon et al.   NATURE NEUROSCIENCE

Genome-wide identification of microRNA expression quantitative trait loci

(2015) Tianxiao Huan et al.   Nature Communications

Role of DNA Methylation in Modulating Transcription Factor Occupancy

(2015) Matthew T. Maurano et al.   Cell Reports

Tissue-Specific Effects of Genetic and Epigenetic Variation on Gene Regulation and Splicing

(2015) Maria Gutierrez-Arcelus et al.   PLoS Genetics

The Genetic and Mechanistic Basis for Variation in Gene Regulation

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

Predicting genome-wide DNA methylation using methylation marks, genomic position, and DNA regulatory elements

(2015) Weiwei Zhang et al.   GENOME BIOLOGY

GeMes, Clusters of DNA Methylation under Genetic Control, Can Inform Genetic and Epigenetic Analysis of Disease

(2014) Yun Liu et al.   AMERICAN JOURNAL OF HUMAN 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

Bayesian Test for Colocalisation between Pairs of Genetic Association Studies Using Summary Statistics

(2014) Claudia Giambartolomei et al.   PLoS Genetics

Global Analysis of DNA Methylation Variation in Adipose Tissue from Twins Reveals Links to Disease-Associated Variants in Distal Regulatory Elements

(2013) Elin Grundberg et al.   AMERICAN JOURNAL OF HUMAN GENETICS

ChAMP: 450k Chip Analysis Methylation Pipeline

(2013) Tiffany J. Morris et al.   BIOINFORMATICS

Intragenic DNA methylation modulates alternative splicing by recruiting MeCP2 to promote exon recognition

(2013) Alika K Maunakea et al.   CELL RESEARCH

Charting a dynamic DNA methylation landscape of the human genome

(2013) Michael J. Ziller et al.   NATURE

Multiple independent variants at the TERT locus are associated with telomere length and risks of breast and ovarian cancer

(2013) Stig E Bojesen et al.   NATURE GENETICS

Low-level processing of Illumina Infinium DNA Methylation BeadArrays

(2013) Timothy J. Triche et al.   NUCLEIC ACIDS RESEARCH

Passive and active DNA methylation and the interplay with genetic variation in gene regulation

(2013) Maria Gutierrez-Arcelus et al.   eLife

A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data

(2012) Andrew E. Teschendorff et al.   BIOINFORMATICS

Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses

(2012) Oliver Stegle et al.   Nature Protocols

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

(2011) Jordana T Bell et al.   GENOME BIOLOGY

A genome-wide association study identifies susceptibility loci for ovarian cancer at 2q31 and 8q24

(2010) Ellen L Goode et al.   NATURE GENETICS

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

DNA methylation profiles in monozygotic and dizygotic twins

(2009) Zachary A Kaminsky et al.   NATURE GENETICS

X Chromosome Dosage Compensation: How Mammals Keep the Balance

(2008) Bernhard Payer et al.   Annual Review of Genetics