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Brain xQTL map: Integrating the genetic architecture of the human brain transcriptome and epigenome

https://doi.org/10.1101/142927
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Improving power in genome‐wide association studies: weights tip the scale
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Histone H3 acetylated at lysine 9 in promoter is associated with low nucleosome density in the vicinity of transcription start site in human cell
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A Unified Approach to Genotype Imputation and Haplotype-Phase Inference for Large Data Sets of Trios and Unrelated Individuals
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Mechanisms and Disease Associations of Haplotype-Dependent Allele-Specific DNA Methylation
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Histone Acetylome-wide Association Study of Autism Spectrum Disorder
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A genome-wide scan for common variants affecting the rate of age-related cognitive decline
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Further evidence for the association between the LSM1 gene and schizophrenia
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Polygenic dissection of diagnosis and clinical dimensions of bipolar disorder and schizophrenia
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Functional screening of Alzheimer risk loci identifies PTK2B as an in vivo modulator and early marker of Tau pathology
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Understanding mechanisms underlying human gene expression variation with RNA sequencing
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Transcriptome genetics using second generation sequencing in a Caucasian population
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An integrated map of genetic variation from 1,092 human genomes
inferredcites →https://doi.org/10.1038/nature12531openalex-snapshot
Transcriptome and genome sequencing uncovers functional variation in humans
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Biological insights from 108 schizophrenia-associated genetic loci
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The contribution of de novo coding mutations to autism spectrum disorder
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The Genotype-Tissue Expression (GTEx) project
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Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease
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A gene-based association method for mapping traits using reference transcriptome data
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Partitioning heritability by functional annotation using genome-wide association summary statistics
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Genetic fine mapping and genomic annotation defines causal mechanisms at type 2 diabetes susceptibility loci
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A spectral approach integrating functional genomic annotations for coding and noncoding variants
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Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets
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Common variants on 8p12 and 1q24.2 confer risk of schizophrenia
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ChromHMM: automating chromatin-state discovery and characterization
inferredcites →https://doi.org/10.1038/nn.3786openalex-snapshot
Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci
inferredcites →https://doi.org/10.1038/nn.3801openalex-snapshot
Genetic variability in the regulation of gene expression in ten regions of the human brain
inferredcites →https://doi.org/10.1038/nn.4182openalex-snapshot
Methylation QTLs in the developing brain and their enrichment in schizophrenia risk loci
inferredcites →https://doi.org/10.1038/nn.4399openalex-snapshot
Gene expression elucidates functional impact of polygenic risk for schizophrenia
inferredcites →https://doi.org/10.1038/nrg2814openalex-snapshot
Annotating non-coding regions of the genome
inferredcites →https://doi.org/10.1038/nrn3638openalex-snapshot
Inflammasomes in the CNS
inferredcites →https://doi.org/10.1056/nejmp0806284openalex-snapshot
Common Genetic Variation and Human Traits
inferredcites →https://doi.org/10.1073/pnas.0307349101openalex-snapshot
Down-regulation of DENN/MADD, a TNF receptor binding protein, correlates with neuronal cell death in Alzheimer's disease brain and hippocampal neurons
inferredcites →https://doi.org/10.1073/pnas.0806296105openalex-snapshot
The RNA binding protein CPEB regulates dendrite morphogenesis and neuronal circuit assembly in vivo
inferredcites →https://doi.org/10.1073/pnas.1530509100openalex-snapshot
Statistical significance for genomewide studies
inferredcites →https://doi.org/10.1093/nar/gkt1229openalex-snapshot
The NHGRI GWAS Catalog, a curated resource of SNP-trait associations
inferredcites →https://doi.org/10.1097/fpc.0b013e3283050107openalex-snapshot
Polymorphisms affecting gene transcription and mRNA processing in pharmacogenetic candidate genes: detection through allelic expression imbalance in human target tissues
inferredcites →https://doi.org/10.1097/wad.0b013e318231a8acopenalex-snapshot
NALP1/NLRP1 Genetic Variants are Associated With Alzheimer Disease
inferredcites →https://doi.org/10.1101/gr.155192.113openalex-snapshot
Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals
inferredcites →https://doi.org/10.1126/science.1174148openalex-snapshot
Common Regulatory Variation Impacts Gene Expression in a Cell Type–Dependent Manner
inferredcites →https://doi.org/10.1126/science.1242429openalex-snapshot
Identification of Genetic Variants That Affect Histone Modifications in Human Cells
inferredcites →https://doi.org/10.1126/science.1249547openalex-snapshot
Polarization of the Effects of Autoimmune and Neurodegenerative Risk Alleles in Leukocytes
inferredcites →https://doi.org/10.1126/science.1262110openalex-snapshot
The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans
inferredcites →https://doi.org/10.1186/1471-2156-10-23openalex-snapshot
Disentangling molecular relationships with a causal inference test
inferredcites →https://doi.org/10.1186/gb-2012-13-1-r7openalex-snapshot
Dissecting the regulatory architecture of gene expression QTLs
inferredcites →https://doi.org/10.1186/s13742-015-0047-8openalex-snapshot
Second-generation PLINK: rising to the challenge of larger and richer datasets
inferredcites →https://doi.org/10.1371/journal.pcbi.1000770openalex-snapshot
A Bayesian Framework to Account for Complex Non-Genetic Factors in Gene Expression Levels Greatly Increases Power in eQTL Studies
inferredcites →https://doi.org/10.1371/journal.pgen.1000888openalex-snapshot
Trait-Associated SNPs Are More Likely to Be eQTLs: Annotation to Enhance Discovery from GWAS
inferredcites →https://doi.org/10.1371/journal.pgen.1000952openalex-snapshot
Abundant Quantitative Trait Loci Exist for DNA Methylation and Gene Expression in Human Brain
inferredcites →https://doi.org/10.1371/journal.pgen.1003649openalex-snapshot
Integrative Modeling of eQTLs and Cis-Regulatory Elements Suggests Mechanisms Underlying Cell Type Specificity of eQTLs
inferredcites →https://doi.org/10.1371/journal.pgen.1004663openalex-snapshot
Methylation QTLs Are Associated with Coordinated Changes in Transcription Factor Binding, Histone Modifications, and Gene Expression Levels
inferredcites →https://doi.org/10.1371/journal.pgen.1005223openalex-snapshot
Cell Specific eQTL Analysis without Sorting Cells
inferredcites →https://doi.org/10.1371/journal.pone.0068141openalex-snapshot
Normalizing RNA-Sequencing Data by Modeling Hidden Covariates with Prior Knowledge
inferredcites →https://doi.org/10.1371/journal.pone.0099313openalex-snapshot
Characterization of Genome-Methylome Interactions in 22 Nuclear Pedigrees
inferredcites →https://doi.org/10.1371/journal.pone.0148717openalex-snapshot
Alzheimer’s Disease Risk Polymorphisms Regulate Gene Expression in the ZCWPW1 and the CELF1 Loci
inferredcites →https://doi.org/10.2174/156720512801322573openalex-snapshot
Overview and Findings from the Religious Orders Study
inferredcites →https://doi.org/10.2174/156720512801322663openalex-snapshot
Overview and Findings from the Rush Memory and Aging Project
inferredcites →https://doi.org/10.7554/elife.00523openalex-snapshot
Passive and active DNA methylation and the interplay with genetic variation in gene regulation

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1007/s12031-018-1144-9openalex-snapshot
Alzheimer’s Disease Risk Variant rs2373115 Regulates GAB2 and NARS2 Expression in Human Brain Tissues
inferred← citeshttps://doi.org/10.1016/b978-0-444-63639-3.00017-7openalex-snapshot
Epigenetic analysis of human postmortem brain tissue
inferred← citeshttps://doi.org/10.1038/s41398-018-0337-xopenalex-snapshot
Replicated associations of FADS1, MAD1L1, and a rare variant at 10q26.13 with bipolar disorder in Chinese population
inferred← citeshttps://doi.org/10.1038/s41398-019-0577-4openalex-snapshot
Genetic risk for Alzheimer’s dementia predicts motor deficits through multi-omic systems in older adults
inferred← citeshttps://doi.org/10.1038/s41398-021-01348-0openalex-snapshot
Mendelian randomization integrating GWAS and eQTL data revealed genes pleiotropically associated with major depressive disorder
inferred← citeshttps://doi.org/10.1038/s41398-021-01436-1openalex-snapshot
Genetic underpinnings of affective temperaments: a pilot GWAS investigation identifies a new genome-wide significant SNP for anxious temperament in ADGRB3 gene
inferred← citeshttps://doi.org/10.1038/s41467-018-04558-1openalex-snapshot
Identifying gene targets for brain-related traits using transcriptomic and methylomic data from blood
inferred← citeshttps://doi.org/10.1038/s41467-018-07524-zopenalex-snapshot
Genome-wide mega-analysis identifies 16 loci and highlights diverse biological mechanisms in the common epilepsies
inferred← citeshttps://doi.org/10.1038/s41467-019-08912-9openalex-snapshot
Prioritizing Parkinson’s disease genes using population-scale transcriptomic data
inferred← citeshttps://doi.org/10.1038/s41467-020-20337-3openalex-snapshot
The patterns of deleterious mutations during the domestication of soybean
inferred← citeshttps://doi.org/10.1038/s41467-021-21854-5openalex-snapshot
Global discovery of lupus genetic risk variant allelic enhancer activity
inferred← citeshttps://doi.org/10.1038/s41467-021-22262-5openalex-snapshot
Human-lineage-specific genomic elements are associated with neurodegenerative disease and APOE transcript usage
inferred← citeshttps://doi.org/10.1038/s41467-021-23243-4openalex-snapshot
A meta-analysis of epigenome-wide association studies in Alzheimer’s disease highlights novel differentially methylated loci across cortex
inferred← citeshttps://doi.org/10.1038/s41467-021-25392-yopenalex-snapshot
Multi-omics integration analysis identifies novel genes for alcoholism with potential overlap with neurodegenerative diseases
inferred← citeshttps://doi.org/10.1038/s41540-021-00177-7openalex-snapshot
ADAS-viewer: web-based application for integrative analysis of multi-omics data in Alzheimer’s disease
inferred← citeshttps://doi.org/10.1038/s41562-020-00956-yopenalex-snapshot
Genome-wide association study identifies 48 common genetic variants associated with handedness
inferred← citeshttps://doi.org/10.1038/s41588-018-0090-3openalex-snapshot
Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression
inferred← citeshttps://doi.org/10.1038/s41588-018-0238-1openalex-snapshot
Integrative transcriptome analyses of the aging brain implicate altered splicing in Alzheimer’s disease susceptibility
inferred← citeshttps://doi.org/10.1038/s41588-018-0311-9openalex-snapshot
Genome-wide meta-analysis identifies new loci and functional pathways influencing Alzheimer’s disease risk
inferred← citeshttps://doi.org/10.1038/s41588-020-00776-wopenalex-snapshot
Genome-wide meta-analysis, fine-mapping and integrative prioritization implicate new Alzheimer’s disease risk genes
inferred← citeshttps://doi.org/10.1038/s41588-021-00835-wopenalex-snapshot
Uncovering genetic mechanisms of hypertension through multi-omic analysis of the kidney
inferred← citeshttps://doi.org/10.1038/s41588-021-00921-zopenalex-snapshot
A genome-wide association study with 1,126,563 individuals identifies new risk loci for Alzheimer’s disease
inferred← citeshttps://doi.org/10.1038/s41588-021-00924-wopenalex-snapshot
A compendium of uniformly processed human gene expression and splicing quantitative trait loci
inferred← citeshttps://doi.org/10.1038/s41591-019-0579-zopenalex-snapshot
Genome-wide germline correlates of the epigenetic landscape of prostate cancer
inferred← citeshttps://doi.org/10.1038/s41593-018-0187-0openalex-snapshot
Cell-specific histone modification maps in the human frontal lobe link schizophrenia risk to the neuronal epigenome
inferred← citeshttps://doi.org/10.1038/s41593-018-0240-zopenalex-snapshot
Deconstructing and targeting the genomic architecture of human neurodegeneration
inferred← citeshttps://doi.org/10.1038/s41593-021-00886-6openalex-snapshot
Genomic atlas of the proteome from brain, CSF and plasma prioritizes proteins implicated in neurological disorders
inferred← citeshttps://doi.org/10.1038/s41597-020-00642-8openalex-snapshot
Large eQTL meta-analysis reveals differing patterns between cerebral cortical and cerebellar brain regions
inferred← citeshttps://doi.org/10.1038/s41598-019-54782-yopenalex-snapshot
Investigating the energy crisis in Alzheimer disease using transcriptome study
inferred← citeshttps://doi.org/10.1038/s41598-021-82169-5openalex-snapshot
Transcriptome-wide Mendelian randomization study prioritising novel tissue-dependent genes for glioma susceptibility
inferred← citeshttps://doi.org/10.1038/s43587-021-00110-xopenalex-snapshot
Dysregulation of mitochondrial and proteolysosomal genes in Parkinson’s disease myeloid cells
inferred← citeshttps://doi.org/10.1101/192922openalex-snapshot
Chromatin accessibility profiling uncovers genetic- and T2D disease state-associated changes in cis -regulatory element use in human islets
inferred← citeshttps://doi.org/10.1101/2020.10.21.349019openalex-snapshot
Genetic effects on brain traits impact cell-type specific gene regulation during neurogenesis
inferred← citeshttps://doi.org/10.1101/2020.11.20.20235275openalex-snapshot
Largest GWAS (N=1,126,563) of Alzheimer’s Disease Implicates Microglia and Immune Cells
inferred← citeshttps://doi.org/10.1101/2021.01.21.426000openalex-snapshot
Single-cell deconvolution of 3,000 post-mortem brain samples for eQTL and GWAS dissection in mental disorders
inferred← citeshttps://doi.org/10.1186/s13024-018-0272-6openalex-snapshot
Polygenic analysis of inflammatory disease variants and effects on microglia in the aging brain
inferred← citeshttps://doi.org/10.1371/journal.pgen.1007607openalex-snapshot
Identification of expression quantitative trait loci associated with schizophrenia and affective disorders in normal brain tissue
inferred← citeshttps://doi.org/10.1371/journal.pgen.1009918openalex-snapshot
Cascading epigenomic analysis for identifying disease genes from the regulatory landscape of GWAS variants
inferred← citeshttps://doi.org/10.37349/emed.2024.00216openalex-snapshot
The association between circulating CD34+CD133+ endothelial progenitor cells and reduced risk of Alzheimer’s disease in the Framingham Heart Study
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