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Allelic imbalance reveals widespread germline-somatic regulatory differences and prioritizes risk loci in Renal Cell Carcinoma

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What this work says

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

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Partitioning Heritability of Regulatory and Cell-Type-Specific Variants across 11 Common Diseases

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A Lentiviral RNAi Library for Human and Mouse Genes Applied to an Arrayed Viral High-Content Screen

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Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

inferredcites →https://doi.org/10.1016/j.cell.2013.03.036openalex-snapshot

Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers

inferredcites →https://doi.org/10.1016/j.cell.2015.07.048openalex-snapshot

Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions

inferredcites →https://doi.org/10.1016/j.cell.2015.08.001openalex-snapshot

Population Variation and Genetic Control of Modular Chromatin Architecture in Humans

inferredcites →https://doi.org/10.1016/j.cell.2016.10.026openalex-snapshot

Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells

inferredcites →https://doi.org/10.1016/j.cell.2017.05.038openalex-snapshot

An Expanded View of Complex Traits: From Polygenic to Omnigenic

inferredcites →https://doi.org/10.1016/j.celrep.2017.03.078openalex-snapshot

Systematic Epigenomic Analysis Reveals Chromatin States Associated with Melanoma Progression

inferredcites →https://doi.org/10.1016/j.molcel.2017.03.007openalex-snapshot

Multiplexed Engineering and Analysis of Combinatorial Enhancer Activity in Single Cells

inferredcites →https://doi.org/10.1038/cdd.2010.153openalex-snapshot

GRAMD4 mimics p53 and mediates the apoptotic function of p73 at mitochondria

inferredcites →https://doi.org/10.1038/nature08672openalex-snapshot

Systematic sequencing of renal carcinoma reveals inactivation of histone modifying genes

inferredcites →https://doi.org/10.1038/nature12222openalex-snapshot

Comprehensive molecular characterization of clear cell renal cell carcinoma

inferredcites →https://doi.org/10.1038/nature13602openalex-snapshot

Putative cis-regulatory drivers in colorectal cancer

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Genetic effects on gene expression across human tissues

inferredcites →https://doi.org/10.1038/nbt.3437openalex-snapshot

Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9

inferredcites →https://doi.org/10.1038/ncomms12098openalex-snapshot

Functional characterization of the 12p12.1 renal cancer-susceptibility locus implicates BHLHE41

inferredcites →https://doi.org/10.1038/ncomms13183openalex-snapshot

Genetic variation at the 8q24.21 renal cancer susceptibility locus affects HIF binding to a MYC enhancer

inferredcites →https://doi.org/10.1038/ncomms15724openalex-snapshot

Genome-wide association study identifies multiple risk loci for renal cell carcinoma

inferredcites →https://doi.org/10.1038/ng.237openalex-snapshot

Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs

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Genome-wide association analysis of more than 120,000 individuals identifies 15 new susceptibility loci for breast cancer

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

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The androgen receptor cistrome is extensively reprogrammed in human prostate tumorigenesis

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Regulators of genetic risk of breast cancer identified by integrative network analysis

inferredcites →https://doi.org/10.1038/ng.3467openalex-snapshot

Fine-mapping cellular QTLs with RASQUAL and ATAC-seq

inferredcites →https://doi.org/10.1038/ng.3523openalex-snapshot

Gene regulatory mechanisms underpinning prostate cancer susceptibility

inferredcites →https://doi.org/10.1038/ng.3679openalex-snapshot

Reference-based phasing using the Haplotype Reference Consortium panel

inferredcites →https://doi.org/10.1038/nm.3975openalex-snapshot

CAUSEL: an epigenome- and genome-editing pipeline for establishing function of noncoding GWAS variants

inferredcites →https://doi.org/10.1038/nmeth.3582openalex-snapshot

WASP: allele-specific software for robust molecular quantitative trait locus discovery

inferredcites →https://doi.org/10.1038/nmeth.3853openalex-snapshot

Growth rate inhibition metrics correct for confounders in measuring sensitivity to cancer drugs

inferredcites →https://doi.org/10.1038/nmeth.4298openalex-snapshot

Allele-specific expression reveals interactions between genetic variation and environment

inferredcites →https://doi.org/10.1038/nmeth.4396openalex-snapshot

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

inferredcites →https://doi.org/10.1038/nprot.2012.101openalex-snapshot

Identifying ChIP-seq enrichment using MACS

inferredcites →https://doi.org/10.1038/s41588-018-0092-1openalex-snapshot

Transcriptome-wide association study of schizophrenia and chromatin activity yields mechanistic disease insights

inferredcites →https://doi.org/10.1038/s41588-018-0142-8openalex-snapshot

Association analyses of more than 140,000 men identify 63 new prostate cancer susceptibility loci

inferredcites →https://doi.org/10.1038/s41588-018-0144-6openalex-snapshot

Mixed-model association for biobank-scale datasets

inferredcites →https://doi.org/10.1038/s41588-018-0148-2openalex-snapshot

Leveraging molecular quantitative trait loci to understand the genetic architecture of diseases and complex traits

inferredcites →https://doi.org/10.1038/s41588-018-0156-2openalex-snapshot

Genetic determinants of co-accessible chromatin regions in activated T cells across humans

inferredcites →https://doi.org/10.1038/s41588-018-0196-7openalex-snapshot

Detecting genome-wide directional effects of transcription factor binding on polygenic disease risk

inferredcites →https://doi.org/10.1038/s41588-018-0278-6openalex-snapshot

High-resolution genetic mapping of putative causal interactions between regions of open chromatin

inferredcites →https://doi.org/10.1093/bioinformatics/btp616openalex-snapshot

edgeR : a Bioconductor package for differential expression analysis of digital gene expression data

inferredcites →https://doi.org/10.1093/bioinformatics/btu802openalex-snapshot

QuASAR: quantitative allele-specific analysis of reads

inferredcites →https://doi.org/10.1093/bioinformatics/btv470openalex-snapshot

motifbreakR : an R/Bioconductor package for predicting variant effects at transcription factor binding sites

inferredcites →https://doi.org/10.1093/bioinformatics/btv722openalex-snapshot

Fast and efficient QTL mapper for thousands of molecular phenotypes

inferredcites →https://doi.org/10.1101/225441openalex-snapshot

Assessing the Gene Regulatory Landscape in 1,188 Human Tumors

inferredcites →https://doi.org/10.1101/gr.209759.116openalex-snapshot

High-throughput allele-specific expression across 250 environmental conditions

inferredcites →https://doi.org/10.1111/j.1467-9868.2004.00439.xopenalex-snapshot

Strong Control, Conservative Point Estimation and Simultaneous Conservative Consistency of False Discovery Rates: A Unified Approach

inferredcites →https://doi.org/10.1126/science.1117679openalex-snapshot

Recurrent Fusion of TMPRSS2 and ETS Transcription Factor Genes in Prostate Cancer

inferredcites →https://doi.org/10.1126/science.1222794openalex-snapshot

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

inferredcites →https://doi.org/10.1126/science.1242429openalex-snapshot

Identification of Genetic Variants That Affect Histone Modifications in Human Cells

inferredcites →https://doi.org/10.1158/2159-8290.cd-17-0375openalex-snapshot

VHL Deficiency Drives Enhancer Activation of Oncogenes in Clear Cell Renal Cell Carcinoma

inferredcites →https://doi.org/10.1186/gb-2008-9-9-r137openalex-snapshot

Model-based Analysis of ChIP-Seq (MACS)

inferredcites →https://doi.org/10.1186/s12885-017-3761-zopenalex-snapshot

Up-regulation of SR-BI promotes progression and serves as a prognostic biomarker in clear cell renal cell carcinoma

inferredcites →https://doi.org/10.1186/s13059-015-0762-6openalex-snapshot

Tools and best practices for data processing in allelic expression analysis

inferredcites →https://doi.org/10.1194/jlr.m083311openalex-snapshot

Scavenger receptor BI promotes cytoplasmic accumulation of lipoproteins in clear-cell renal cell carcinoma

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.1006872openalex-snapshot

Multiple renal cancer susceptibility polymorphisms modulate the HIF pathway

inferredcites →https://doi.org/10.3389/fphar.2016.00326openalex-snapshot

Targeting SR-BI for Cancer Diagnostics, Imaging and Therapy

inferredcites →https://doi.org/10.3389/fphar.2016.00338openalex-snapshot

SR-BI: Linking Cholesterol and Lipoprotein Metabolism with Breast and Prostate Cancer

inferredcites →https://doi.org/10.3389/fphar.2016.00466openalex-snapshot

Targeting the SR-B1 Receptor as a Gateway for Cancer Therapy and Imaging

What points at this work

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

inferred← citeshttps://doi.org/10.1002/ijc.34761openalex-snapshot

Regulome‐wide association study identifies genetically driven accessible regions associated with pancreatic cancer risk

inferred← citeshttps://doi.org/10.1016/j.ajhg.2019.12.011openalex-snapshot

Allele-Specific QTL Fine Mapping with PLASMA

inferred← citeshttps://doi.org/10.1016/j.ajhg.2021.09.008openalex-snapshot

Allele-specific epigenetic activity in prostate cancer and normal prostate tissue implicates prostate cancer risk mechanisms

inferred← citeshttps://doi.org/10.1016/j.compbiomed.2025.110890openalex-snapshot

Allele-specific expression analysis: pipelines, applications, challenges, and unmet needs

inferred← citeshttps://doi.org/10.1016/j.gde.2020.10.007openalex-snapshot

Allele-specific expression: applications in cancer and technical considerations

inferred← citeshttps://doi.org/10.1038/s41467-023-35833-5openalex-snapshot

Epigenomic charting and functional annotation of risk loci in renal cell carcinoma

inferred← citeshttps://doi.org/10.1038/s41588-022-01075-2openalex-snapshot

Allelic imbalance of chromatin accessibility in cancer identifies candidate causal risk variants and their mechanisms

inferred← citeshttps://doi.org/10.1038/s41588-022-01168-yopenalex-snapshot

Genetic determinants of chromatin reveal prostate cancer risk mediated by context-dependent gene regulation

inferred← citeshttps://doi.org/10.1038/s41598-023-42637-6openalex-snapshot

Allele specific binding of histone modifications and a transcription factor does not predict allele specific expression in correlated ChIP-seq peak-exon pairs

inferred← citeshttps://doi.org/10.1093/gpbjnl/qzae077openalex-snapshot

Multiome-wide Association Studies: Novel Approaches for Understanding Diseases

inferred← citeshttps://doi.org/10.1101/2021.11.11.468278openalex-snapshot

A novel method to identify cell-type specific regulatory variants and their role in cancer risk

inferred← citeshttps://doi.org/10.1101/2025.11.12.688010openalex-snapshot

Circulating chromatin reveals the effects of disease-associated variants on gene regulation

inferred← citeshttps://doi.org/10.1126/science.adp4753openalex-snapshot

Kidney multiome-based genetic scorecard reveals convergent coding and regulatory variants

inferred← citeshttps://doi.org/10.1186/s13059-022-02708-9openalex-snapshot

DeCAF: a novel method to identify cell-type specific regulatory variants and their role in cancer risk

inferred← citeshttps://doi.org/10.64898/2026.05.05.26352448openalex-snapshot

In vivo measurement and prediction of cell-type-resolved non-coding variant effects in human immunity

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