ArticleNature communications2024
Identifying genetic variants associated with chromatin looping and genome function.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Single-allele nanoscale mapping of regulatory variants.Nature genetics · 2026Article
- CLASH (Chromatin Loop Across-sample Score Harmonizer) quantifies the relative contributions of genetic variation, methylation, and CTCF occupancy on chromatin loop strength across individuals.bioRxiv : the preprint server for biology · 2026Article
- Molecular systems, human noncoding sequence variants, and blood pressure.Physiological reviews · 2026Review
- A meta-analysis of chromatin-associated loci provides insights into mechanistic interpretations of trait heritability.bioRxiv : the preprint server for biology · 2026Article
- Genetic and epigenetic markers in the METTL21C gene associated with umbilical hernia in pigs.BMC genomics · 2025Article
- Genetic coupling of enhancer activity and connectivity in gene expression control.Nature communications · 2025Article
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Authors and funding
2 authors.
Funding
Abstract
Here we present a comprehensive HiChIP dataset on naïve CD4 T cells (nCD4) from 30 donors and identify QTLs that associate with genotype-dependent and/or allele-specific variation of HiChIP contacts defining loops between active regulatory regions (iQTLs). We observe a substantial overlap between iQTLs and previously defined eQTLs and histone QTLs, and an enrichment for fine-mapped QTLs and GWAS variants. Furthermore, we describe a distinct subset of nCD4 iQTLs, for which the significant variation of chromatin contacts in nCD4 are translated into significant eQTL trends in CD4 T cell memory subsets. Finally, we define connectivity-QTLs as iQTLs that are significantly associated with concordant genotype-dependent changes in chromatin contacts over a broad genomic region (e.g., GWAS SNP in the RNASET2 locus). Our results demonstrate the importance of chromatin contacts as a complementary modality for QTL mapping and their power in identifying previously uncharacterized QTLs linked to cell-specific gene expression and connectivity.
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Registered trials
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