Knowledgebases now map regulatory elements and GWAS variants onto genes and traits

Published papers

• An expanded registry of candidate cis-regulatory elements.

  Nature2026-01-07Jill E Moore et al.

  Expands the ENCODE cCRE registry to 2.37M human and 967k mouse candidate cis-regulatory elements, with functional validation and silencer annotations.

• Protein-protein interactions shape trans-regulatory impact of genetic variation on protein expression and complex traits.

  Nature genetics2026-01-07Jinghui Li et al.

  Re-analyzes large pQTL maps and uses PPI annotations to guide trans-pQTL mapping, identifying 17,662 trans-pQTLs linked to GWAS loci.

• Enhancing TFEA.ChIP with ENCODE regulatory maps for generalizable transcription factor enrichment.

  Briefings in bioinformatics2026-01-07Yosra Berrouayel et al.

  TFEA.ChIP update links ReMap2022 TF binding to ENCODE rE2G/CREdb regulatory maps with recurrence filtering; benchmarked on 342 MSigDB C2 sets, R/Bioconductor.

• Spatial2GWAS: a database for linking spatial transcriptomic regions with GWAS traits.

  Nucleic acids research2026-01-06Xi Hu et al.

  Spatial heterogeneity of gene expression within tissue regions has a critical influence on biological functions, thereby affecting disease pathogenesis.

• GENEasso: a curated resource of credible disease-gene associations across complex diseases from GWAS summary statistics.

  Nucleic acids research2026-01-06Tao Jiang et al.

  Gene-based association analysis has become a powerful strategy to improve the biological interpretability of genome-wide association studies (GWAS) by aggregati

• Spatial GWAS Atlas: a knowledgebase for decoding the genetic architecture of complex traits in spatial resolution.

  Nucleic acids research2026-01-06Hongen Kang et al.

  Spatial GWAS Atlas is a knowledgebase linking 3854 GWAS summary statistics to 635 spatial transcriptomics datasets to map trait-associated cells and spatial…

• scVMAP: a comprehensive platform for integrating single-cell chromatin accessibility regions with causal variants.

  Nucleic acids research2026-01-06Zheng-Min Yu et al.

  Integrating causal variant effects with single-cell assay for transposase-accessible chromatin with high-throughput sequencing (scATAC-seq) enables a more effec

• SEA version 4.0: a major expansion and update of the Super-Enhancer Archive.

  Nucleic acids research2026-01-06Bowen Shi et al.

  SEA v4.0 updates the Super-Enhancer Archive: uniform SE calling from five histone/cofactor marks across 14 species, plus regulatory networks and a…

• DisCP-Atlas: a comprehensive resource mapping cellular processes to complex diseases.

  Nucleic acids research2026-01-06Frank Qingyun Wang et al.

  Genome-wide association studies (GWAS) have identified thousands of disease-associated loci, yet translating these findings into biological mechanisms remains c

• JASPAR 2026: expansion of transcription factor binding profiles and integration of deep learning models.

  Nucleic acids research2026-01-06Damla Ovek Baydar et al.

  JASPAR 2026 expands curated TF binding profiles (CORE, UNVALIDATED) and adds a deep learning collection of 1259 BPNet models trained on ENCODE ChIP-seq data.

• ATACdb 2.0: a comprehensive chromatin accessibility database of human and mouse.

  Nucleic acids research2026-01-06Qiao-Li Fang et al.

  ATACdb 2.0 is an updated chromatin accessibility database for human and mouse, expanding samples and regions with annotations, SNP search, and enrichment tools.

• TWAS atlas 2.0: an updated data resource for transcriptome-wide association studies.

  Nucleic acids research2026-01-06Hao Gao et al.

  Transcriptome-wide association studies (TWAS), which combine large-scale GWAS and expression quantitative trait loci (eQTL) datasets to predict gene expression

• SEdb 3.0: a comprehensive super-enhancer database across multiple species.

  Nucleic acids research2026-01-06Shuang Song et al.

  Super-enhancers (SEs) are key DNA cis-regulatory elements that play a central role in regulating tissue/cell-specific gene expression, thereby maintaining cellu

• Chinese Immune Multi-Omics Atlas.

  Science (New York, N.Y.)2026-01-08Jianhua Yin et al.

  CIMA is a multi-omics atlas of over 10 million circulating immune cells from 428 Chinese adults, with a gene regulatory network, eQTL/caQTL maps, and a cell…

Preprints

• A cohesin-centric gene regulatory network resource with regulatory site annotations

  bioRxiv2026-01-07Ding, J. et al.

  Presents Cohesin-GRN, a database module in CohesinDB linking TF binding, cohesin-associated regulatory sites, and target genes into over 270 million…

Related topics

• Functional Genomics Resources Linking Variants
• Cell Type Resolved Omics Atlases
• Curated Biological Reference Databases

Topic history