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Loop Catalog: a comprehensive HiChIP database of human and mouse samples.

Joaquin Reyna1,2, Kyra Fetter1,3, Romeo Ignacio1,4

  • 1Centers for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA.

Genome Biology
|June 20, 2025
PubMed
Summary

Loop Catalog is a new database that makes it easy to find and analyze chromatin loops from HiChIP and Hi-C data. It helps researchers interpret genetic variants and understand gene regulation.

Keywords:
Chromatin loopsDatabaseGWASHiChIPSNP-to-gene linking

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • High-throughput chromatin interaction capture (HiChIP) provides high-resolution chromatin loop profiling.
  • An increasing volume of HiChIP data necessitates centralized resources for analysis.

Purpose of the Study:

  • To develop Loop Catalog, a web-based database for HiChIP and Hi-C loop calls.
  • To provide a comprehensive resource for exploring and analyzing chromatin interaction data.

Main Methods:

  • Aggregated loop calls from over 1000 human and mouse HiChIP samples and 44 Hi-C samples.
  • Integrated analysis modules for SNP-to-gene linking, motif analysis, and network generation.

Main Results:

  • The catalog contains over 4.19 million unique chromatin loops.
  • Demonstrated utility in interpreting GWAS and eQTL variants.
  • Facilitated identification of regulatory networks and sequence motifs.

Conclusions:

  • Loop Catalog is a valuable resource for the genomics community.
  • Enables deeper understanding of chromatin structure and gene regulation.
  • Supports interpretation of genetic variants in the context of 3D genome organization.