G-四链体（G4）是非典型的四链结构，正在作为新型遗传调控元件出现。然而，内源性 G4 (eG4) 的全面基因组注释及其调控网络的系统表征仍然缺乏，这给 eG4 研究带来了重大挑战。在这里，我们提出了 EndoQuad (https://EndoQuad.chenzxlab.cn/)，通过整合高通量实验数据来解决这些紧迫的问题。首先，基于 G4 ChIP-seq/CUT 生成的高质量全基因组 eG4s 作图数据集（人类：1181；小鼠：24；鸡：2）

G-quadruplexes (G4s) are non-canonical four-stranded structures and are emerging as novel genetic regulatory elements. However, a comprehensive genomic annotation of endogenous G4s (eG4s) and systematic characterization of their regulatory network are still lacking, posing major challenges for eG4 research. Here, we present EndoQuad (https://EndoQuad.chenzxlab.cn/) to address these pressing issues by integrating high-throughput experimental data. First, based on high-quality genome-wide eG4s mapping datasets (human: 1181; mouse: 24; chicken: 2) generated by G4 ChIP-seq/CUT&Tag, we generate a reference set of genome-wide eG4s. Our multi-omics analyses show that most eG4s are identified in one or a few cell types. The eG4s with higher occurrences across samples are more structurally stable, evolutionarily conserved, enriched in promoter regions, mark highly expressed genes and associate with complex regulatory programs, demonstrating higher confidence level for further experiments. Finally, we integrate millions of functional genomic variants and prioritize eG4s with regulatory functions in disease and cancer contexts. These efforts have culminated in the comprehensive and interactive database of experimentally validated DNA eG4s. As such, EndoQuad enables users to easily access, download and repurpose these data for their own research. EndoQuad will become a one-stop resource for eG4 research and lay the foundation for future functional studies.© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.