What is EWAS Open Platform?

With the explosive growth of epigenome-wide association studies (EWAS), a large amount of data and knowledge related to EWAS have been accumulated. Although these data hold great potential for clinical translation, a standardized platform for data archiving, retrieving and exploration is indispensable. For this reason, we updated the existing data resources, EWAS Atlas (Nucleic Acids Res 2019, https://ngdc.cncb.ac.cn/ewas/atlas) and EWAS Data Hub (Nucleic Acids Res 2020, https://ngdc.cncb.ac.cn/ewas/datahub), and proposed EWAS Toolkit (https://ngdc.cncb.ac.cn/ewas/toolkit), an online tool for downstream analysis of EWAS result. Focusing on EWAS research, these three resources provide knowledge, data and tools respectively. More importantly, the quality and functionality for each component are enhanced by cross-linking information from each other. To this end, we present EWAS Open Platform , an integrated one-stop analysis platform for EWAS research.
EWAS Open Platform aims to integrate large, diverse and continually arriving EWAS data. There are three parts in this major release:
1. As a curated knowledgebase of EWAS, EWAS Atlas (updated) systematically curated and integrated 806,860 high-quality EWAS associations and 17,494 causations reported in 1568 articles (as of August 25, 2025), involving 248 tissues/cell types, 877 traits and 35,598 genes.
2. As a normalized data portal of EWAS, EWAS Data Hub (updated) integrates DNA methylation data of 180,317 samples from public sources and standardizes the metadata of each sample via a specific data normalization procedure. These data cover 1,413 different types of tissues and cells, as well as 842 different diseases.
3. Taking advantage of integrated knowledge and data in EWAS Atlas, EWAS Data Hub, and Roadmap Epigenomics Project,the EWAS Toolkit has been developed as an online analysis platform covering both upstream and downstream analyses. Upstream, the GMQN tool addresses batch effects in EWAS data, while downstream offers one-click analysis functions, including trait enrichment, genomic location enrichment, GO & KEGG enrichment, chromatin state & histone modification enrichment, tissue methylation, expression regulation and motif enrichment. It provides a one-stop solution for downstream analysis of EWAS and requires no bioinformatics background.

EWAS Atlas

EWAS Atlas, a curated knowledgebase of EWAS. As one of core resources in the the National Genomics Data Center, China National Center for Bioinformation, EWAS Atlas is devoted to providing a comprehensive collection of high-quality EWAS associations and causations in support of systematic investigations of complex molecular mechanisms associated with different biological traits. Unlike extant data-oriented epigenetic resources, EWAS Atlas features manual curation of EWAS knowledge from extensive publications and accordingly incorporates a large number of high-quality EWAS data and a diversity of traits and ontology entities. EWAS Atlas provides open access to all curated data and thus would serve as a valuable resource for the global research community.
More details about EWAS Atlas are in EWAS Atlas documentation

EWAS Data Hub

To provide the epigenetic research community with a unified data repository that enables data sharing across EWAS, we develop EWAS Data Hub, a public repository that integrates DNA methylation array data (including 450K , 850K and 935K in current version) and comprehensive metadata from various data source (GEO, TCGA, ENCODE and ArrayExpress) based on a standard pipeline to minimize batch effects from distinct sources. Besides, taking advantage of big and high quality data, abundant of baseline data on different tissues and conditions are also provided in EWAS Data Hub.
More details about EWAS Data Hub are in EWAS Data Hub documentation

EWAS Toolkit

Taking advantage of integrated knowledge and data in EWAS Atlas, EWAS Data Hub, and Roadmap Epigenomics Project, EWAS Toolkit is newly developed to provides an online analysis platform for EWAS downstream analysis which includes trait enrichment, genomic location enrichment, GO & KEGG enrichment, chromatin state & histone modification enrichment, tissue methylation, expression regulation and motif enrichment. It provides a one-stop solution for downstream analysis of EWAS and requires no bioinformatics background.
More details about EWAS Toolkit are in EWAS toolkit documentation

Unified Retrieval

To address the fragmentation of data, knowledge, and toolkit on EWAS Open Platform and to enable efficient, integrated access, we developed a seamless cross-module unified retrieval that combines quantitative summaries with interactive visualizations. This interface leverages a unified API, integrates heterogeneous data through semantic parsing, and employs standardized data modeling, ensuring consistency, interoperability, and robust query support across diverse data types. Users can query by traits, genes, or CpG probe IDs, with results delivered through concise summaries and intuitive visual outputs.
More details about Unified Retrieval are in Unified Retrieval

AI-based Q&A Assistant

To enable researchers to access epigenetic information on complex traits including diseases in a more flexible and intuitive manner, we developed an intelligent agent–based question–answering assistant within EWAS Open Platform, using the LangChain and LangGraph frameworks along with Vue3. The assistant supports conversational queries in natural language and automatically returns structured answers derived from integrated EWAS resources, covering disease associations, methylation patterns, and multidimensional factors such as age, sex, ethnicity, and tissue.
More details about AI-based Q&A Assistant are in AI-based Q&A Assistant

How to cite?

EWAS Open Platform 2026: a deeply integrated resource for epigenome-wide association studies. Nucleic Acids Res. Nucleic Acids Res 2026. [PMID=41243956]

Disclaimer

The information on this website is curated from publications and not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have any question about the information contained on this website, please see a health care professional.

Licenses

EWAS Open Platform is free for academic use only. For any commercial use, please contact us for commercial licensing terms.