Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a debilitating female-biased disease with neither diagnostic biomarkers nor effective treatment nor well-understood aetiology. To investigate its biological basis, we used TarGene to perform a genome-wide association study in the UK Biobank with 1,268 ME/CFS cases, using electronic health records and survey responses to affirm ME/CFS status in cases, and non-ME/CFS status in controls. This analysis identified 176 variants as significantly associated with ME/CFS (false discovery rate < 5%). We then performed two replication studies, with similar phenotyping, in two disjoint, smaller cohorts in the UK Biobank and in the All of Us Research Program with 319 and 371 cases, respectively. Seven genomic ME/CFS risk loci replicated, although none were significant across all three cohorts. Fine-mapping at one replicated locus resolved a credible set colocalising with reduced CLYBL expression in putamen, in linkage disequilibrium with the replicated variant. However, the CLYBL Arg259 stop-gain variant was not associated with ME/CFS risk. Other replicated loci contained BICD1 , GRIN2A , CSMD1 and RORA genes. No gene-by-sex or gene-by-deprivation interactions survived multiple-testing correction. ![Figure][1]</img> No genomic risk loci for myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) have previously replicated across independent cohorts. We find seven variants associated with ME/CFS that replicate in disjoint biobank cohorts. Lay summary Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a common and disabling illness with a variety of symptoms. Additionally, little is known about the biological mechanisms that cause ME/CFS. The variety of symptoms and its unknown cause can make it difficult for healthcare professionals to diagnose people with ME/CFS reliably. This poses a significant challenge for ME/CFS research, as misdiagnoses may lead to errors in conclusions drawn from its study. Previously, studies have attempted to find biological mechanisms for ME/CFS by comparing the DNA of people with ME/CFS with the DNA of people without ME/CFS. These studies have identified regions of DNA linked to the illness; however, none of these links have been found in other ME/CFS studies. In our work, we compare the DNA of people with ME/CFS to the DNA of people without ME/CFS, where ME/CFS status is supported by multiple lines of evidence to reduce the likelihood of misdiagnoses in the participants selected for the study. We then use similar selection strategies, using multiple lines of evidence to repeat the study in independent groups of people. By doing so, we found seven regions of DNA linked to ME/CFS status in more than one study. Some of these links are close to or located in regions of DNA called genes. Genes produce molecules known as proteins, which are responsible for many functions in the human body. It is not currently possible to determine exactly whether genes near disease-linked regions of DNA cause disease, so we report nearby genes with the highest likelihood of linkage to ME/CFS. We also investigated whether the linkage of these regions changed when we further compared groups based on sex or socioeconomic status, but no conclusive results were found. Comparison with the larger DecodeME study showed no overlapping results. ### Competing Interest Statement The authors have declared no competing interest. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Only existing public datasets (UK Biobank and All of Us Research Program) were used. In accordance with UK Biobank regulations, we have included the statement “This research has been conducted using the UK Biobank Resource under Application Number 76173.” in the manuscript's Acknowledgement section, and notified the access management team of UK Biobank at least 2 weeks prior to this submission. Similarly, for All of Us, we included the statement “We also thank the National Institute of Health’s All of Us Research Program... for making available the participant data examined in this study.” and notified the All of Us Research Program at least 2 weeks prior to this submission. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes This study used data from the All of Us Research Program’s Controlled Tier Dataset v8, available to authorised users on the Researcher Workbench. This study also used data from the UK Biobank Resource under Application Number 76173, available to users on the UK Biobank Research Analysis Platform. The datasets and computed code produced in this study are available in the following repositories: NIHR MRC, MC\_PC\_20005 UKRI AI programme Engineering and Physical Sciences Research Council, for CHAI - EPSRC AI hub for Causality in Healthcare AI with real data, EP/Y028856/1 The study was also funded by generous philanthropic donations [1]: pending:yes