The STAAR PheWAS UKBB Portal is a public web portal providing access to rare coding and noncoding variant associations derived from whole-genome sequencing (WGS) data of up to 490,549 UK Biobank participants. Using the STAARpipelinePheWAS framework, we conducted a phenome-wide association study (PheWAS) of rare coding and noncoding variants across 1,342 phenotypes, including 944 diseases, 76 clinical biomarkers, and 322 metabolomic traits.
STAARpipelinePheWAS is a scalable and computationally efficient framework for phenome-wide functionally informed rare variant association studies across thousands of traits, to enable our cloud-based analysis. Evaluation on the UK Biobank Research Analysis Platform demonstrates that this framework supports comprehensive phenome-wide analyses across 14 coding and noncoding functional categories for protein-coding genes and one functional category for ncRNA genes, enabling rare variant association studies at phenome-wide scale.
All genomic coordinates in this Portal are based on GRCh38. Continuous phenotypes are rank-based inverse normal transformed before analysis. Instructions for navigating and using the portal are provided on the Tutorial page.
If you have any question, please send an email to:
Zilin Li (lizl@nenu.edu.cn)
Xihao Li (xihaoli@unc.edu)
Xihong Lin (xlin@hsph.harvard.edu)
Title: Streamlining large-scale genomic data management: Insights from the UK Biobank whole-genome sequencing data
Journal: Cell Genomics
Year: 2025
Volume: 5 (12)
Pages: 101009
DOI: 10.1016/j.xgen.2025.101009
PMID: 40972583
Title: STAARpipeline: an all-in-one rare-variant tool for biobank-scale whole-genome sequencing data
Journal: Nature Methods
Year: 2022
Volume: 19 (12)
Pages: 1532-1533
DOI: 10.1038/s41592-022-01641-w
PMID: 36316564
Title: A framework for detecting noncoding rare variant associations of large-scale whole-genome sequencing studies
Journal: Nature Methods
Year: 2022
Volume: 19 (12)
Pages: 1599-1611
DOI: 10.1038/s41592-022-01640-x
PMID: 36303018 PMCID: PMC10008172
Title: Dynamic incorporation of multiple in silico functional annotations empowers rare variant association analysis of large whole-genome sequencing studies at scale
Journal: Nature Genetics
Year: 2020
Volume: 52 (9)
Pages: 969-983
DOI: 10.1038/s41588-020-0676-4
PMID: 32839606 PMCID: PMC7483769
