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This score, defined as the Haplotype Function Score (HFS), replaces the original genotype in association studies. Applying the HFS framework to 14 complex traits in the UK Biobank, we identified 3619 independent HFS\u2013trait associations with a significance of p &lt; 5 \u00d7 10\n                    <jats:sup>\u22128<\/jats:sup>\n                    . Fine-mapping revealed 2699 causal associations, corresponding to a median increase of 63 causal findings per trait compared with single-nucleotide polymorphism (SNP)-based analysis. HFS-based enrichment analysis uncovered 727 pathway\u2013trait associations and 153 tissue\u2013trait associations with strong biological interpretability, including \u2018circadian pathway-chronotype\u2019 and \u2018arachidonic acid-intelligence\u2019. Lastly, we applied least absolute shrinkage and selection operator (LASSO) regression to integrate HFS prediction score with SNP-based polygenic risk scores, which showed an improvement of 16.1\u201339.8% in cross-ancestry polygenic prediction. We concluded that HFS is a promising strategy for understanding the genetic basis of human complex traits.\n                  <\/jats:p>","DOI":"10.7554\/elife.92574","type":"journal-article","created":{"date-parts":[[2023,12,5]],"date-time":"2023-12-05T10:40:17Z","timestamp":1701772817000},"update-policy":"https:\/\/doi.org\/10.7554\/elife.92574","source":"Crossref","is-referenced-by-count":2,"title":["Haplotype function score improves biological interpretation and cross-ancestry polygenic prediction of human complex traits"],"prefix":"10.7554","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3197-6236","authenticated-orcid":true,"given":"Weichen","family":"Song","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/0220qvk04","id-type":"ROR","asserted-by":"publisher"}],"name":"Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Bioengineering, Shanghai Jiao Tong University","place":["Shanghai, 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