Background Genome-wide association studies (GWAS) have identified hundreds of loci underlying adult-onset asthma (AOA) and childhood-onset asthma (COA). However, the causal variants, regulatory elements, and effector genes at these loci are largely unknown. Methods We performed heritability enrichment analysis to determine relevant cell types for AOA and COA, respectively. Next, we fine-mapped putative causal variants at AOA and COA loci. To improve the resolution of fine-mapping, we integrated ATAC-seq data in blood and lung cell types to annotate variants in candidate cis-regulatory elements (CREs). We then computationally prioritized candidate CREs underlying asthma risk, experimentally assessed their enhancer activity by massively parallel reporter assay (MPRA) in bronchial epithelial cells (BECs) and further validated a subset by luciferase assays. Combining chromatin interaction data and expression quantitative trait loci, we nominated genes targeted by candidate CREs and prioritized effector genes for AOA and COA. Results Heritability enrichment analysis suggested a shared role of immune cells in the development of both AOA and COA while highlighting the distinct contribution of lung structural cells in COA. Functional fine-mapping uncovered 21 and 67 credible sets for AOA and COA, respectively, with only 16% shared between the two. Notably, one-third of the loci contained multiple credible sets. Our CRE prioritization strategy nominated 62 and 169 candidate CREs for AOA and COA, respectively. Over 60% of these candidate CREs showed open chromatin in multiple cell lineages, suggesting their potential pleiotropic effects in different cell types. Furthermore, COA candidate CREs were enriched for enhancers experimentally validated by MPRA in BECs. The prioritized effector genes included many genes involved in immune and inflammatory responses. Notably, multiple genes, including TNFSF4, a drug target undergoing clinical trials, were supported by two independent GWAS signals, indicating widespread allelic heterogeneity. Four out of six selected candidate CREs demonstrated allele-specific regulatory properties in luciferase assays in BECs. Conclusions We present a comprehensive characterization of causal variants, regulatory elements, and effector genes underlying AOA and COA genetics. Our results supported a distinct genetic basis between AOA and COA and highlighted regulatory complexity at many GWAS loci marked by both extensive pleiotropy and allelic heterogeneity.

The authors have declared no competing interest.

This study was supported by U19 AI62310 (C.O., M.A.N., A.I.S.), R01 MH110531, R01 MH116281, R01 HG010773, R01 HL163523 (X.H.), and UG3/UH3 OD023282 and UM1 AI160040 (C.O.). I.M.S. was supported by T32 HL007605. N.S. was supported by K08 HL153955.

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:

The Institutional Review Board (IRB) at the University of Chicago waived ethical approval for this study.

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 uses genotype and phenotype data from the UK Biobank under application number 44300. Access to UK Biobank resource is available with application at http://www.ukbiobank.ac.uk. Summary statistics of AOA and COA GWAS performed with UK Biobank version 3 genotypes will be made available prior to publication of the manuscript. The sequencing data generated in this study were deposited in EMBL-EBI's Array Express database (https://www.ebi.ac.uk/biostudies/arrayexpress) under accession numbers E-MTAB-14267 (ASMCs ATAC-seq), E-MTAB-14273 (BECs MPRA), and E-MTAB-14295 (ASMCs PCHi-C). The snATAC-seq data from 18 lung cell types were downloaded from https://www.lungepigenome.org. The ATAC-seq data from seven blood cell types were downloaded from https://github.com/caleblareau/singlecell_bloodtraits/tree/master/data/bulk/ATAC/narrowpeaks. The BECs ATAC-seq data are available as supplementary material from the original publication: https://doi.org/10.1038/s42003-020-01411-4. The PCHi-C datasets are available as supplementary material from the original publications: https://doi.org/10.1016/j.cell.2016.09.037 (blood immune cells), https://doi.org/10.1038/s42003-020-01411-4 (BECs), and https://doi.org/10.1038/s42003-020-01411-4 (bulk lung). The ABC models are available on Engreitz Lab website: https://www.engreitzlab.org/resources/. GTEx V8 eQTLs were downloaded from https://www.gtexportal.org/home/downloads/adult-gtex/qtl. DICE eQTLs were downloaded from https://dice-database.org/downloads#eqtl_download. OneK1K single-cell eQTLs in peripheral blood mononuclear cells were downloaded from https://onek1k.org/. Single-cell eQTLs in lung were downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE227136. All analysis code is available on GitHub: https://github.com/ez-xyz/asthma_finemapping.