Research Object Crate for Use case 9: Explore regulatory information associated with a regulatory element

The workflow starts with selecting EH38E2924876 as the search term. Genomic position of provided unique regulatory element identifier was retrieved from CFDE Linked Data Hub[1]. A list of variants in the region of the regulatory element was retrieved from CFDE Linked Data Hub[1]. Variant/variant set associated allele specific epigenomic signatures were retrieved from CFDE LDH[5] based on Roadmap and ENTEx data[6], [4]. GTEx eQTL and sQTL evidence for the given variant(s) were retrieved from CFDE LDH[5][3]. MyVariant.info, dbSNP, gnomAD, and other common identifiers for the given variant(s) were retrieved from ClinGen Allele Registry[7]. Gene(s) in the vicinity of the given variant(s) were retrieved from MyVariant.info API results[8]. A list of genes in the 10kbps region of the given regulatory element was retrieved from CFDE Linked Data Hub[1]. 1. CFDE Linked Data Hub, https://ldh.genome.network/cfde/ldh/ 3. The GTEx Consortium atlas of genetic regulatory effects across human tissues. Science vol. 369 1318–1330 (2020). doi:10.1126/science.aaz1776 4. Onuchic, V. et al. Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci. Science vol. 361 (2018). doi:10.1126/science.aar3146 5. Genomic Location Registry, https://reg.genome.network/reg/loc/ 6. Integrative analysis of 111 reference human epigenomes. Nature vol. 518 317–330 (2015). doi:10.1038/nature14248 7. Pawliczek, P. et al. ClinGen Allele Registry links information about genetic variants. Human Mutation vol. 39 1690–1701 (2018). doi:10.1002/humu.23637 8. Lelong, S. et al. BioThings SDK: a toolkit for building high-performance data APIs in biomedical research. Bioinformatics vol. 38 2077–2079 (2022). doi:10.1093/bioinformatics/btac017

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