Use case 9: Explore regulatory information associated with a regulatory element
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Download RO-CrateThe 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].
- CFDE Linked Data Hub, https://ldh.genome.network/cfde/ldh/
- The GTEx Consortium atlas of genetic regulatory effects across human tissues. Science vol. 369 1318–1330 (2020). doi:10.1126/science.aaz1776
- 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
- Genomic Location Registry, https://reg.genome.network/reg/loc/
- Integrative analysis of 111 reference human epigenomes. Nature vol. 518 317–330 (2015). doi:10.1038/nature14248
- Pawliczek, P. et al. ClinGen Allele Registry links information about genetic variants. Human Mutation vol. 39 1690–1701 (2018). doi:10.1002/humu.23637
- 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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Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| step-1-data | Regulatory Element Input | Start with a Regulatory Element |
|
| step-6-data | Select One Variant | Select one Variant |
|
Steps
| ID | Name | Description |
|---|---|---|
| step-1 | Regulatory Element Input | Start with a Regulatory Element |
| step-2 | Retrieve regulatory element position | Find regulatory element postion (GRCh38) |
| step-3 | Identify Variants Within Regulatory Element | Retrieve registered variants in the region of given regulatory element from Allele Registry |
| step-4 | Identify Associated Allele Specific Epigenomic Signature | Retrieve variant/variant set associated allele specific epigenomic signatures based on Roadmap and ENTEx data. |
| step-5 | Identify eQTLs and sQTLs and retrieve evidence | Identify eQTL and sQTL information for the given variant(s) based on GTEx data. |
| step-6 | Select One Variant | Select one Variant |
| step-7 | Retrieve alternative identifiers for variant | Retrieve MyVariant.info, dbSNP, gnomAD, and other common identifiers for given variant from ClinGen Allele Registry. |
| step-8 | Identify Variant And Gene Association (HG38) | Get Associated Gene info for a given Variant. |
| step-9 | Identify Genes In Vicinity | Identify genes in 10kbps distance of regulatory element. |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| step-1-output | Regulatory Element | Regulatory Element Term |
|
| step-2-output | Regulatory Element position | Regulatory Element position |
|
| step-3-output | Variant Set | Set of Variants |
|
| step-4-output | Allele Specific Evidence For Variant Set | n/a |
|
| step-5-output | xQTL Evidence For Variant Set | n/a |
|
| step-6-output | Variant | Variant Term |
|
| step-7-output | Allele Registry External Records Table | n/a |
|
| step-8-output | Gene Associations (HG38) | n/a |
|
| step-9-output | Gene Set | Set of Genes |
|
Version History
Version 2 (latest) Created 16th Jan 2025 at 20:58 by Daniel Clarke
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Version 1 (earliest) Created 16th Jan 2025 at 20:55 by Daniel Clarke
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Created: 16th Jan 2025 at 20:55
Last updated: 16th Jan 2025 at 20:57
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