variant-annotation skillA
variant-annotation is agent-read markdown (skill) from ammawla/encode-toolkit: Annotate genetic variants (GWAS hits, eQTLs, rare variants) with ENCODE functional data to interpret non-coding variation. Use when the user has variants of interest and wants to understand their regulatory context, identify causal variants from GWAS loci, assess variant impact on regulatory elements, perform enrichment testing of variant sets in tissue-specific annotations, or link variants to target genes through enhancer-gene maps. Handles the full post-GWAS workflow from variant set → tissue.
Indexed from public GitHub and served as immutable, content-addressed versions. Install it pinned to an exact SHA-256 with the mdr CLI, and every file is verified against the hash recorded here before it reaches your agent. The deterministic audit below grades the latest version, and the same file always earns the same grade.
What the file says
# Functional Annotation of Genetic Variants with ENCODE Data ## When to Use - User wants to annotate genetic variants with ENCODE regulatory element overlap and functional evidence - User asks about "variant annotation", "regulatory variants", "non-coding variants", or "variant prioritization" - User needs to assess whether a variant falls in an active enhancer, promoter, or TF binding site - User wants to build a multi-evidence variant interpretation combining ENCODE + ClinVar + gnomAD - Example queries: "annotate my GWAS hits with ENCODE regulatory data", "does this variant disrupt a TF binding site?", "prioritize non-coding variants by regulatory impact" Interpret non-coding genetic variation by layering ENCODE functional genomics annotations to identify causal regulatory variants and link them to target genes. ## Scientific Rationale **The question**: "Which of my GWAS/eQTL variants actually disrupt regulatory elements, and what genes do they affect?" …
Read the whole file at its exact version.
How to install
mdr add ammawla/encode-toolkit/variant-annotation@git:20260920.6050003mdr add ammawla/encode-toolkit/variant-annotation@sha256:355c7f451018a9bcPin to a label to follow the author's releases, or to a sha256 to freeze the exact bytes forever. Either way the resolved hash is written to mdr.lock, and mdr install reproduces it on any machine.
[](https://markdownregistry.com/a/art_shayhrrhpjefl2jr)
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Versions
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260920.6050003 latest | 2026-09-20 | 6050003 | 29,830 B | A | view · diff |
| git:20260920.ce7840d | 2026-09-20 | ce7840d | 29,365 B | A | view · diff |
| git:20260321.d9029d0 | 2026-03-21 | d9029d0 | 29,349 B | A | view · diff |
| git:20260312.be32706 | 2026-03-12 | be32706 | 29,343 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (29830 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
ammawla/encode-toolkit · 20 stars · license AGPL-3.0 · pushed 2026-09-21 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_shayhrrhpjefl2jr GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/variant-annotation GET https://markdownregistry.com/api/v1/blob/355c7f451018a9bc4a0cc31ff9b505553d9459d6bd11a539eec8206d993817e3
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