EpiMark: Epigenomic Annotation from Sequence

EpiMark is a 420M parameter epigenomic annotation model. Given a genomic region and cell type, it predicts histone marks, CpG methylation, and chromatin accessibility from sequence context alone. No ChIP-seq or ATAC-seq data required.

At a glance

Field	Value
Category	Genomics
Parameters	420M
Version	v1.1
Endpoint	`POST /v1/models/epimark/predict`
Supported cell types	300+ ENCODE and Roadmap reference cell lines

Install

pip install bunker-fold

See Installation for full setup, including uv and poetry.

When to use

Annotate regulatory elements in a locus without running assays.
Compare predicted epigenomic state across cell types.
Prioritize non-coding variants by predicted regulatory impact.

Example

curl -X POST https://api.bunkerbio.com/v1/models/epimark/predict \
  -H "Authorization: Bearer $BUNKER_API_KEY" \
  -H "Content-Type: application/json" \
  -d '{
    "region": "chr11:5225000-5250000",
    "cell_type": "K562",
    "marks": ["H3K27ac", "H3K4me3", "ATAC", "CpG_methyl"]
  }'

import requests, os

r = requests.post(
    "https://api.bunkerbio.com/v1/models/epimark/predict",
    headers={"Authorization": f"Bearer {os.environ['BUNKER_API_KEY']}"},
    json={
        "region": "chr11:5225000-5250000",
        "cell_type": "K562",
        "marks": ["H3K27ac", "H3K4me3", "ATAC", "CpG_methyl"],
    },
)
print(r.json())

Response

{
  "H3K27ac": {"state": "active_enhancer", "peaks": 3, "p_value": 1e-8},
  "H3K4me3": {"state": "active_promoter"},
  "ATAC": {"state": "open_chromatin"},
  "CpG_methyl": {"level": 0.12, "state": "hypomethylated"},
  "overall_state": "active_regulatory"
}

Parameters

string

required

Genomic region in chrN:start-end format. Maximum window 100 kb.

string

required

ENCODE or Roadmap cell type identifier (for example, K562, GM12878).

string[]

Marks to predict. Defaults to a standard panel. Valid values include H3K27ac, H3K4me3, H3K4me1, H3K27me3, ATAC, DNase, CpG_methyl.

Response fields

object

Prediction for the H3K27ac mark with state, peaks, and p_value fields.

object

Chromatin accessibility prediction. state is one of open_chromatin or closed_chromatin.

object

CpG methylation prediction with a fractional level and categorical state.

string

Aggregated regulatory state for the region: active_regulatory, poised, repressed, or quiescent.

Get Started

Models

API Reference

Installation

EpiMark: Epigenomic Annotation from Sequence

At a glance

Install

When to use

Example

Parameters

Response fields