# Decoding the regulatory architecture of the human genome across cell types, individuals and disease

> **NIH NIH U01** · STANFORD UNIVERSITY · 2021 · $619,508

## Abstract

PROJECT DESCRIPTION
While accurate annotations of protein-coding regions in the human genome have been available for
many years, annotation and interpretation of regulatory sequences has lagged far behind. This is
because—in contrast to protein-coding sequences—the “rules” that govern links from genome
sequence to regulatory function are fuzzy, complex, and highly context-specific. Our limited
understanding of regulatory regions presents a fundamental challenge for the identification and
interpretation of disease variation, especially in the context of personal genome interpretation. Work
from ENCODE and other groups has started to close this gap through experimental work, including
high-resolution maps of regulatory sites in a variety of cell types, and modeling of the cell-type
specific mappings from genome sequence to regulatory function. In our funded project so far we have
developed new computational tools to understand gene regulation, and how this may be impacted by
genetic variation; as well as new methods for high throughput validation. In the Supplement year, we
propose to extend this work with additional projects focusing in this area, including work on zinc finger
proteins; connections between genetic variation, RNA expression, and GWAS; and, finally, high
throughput CRISPR-based validation experiments.

## Key facts

- **NIH application ID:** 10241018
- **Project number:** 3U01HG009431-04S1
- **Recipient organization:** STANFORD UNIVERSITY
- **Principal Investigator:** JONATHAN K PRITCHARD
- **Activity code:** U01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $619,508
- **Award type:** 3
- **Project period:** 2017-02-01 → 2022-01-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10241018

## Citation

> US National Institutes of Health, RePORTER application 10241018, Decoding the regulatory architecture of the human genome across cell types, individuals and disease (3U01HG009431-04S1). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10241018. Licensed CC0.

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