---
title: "ADSP FunGen xQTL Atlas"
id: "9023"
type: "study"
slug: "sa000078"
published_at: "2026-06-15T20:18:27+00:00"
modified_at: "2026-06-15T20:56:48+00:00"
url: "https://dss.niagads.org/studies/sa000078/"
markdown_url: "https://dss.niagads.org/studies/sa000078.md"
excerpt: "This study constructs the largest brain-centric xQTL atlas to date, spanning five molecular phenotypes (expression, splicing, protein abundance, DNA methylation, histone acetylation) across 13 brain regions and 7 cell types from thousands of individuals in four cohorts (ROSMAP, MSBB, Knight-ADRC,..."
---

## Description

This study constructs the largest brain-centric xQTL atlas to date, spanning five molecular phenotypes (expression, splicing, protein abundance, DNA methylation, histone acetylation) across 13 brain regions and 7 cell types from thousands of individuals in four cohorts (ROSMAP, MSBB, Knight-ADRC, MiGA). All xQTLs were generated using standardized pipelines developed by the FunGen-AD xQTL Workgroup with stringent quality control. The results were harmonized using a common set of ADSP genomic references.

The overall goal is to create a unified, high-coverage xQTL resource that improves on existing datasets in both scope and usability. To enhance detection of regulatory variants, cis testing windows leveraged tissue-specific topologically associating domains (TADs) instead of conventional fixed 1 Mb windows, identifying ~40% more QTL associations while enriching for variants with regulatory potential.

## PI

Philip L. De Jager  
 *Columbia University Medical Center*

Gao Wang  
 *Columbia University*

Carlos Cruchaga  
 *Washington University School of Medicine in St. Louis*

Yuk Yee (Fanny) Leung  
 *University of Pennsylvania Perelman School of Medicine*

## Associated Datasets

- [NG00184 – ADSP FunGen xQTL Atlas](https://dss.niagads.org/datasets/ng00184/) This dataset contains brain quantitative trait locus (xQTL) summary statistics across six molecular phenotypes: expression quantitative trait loci (eQTL), histone acetylation quantitative trait loci (haQTL), DNA methylation quantitative trait loci… [Learn more](https://dss.niagads.org/datasets/ng00184/)

## Grants

U01AG072572, R01AG086467, U01AG072577, R01AG076901, U01AG072572, RF1AG066107, R01AG067501, R01AG086467, U01AG072577, R01AG080810, U01AG058654, R35GM146868, U01AG058635

## Acknowledgement

### Acknowledgment statement for any data distributed by NIAGADS:

Data for this study were prepared, archived, and distributed by the National Institute on Aging Alzheimer's Disease Data Storage Site (NIAGADS) at the University of Pennsylvania (U24-AG041689), funded by the National Institute on Aging.

### For investigators using ADSP FunGen xQTL Atlas data:

The data described here would not be possible without the participation of research volunteers and the contributions of collaborating investigators across multiple institutions. We gratefully acknowledge all researchers and staff involved in data generation, processing, and sharing.

These data are made available as Open-Access. Individual-level human subject data are provided under Controlled Access and can be accessed at ng00067.v14, ng00105, ng00127, ng00083, ng00102, ng00104.

Relevant support includes, but is not limited to, the following grants:   
NIH funding: R01AG076901, U01AG072572, RF1AG066107, R01AG067501, R01AG086467, U01AG072577, R01AG080810, U01AG058654, R35GM146868, U01AG058635, and support from the Freedom Together Foundation.