Overview
All data provided in this dataset are open access and are available publicly in the “Open Access Dataset” tab.
Description
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 (mQTL), protein quantitative trait loci (pQTL), splicing quantitative trait loci (sQTL), and single-nucleus expression quantitative trait loci (snuc-eQTL). The data were generated from four cohorts (ROSMAP, MSBB, Knight-ADRC, MiGA NBB, MiGA MSSM) and 20 brain cell types and regions, including microglia, monocytes, and multiple cortical areas. xQTLs were derived using a standardized Alzheimer’s Disease Sequencing Project Functional Genomics (ADSP FunGen-AD) pipeline with stringent quality control, followed by harmonization to a common set of genomic references to maximize accessibility and interoperability.
Unlike previous xQTL resources, all summary statistics in this atlas provide consistent information on effect alleles, allele frequencies, and effect directions in uniform file formats, and include both full and significance-filtered result sets. This consistency is intended to remove common barriers to downstream applications such as colocalization, Mendelian randomization, and integrative fine-mapping, where heterogeneous formats and partial releases have been a major limitation.
The atlas also extends cis-testing windows using brain topologically associating domains (TADs), yielding additional xQTLs beyond conventional fixed 1 megabase (Mb) windows and supporting more complete detection of regulatory variants. Variants and non-genic molecular features are annotated with overlapping or nearest genes to simplify gene-centric investigation.
The ADSP Functional Genomics xQTL Atlas provides fully quality-controlled xQTL results, high-quality significant xQTL associations using Benjamini–Hochberg and Hierarchical Multiple Testing (HMT) adjustments, and single-context fine-mapping results generated via SuSiE and fSuSiE. All results are in standardized gzipped browser extensible data (BED–like) formats that are also browsable through the companion web portal at https://xqtl.niagads.org/.
Available Filesets
| Name | Accession | Latest Release | Description |
|---|---|---|---|
| ADSP FunGen xQTL Atlas (open access) | fsa000172 | NG00184.v1 | QTL Summary Statistics |
View the File Manifest for a full list of files released in this dataset.
ADSP FunGen xQTL Atlas Download Guide
xQTL Atlas files are not currently available as individual files, but instead as packaged .tar archives. Archives are named as:
ADSP_FunGen_xQTL.v1.<QTL type>.<result type>.tar
Example: ADSP_FunGen_xQTL.v1.pQTL.hmt_significant.tar
| User goal | Recommended result type | Use case |
| Start with high-confidence xQTL associations | hmt_significant | Best default choice for most users |
| Use a broader significant association set | bh_significant | More inclusive than HMT; still FDR-filtered |
| Access all tested associations | all | Complete summary statistics for custom analyses |
| Prioritize likely causal variants | single_context_finemapping_cs95 | Fine-mapped variants in 95% credible sets |
| Review all fine-mapping output | single_context_finemapping_all | Advanced fine-mapping analyses |
Choose the QTL type based on the molecular layer of interest:
| QTL type | Molecular layer |
| eQTL | Bulk gene expression |
| snuc-eQTL | Cell-type-specific single-nucleus expression |
| sQTL | Alternative splicing |
| pQTL | Protein abundance |
| mQTL | DNA methylation |
| haQTL | H3K9ac histone acetylation |
Recommended starting point: download <QTL type>.hmt_significant.tar for association results, or <QTL type>.single_context_finemapping_cs95.tar for fine-mapping results.
Each .tar archive includes harmonized .bed.gz files, .bed.gz.tbi index files, metadata, and a manifest.