ROSMAP Single-Nucleus Chromatin Accessibility QTL (caQTL)
Single-nucleus ATAC-seq chromatin accessibility QTL analysis from ROSMAP donors, using the MIT snATAC-seq dataset described in Xiong et al., Cell 186, 4422–4437 (2023).
Please refer to this document for an overview of the ROSMAP project.
Access
Controlled access. Request data access for ROSMAP on the AD Knowledge Portal; you need a Synapse account. See How to get the data.
| Where | ID | Access | What you get |
|---|---|---|---|
| Synapse | syn69670592 | Controlled | Results described below |
Other Synapse IDs on this page syn69670597 syn69865816 syn69670630
pip install synapseclient
synapse login
synapse get -r syn69670592Contact
FunGen-xQTL Analysis Team
Study Overview
- Study name: ROSMAP snATAC-seq caQTL
- Study Description: Chromatin accessibility quantitative trait loci (caQTL) using pseudo-bulk ATAC-seq profiles per cell type. Data are from the MIT snATAC-seq dataset (Mic, Ast, Oli, OPC, Exc, Inh). A response caQTL (r-caQTL) analysis was also performed to identify variants affecting chromatin remodeling in context of co-measured gene expression.
- Cell types: Microglia (Mic), Astrocytes (Ast), Oligodendrocytes (Oli), OPCs (OPC), Excitatory neurons (Exc), Inhibitory neurons (Inh)
- Assay: single-nucleus ATAC-seq (snATAC-seq)
Analysis Details
Path(s) to fine-mapping with fSuSiE / SuSiE RSS model
Fine-mapping model objects (fSuSiE/SuSiE-RSS, .rds) are available in the finemapping models folder (syn69670592).
Path(s) to colocalization
Pairwise colocalization models (SuSiE-coloc): syn69670597
AD GWAS–xQTL colocalization results: syn69865816
AD GWAS–xQTL colocalization models: syn69670630
Analyses
- cis-QTLDone
Read from the methods: map in this page's metadata header, the same data as the analysis coverage grid.