Processed data for the study on "Chromatin 3D interactions mediate genetic effects on gene expression"

This repository contains the processed data that was generated as part of the following study:

Delaneau et al. (2019) Chromatin 3D interactions mediate genetic effects on gene expression.

Abstract: Studying the genetic basis of gene expression and chromatin organization is key to characterize the effect of genetic variability on the function and structure of the human genome. Here, we unravel how genetic variation perturbs gene regulation using a dataset combining activity of regulatory elements, gene expression and genetic variants across 317 individuals and two cell types. We show that variability in regulatory activity is structured at the intra- and inter-chromosomal levels within 12,583 Cis Regulatory Domains and 30 Trans Regulatory Hubs that highly reflect the local (i.e. Topologically Associating Domains) and global (i.e. open/close chromatin compartments) nuclear chromatin organization. These structures delimit cell type specific regulatory networks that control gene expression/co-expression and mediate the genetic effects of cis- and trans-acting regulatory variants on genes.

This repository contains:

1. Chromatin QTLs for H3K27ac, H3K4me1 and H3K4me3 discovered in 317 Lymphoblastoids Cell Lines (LCLs) and 78 Fibroblasts.
2. Molecular QTLs affecting the activity and structure of Cis Regulatory Domains (CRDs) in LCLs.
3. Basic information about the full set of genetic variants being analyzed in the study.
4. The peak coordinates, their hierarchy based on inter-individual correlation and the CRD calls for both LCLs and Fibroblasts.
5. The functional links discovered in LCLs between CRDs and genes.
6. eQTLs for LCLs.
7. A README file containing the description of the file format for each file.