Treg Colocalisation

Colocalisation plots between Treg QTLs and immune disease GWAS

Overlap of Treg QTLs from gene-expression and chromatine activity  with immune disease GWAS signals. Dataset from Trynka Group

We profiled gene expression (RNA-seq) and chromatin activity (using ATAC-seq, H3K4me3 and H3K27ac assays) in CD4+ regulatory T cells isolated from 124 healthy individuals. We identified between 1,450 and 4,290 QTL effects across the different assays. We performed colocalisation of these QTL signals with variants associated with different immune diseases. Preprint here Paper here

The tool provides a visualisation of the colocalisation plots between Treg-specific QTLs and 133 immune disease GWAS signals. It includes correlation plots between p-values of GWAS variants and QTL SNPs and locus zoom plots to examine the LD structure within the associated loci. You can query peaks, genes (via ENSG or gene symbols).

Study authors:

Lara Bossini-Castillo^1*, Dafni A. Glinos^1,2*,
Natalia Kunowska¹,**, Gosia Golda¹**,

Abigail  Lamikanra^3,4, Michaela Spitzer^5,6, Blagoje Soskic^1,6, Eddie Cano-Gamez^1,6, Deborah J. Smyth^1,6 ,  Claire Cattermole¹ , Kaur Alasoo^1,7, Alice Mann¹, Anna Lorenc¹, Kousik Kundu¹ , Nicole Soranzo¹ , Ian Dunham^5,6 ,  David Roberts^3,4, Gosia Trynka^1,6

1. Wellcome Sanger Institute, Cambridge, UK
2. New York Genome Center, New York, NY, USA
3. NHS Blood and Transplant, Oxford, UK
4. Radcliffe Department of Medicine, University of Oxford, UK
5. European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI),  Wellcome Genome Campus, Hinxton, Cambridge, UK
6. Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, UK
7. Institute of Computer Science, University of Tartu, Tartu, Estonia

* , ** These authors contributed equally

Online tool and web presence helped by Nick Boughton¹