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

Colocalisation plots between Treg QTLs and immune disease GWAS signals

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-Castillo1*, Dafni A. Glinos1,2*,
Natalia Kunowska1,**, Gosia Golda1**,

Abigail  Lamikanra3,4, Michaela Spitzer5,6, Blagoje Soskic1,6, Eddie Cano-Gamez1,6, Deborah J. Smyth1,6 ,  Claire Cattermole1 , Kaur Alasoo1,7, Alice Mann1, Anna Lorenc1, Kousik Kundu1 , Nicole Soranzo1 , Ian Dunham5,6 ,  David Roberts3,4, Gosia Trynka1,6

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

Sanger Institute Contributors

Photo of Kousik Kundu

Kousik Kundu

Postdoctoral Fellow

Photo of Dr Alice Mann

Dr Alice Mann

Head of Academic Programmes

Photo of Dr Blagoje Soskic

Dr Blagoje Soskic

Postdoctoral Fellow

Photo of Dr Gosia Trynka

Dr Gosia Trynka

Group Leader at the Sanger Institute and Experimental Science Director at Open Targets

Previous contributors

Photo of Kaur Alasoo

Kaur Alasoo

PhD Student

Photo of Dr Lara Bossini-Castillo

Dr Lara Bossini-Castillo

Postdoctoral Fellow

Photo of Dr Ian Dunham

Dr Ian Dunham

Former Director of Open Targets

Photo of Dafni Glinos

Dafni Glinos

PhD Student

Photo of Dr Natalia Kunowska

Dr Natalia Kunowska

Senior Research Assistant

Photo of Dr Anna (Ania) Lorenc

Dr Anna (Ania) Lorenc

Principal Bioinformatician

External Contributors

Gosia Golda

Abigail Lamikanra

Michaela Spitzer

David Roberts