GWAS SVatalog is a novel visualization tool and database for structural variants (SV) found in a predominantly European population of 101 individuals with Cystic Fibrosis (CF). Aside from the CF-causing variants on chromosome 7 and the LD block in which they lie, the remainder of the genome is comparable to a the 1000 Genomes healthy European population. This data is a collection of SV calls and their linkage disequilibrium (LD) statistics with GWAS-significant SNPs reported in the GWAS Catalog. The goal of this project is to provide a resource to aid fine mapping of GWAS loci using SVs. GWAS loci are generally identified by SNPs which account for an incomplete proportion of genetic variation and phenotypic heritability. Their relevance to the phenotype might be limited, tagging other polymorphisms, such as SVs, that could be the cause of the association signal. To leverage this data to its full potential, visit the GWAS SVatalog web tool. Here, interactive visualizations can illustrate SVs identified in high LD with GWAS-significant SNPs, suggesting putative causal variation that could guide additional functional investigation. For more information on how to use GWAS SVatalog, visit the documentation. This project was accomplished in collaboration with the Strug Lab at The Hospital for Sick Children (SickKids), The Center for Applied Genomics (TCAG), and University of Toronto.

File descriptions: gwas_catalog_v1.0-associations_e108.tsv : GWAS Catalog v1.0 associations data MANE.GRCh38.v1.0.ensembl_genomic.gtf : MANE dataset v1.0 for genes in the human genome sv_annotations.tsv : SV calls annotated using a pipeline based on CNV/SV callers Dragen 3.8.4, Manta 1.6.0, Delly 0.8.1, CNVnator 0.4 and ERDS 1.1 chr*_allele_freq.txt : Allele frequencies of SNPs and SVs in the CF cohort and gnomAD's Non-Finnish European (NFE) population. Also includes official variant name obtained from dbSNP chr*_ld_stats.txt : LD statistics between SNPs and SVs