Fig. 1

Making sense of GWAS: an overview. Shown is a flow chart of analytical and experimental steps that can be followed to understand how a non-coding SNP can be associated with an increased risk for a specific disease. Index SNPs are identified using GWAS arrays and then expanded to a larger set of SNPs (termed Refined Associated SNPs) using LD scores and fine-mapping. These Refined Associated SNPs are then prioritized using functional annotation to identify Regulatory SNPs (Reg SNPs) or linkage to allele-specific gene expression to identify eQTL SNPs, producing a set of Candidate Functional SNPs. The Candidate Functional SNPs can either be studied directly or further refined by testing the Regulatory SNPs for possible SNP-RNA linkages or by testing the eQTL SNPs for functional annotation. If a Candidate Functional SNP (yellow arrowhead) lies within a distal regulatory element, it can be deleted or modified using genomic nucleases or epigenomic toggle switches (Approach A); putative target genes are then identified using RNA-seq. Distal regulatory elements that cause changes in gene expression when deleted or modified can then be studied using allele-specific analyses (Approach B); promoters harboring risk-associated SNPs (pink arrowhead) can be directly studied using Approach B. As described in the text, cells deleted for the distal regulatory elements can be used to identify an appropriate phenotypic assay for analysis of the candidate target genes. Then, the genes that show expression changes that are linked to distal SNPs and the genes regulated by the promoter SNPs can be studied using those biological assays to identify possible therapeutic targets and/or candidates for diagnostic tests. Finally, looping assays can be performed to distinguish direct from indirect targets of the distal regulatory elements. It is important to note that a gene whose expression is indirectly affected by a non-coding SNP could be a more important diagnostic or therapeutic target than the directly affected gene