The Credible Sets to Cell Type (CS2CT) method, developed internally at the Knowledge Portal Network, identifies credible set variants that are located within regions annotated as potential regulatory elements, such as enhancers or promoters, in specific tissues. This can suggest which variants, genes, and tissues are important for diseases and traits. The results are displayed in a table on the Phenotype page:
In this method, variants grouped into credible sets are cross-referenced with the regions associated with tissue-specific annotations.
- The sum of the posterior probabilities of the variants located within the annotated regions is the Overlap probability; higher overlap probability values indicate a greater probability that the causal SNP is located within the annotated region.
- Genericity is a probability that is normalized across annotation-tissue-biosamples, which represents the tissue specificity of the overlap. Thus a credible set that overlaps an annotation in a single tissue will have a low genericity value (high tissue specificity), while a credible set that overlaps annotations in multiple tissues will have a high genericity value (low tissue specificity).
- The Combined score combines the overlap probability and genericity to highlight credible sets that are present in and specific to an annotation-tissue-biosample set. A high combined score is associated with high presence and specificity.