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Fig. 5 | Genome Biology

Fig. 5

From: PINES: phenotype-informed tissue weighting improves prediction of pathogenic noncoding variants

Fig. 5

A comparison of weighted and unweighted PINES scores reveals cell type-specific variants. We simulate 5000 background variants (black circles) and 100 cell type-specific variants (red circles) and compute both weighted and unweighted PINES scores. Weighting is based on the annotations that are representative for the cell type-specific variants. The red dots are easily distinguishable from the background variants based on their location in the PINES score space (panel a) as well as the angles they form to the main diagonal (panel b). Applying this approach to variants from the inflammatory bowel disease GWAS in [34], we can detect noncoding variants with putative GI-specific activity. As an example, panel c depicts the annotations present at rs6017342 (red: annotation present, green: annotation absent, gray: missing data), a variant rich in GI-specific annotations that has been implicated by fine mapping of IBD GWAS loci [51]

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