Fig. 3: Identification of functional regulatory variants with reproducible and concordant effects in allele-specific stimulation of transcriptional activity. | Nature Communications

Fig. 3: Identification of functional regulatory variants with reproducible and concordant effects in allele-specific stimulation of transcriptional activity.

From: Investigation of inherited noncoding genetic variation impacting the pharmacogenomics of childhood acute lymphoblastic leukemia treatment

Fig. 3: Identification of functional regulatory variants with reproducible and concordant effects in allele-specific stimulation of transcriptional activity.

a 556 of the 1696 SNVs assayed are functional regulatory variants with reproducible (FDR < 0.05 in >2 cell lines) and concordant (same directionality in >2 cell lines) changes in allele-specific activity. b Frequency distribution plot showing the number of cell samples showing concordant and significant MPRA activity of variants. c Plot showing the distribution of log2-adjusted activity between alternative (Alt) and reference (Ref) alleles across 556 functional regulatory variants. 210 SNVs (in blue) mapped to accessible chromatin sites in ALL cell lines and 346 SNVs (in black) mapped only to accessible chromatin sites identified in primary ALL cells and/or PDXs. d Upset plot shows how many functional regulatory variants map to open chromatin in diverse ALL cell models. 210 of the 556 functional regulatory variants are found in accessible chromatin sites that were identified in an ALL cell line. Source data are provided in the Source Data file.

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