Figure 4.

(A) Regulatory activity of a negative control sequence compared to the reference, G, and alternate, A, alleles of rs490972. Each point represents a single replicate and groups are color-coded (p-values from post hoc pairwise t-tests after passing mpralm 5% FDR threshold). (B) Logo plots of the motifs for SP4 (top) and SP1 (bottom). The position corresponding to where rs490972 overlaps both motifs is highlighted by a transparent yellow box. The reference allele of this variant, G, is the consensus nucleotide for both motifs. (C) Scatterplots of variance stabilizing transformation-normalized RNA expression counts for SP4 (top) and SP1 (bottom) compared to log₂(RNA/DNA) for the reference allele of rs490972. Spearman correlation coefficient and p-value are displayed in the top left corner for each comparison. (N = 3 replicates for AICAR-stimulated group, 4 replicates for other three groups for RNA-seq data; N = 4 replicates per group for MPRA data)