Extended Data Fig. 10: Identification of functional regulatory variants near the DDB1 locus.
(a) Plots showing allelic skewed variants in regulatory elements near the DDB1 locus. rs7948623 overlaps an open chromatin region in melanocytes and many other cell types. rs2277285 and rs2943806 are located within CTCF binding sites and TAD boundaries. Blue tracks indicate DNase-seq, ATAC-seq, and ChIP-Seq data from melanocytes; orange tracks indicate ChIP-Seq data from melanoma (501-mel) cells; gray tracks indicate CTCF ChIP-Seq data from three cell lines; and green tracks indicate DNase-Seq data from ENCODE68. (b-d) Allelic skews at rs7948623, rs2277285 and rs2943806 as estimated by MPRA (n = 3). P values were estimated with a random effects model for mpralm and paired t-tests without multiple testing adjustments. For boxplots, central lines are median, with boxes extending from the 25th to the 75th percentiles. Whiskers further extend by ±1.5 times the interquartile range from the limits of each box. (e) rs7948623 disrupts a MITF binding motif and overlaps ChIP-seq peaks from the Cistrome database103. (f, g) LD pattern between the MFVs at the DDB1 locus. LD was calculated using the 180G18 dataset.
