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. 2020 Jun 1;11:2718. doi: 10.1038/s41467-020-16590-1

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© This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply 2020

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Fig. 2 — a Variants that were tested in MPRA from the Chr21q22.3 melanoma locus are shown relative to the genomic position of MX2. Only the 19 variants located in the first intron of MX2 coming from the primary GWAS signal are shown (the other three from a secondary signal are located upstream of the MX2 genic region). ChromHMM annotation (Primary Core Marks segmentation) of Penis Foreskin Melanocyte Primary Cells from Roadmap Epigenomics Project is shown (Red/OrangeRed: Active_TSS/Flanking_Active_TSS, Yellow/GreenYellow: Enhancers/Genic_enhancers, Green/DarkGreen: Strong_transcription/Weak_transcription). Melanoma FAIRE-seq track of 11 samples is from a study by Verfaillie and colleagues²⁶. Ensembl predicted transcripts from archive 75 are shown. b Transcriptional activity of 145 bp sequences encompassing rs398206 from MPRA are shown as normalized tag counts (log₂(RNA TPM/DNA TPM)). Results from UACC903 melanoma cells are shown for both alleles in forward (For) and reverse (Rev) directions, where results from promoter and enhancer constructs were combined. Center lines show the medians; box limits indicate the 25th and 75th percentiles as determined by R software; whiskers extend 1.5 times the interquartile range from the 25th and 75th percentiles, outliers are represented by dots. Density is reflected in the width of the shape. c Individual luciferase activity assays of 145 bp sequences encompassing rs398206 is shown for UACC903. pGL4.23 construct including minimal TATA promoter was used. One representative set is shown from three biological replicates. Mean with SEM, n = 6. All constructs are significantly higher than pGL4.23 (TATA) control (P < 0.0001, two-tailed, unpaired t-test assuming unequal variance). d eQTL plot of MX2 levels in primary melanocytes in relation to rs398206 is shown for three genotype groups. Center lines show the medians; box limits indicate the 25th and 75th percentiles; whiskers extend 1.5 times the interquartile range from the 25th and 75th percentiles. P-value and slope were derived from linear regression with no multiple-testing correction applied. Source data are provided as a Source Data file.