Figure 1. Fine-mapping and epigenomic annotations of melanoma GWAS and melanocyte eQTLs for the 9q34.13 melanoma risk locus.
A. Genetic variants fine-mapped for the melanoma GWAS are annotated, along with Bayesian fine-mapped variant credible sets (CS) from SuSiE and DAP-G for human primary melanocyte eQTLs for RAPGEF1 and UCK1. Roadmap chromatin states (ChromHMM) from primary melanocytes are shown; red and orange denote annotated promoter, yellow and light green enhancer. Chromatin accessibility from DNAse I hypersensitivity sequencing (DHS) and ATAC-sequencing (ATAC) of melanocytes and melanoma cell models is shown. Chromatin interactions between the entire region of association (Capture-HiC baits) in human melanocytes is shown, as are separately only those interactions between fine-mapped variants and gene promoters; fine-mapped variants interact with the promoters of both RAPGEF1, UCK1, and NTNG2 (not shown on figure). B. Zoomed in view of the fine-mapped variants. The locations of small guide RNAs used for CRISPR-inhibition (CRISPRi sgRNAs) experiments are shown. Chromatin interactions between regoins harboring fine-mapped variants and gene promoters in human melanocytes are shown. C. CRISPR-inhibition (CRISPRi) validation of RAPGEF1 and UCK1 as cis-regulatory targets at 9q34.13. Guide RNAs were designed to target three fine-mapped variants within an ~11.3 kb interval. Each guide was individually tested for effects on RAPGEF1 and UCK1 expression relative to the average of two non-targeting guides in immortalized melanocytes stably expressing dCas9-KRAB via a TaqMan quantitative RT-PCR assay. Whiskers show minimum and maximum values. P-values were calculated using a two-sample two-sided paired t-test comparing 2^(delta-Ct) values from individual guides to those from the average of the two non-targeting guides with 10 biological replicates in total.