Fig. 4: Genomic context of identified putative causal variants.
From: Functional dissection of inherited non-coding variation influencing multiple myeloma risk
Based on our functional screens, we identified eight putative causal variants (highlighted in red and with dashed lines) across six loci. The figure shows their association P values (Fig. 1a), with the lead SNP indicated as a triangle, along with ATAC-seq data for plasma cells (blue) and 11 ChromHMM states in the MM plasma cell line KMS11. We also generated PCHi-C data for the MM plasma cell lines KMS11 (yellow), KMS12 (orange), and MM1S (red), and identified chromatin looping interactions using the CHiCAGO tool. Interactions with −log10(CHiCAGO P score) ≥2 are shown. a At the SMARCD3 locus, we detected a chromatin looping interaction between the rs787404585 region and the SMARCD3 promoter. b rs2790444 at WAC, located close to the promoter within the PCHi-C bait region. c rs3777189 and rs3777183-rs3777182 at ELL2, where rs3777182 and rs3777183 are located only 17 bp apart. We detected a chromatin looping interaction between the rs3777183-rs3777182 region and the promoter. d No looping interactions were detected at CDCA7L. e At the PREX1 locus, we detected a looping interaction between the rs6066832 region and the PREX1 promoter. f No looping interactions were detected for the CEP120 association. Vertical lines indicate variant positions. Coordinates are hg38.
