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. 2020 May 21;106(6):748–763. doi: 10.1016/j.ajhg.2020.04.008

Figure 5.

Figure 5

KIF26B, FGD6, and VEGFC Loci

(A) Browser-style track of KIF26B locus with 3D Hi-C data from HUVECs shown by heatmap above with epigenetic tracks shown below. Vertical yellow bar highlights enhancer-like region containing SNP of interest, with KIF26B promoter highlighted in pink. Cell types listed for H3K27ac are from E—NCODE. GM12878human B-lymphocyte-lymphoblastoid cell line; H1-hESC—human embryonic stem cells; HSMM—human skeletal muscle myoblasts; A549—human epithelial lung carcinoma-derived cell line; HUVEC—human umbilical vein endothelial cells; K562—human chronic myelogenous leukemia-derived cell line; NHEK—human epidermal keratinocytes; NHLF—human lung fibroblasts.

(B) The SNP shown in a is an eQTL for KIF26B, a molQTL for chromatin accessibility, H3K27ac (including allele-specific plot), ERG binding, and p65 binding (including allele-specific plot).

(C) rs12028528 mutates an AP-1 motif.

(D) Reduced KIF26B expression in HAECs treated with pooled gRNAs with CRISPR interference (CRISPRi) within 200 bp of rs12028528. n = 5. Expression measured by qPCR and normalized to GAPDH. Data show mean ± standard error of the mean. ∗p < 0.05, ∗∗∗p < 0.001 as determined from unpaired t test.

(E) The functional effect rs12028528 was replicated via luciferase assay in teloHAECs (n = 3 independent experiments; p < 0.05 by unpaired 2-tailed t test).

(F) FGD6 locus with SNP rs7975658 in an enhancer-like region (yellow) within FGD6 intron.

(G) Plots for eQTL for FGD6 in untreated and gene-by-environment eQTL (y axis = oxPL RNA − notx RNA for FGD6). This SNP is also an hmQTL with allele-specificity (within heterozygotes) and an NF-kB bQTL with allele-specificity.

(H) rs7975658 mutates a BACH motif.

(I) CRISPRi and guides at rs7975658 reduced FGD6 compared to control as in (D).

(J) Luciferase reporter assay in teloHAECs as in (E).

(K) VEGFC locus with SNP rs6825977 in an enhancer-like region (yellow), which loops with the VEGFC promotor (pink) based on high-throughput chromatin conformation capture (HiC) data.

(L) The SNP is an eQTL for VEGFC, an hmQTL with allele-specificity, and an NF-kB bQTL with allele-specificity.

(M) rs6825977mutates an ETS motif.

(N) CRISPRi with gRNA targeting rs6825977 reduced VEGFC RNA versus control as in (D).

(O) Luciferase reporter assay in teloHAECs as in (E).