Extended Data Fig. 6: Functional testing of Di-SNPs near LEF1.
(a) MFVs and regulatory elements near LEF1. rs17038630 and rs11939273 are Di-SNPs from the San population. (b) Plot showing allelic skews at rs17038630 in MNT-1 and WM88 cells estimated by MPRA (n = 3). (c) rs17038630 overlaps SOX10 and LEF1 binding sites. Left panel shows that rs17038630 disrupts the binding motif of SOX10 and LEF1. Right panel shows that rs11939273 overlaps ChIP-seq peaks from the Cistrome database103. (d) MPRA and LRA results showing allelic skews at Di-SNP rs11939273 in MNT-1 and WM88 cells, the allele frequency data was from the 180 G18 and 1000 G31 dataset. MPRA (n = 3), LRA (MNT-1, n = 6; WM88, n = 9). LRA data are presented as mean ± SEM, tested with two-tailed paired t-tests. (e) CRISPR-KO of the enhancer E1 of LEF1 does not affect LEF1 expression and melanin levels in MNT-1 cells. Left panel shows genotyping results of CRISPR-KO of the enhancer E1 of LEF1, three independent experiments. Middle panel shows the RT-qPCR results of CRISPR-KO of the enhancer E1 of LEF1 (n = 9). Right panel shows the melanin levels of CRISPR-KO of the enhancer E1 of LEF1 (n = 9). Two-tailed unpaired t-tests. For MPRA boxplots in b and d, 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. MPRA p-values were estimated with a random effects model for mpralm and paired t-tests with multiple testing adjustments.
