Fig. 3: EMSA and luciferase reporter assessment of 52 candidate regulatory SNPs.
From: High-throughput identification of functional regulatory SNPs in systemic lupus erythematosus
A Seven biallelic and two triallelic (rs2297550 and rs936394) SNPs showed consistent allele-imbalanced binding for nuclear by EMSA. Allele-specific gel shift/binding marked with red circles. Experiments were repeated three times using distinct nuclear extracts. Representative blots from PBMCs are shown here; BL2 data and negative SNPs are provided in Supplementary Fig. 4 and Supplementary Data 6. B Luciferase reporter assay between the reference (red) and alternative (blue) alleles of nine candidate regulatory SNPs from A in Daudi B cells (mean \(\pm\) s.d, n = 8 biological replicates, Mann–Whitney two-tailed U-test with two-stage step-up correction for multiple hypothesis testing: rs2297550 p = 0.00047, rs906868 p = 0.0013, rs936394 p = 0.00047, rs9907966 p = 0.0071, rs13213604 p = 0.0085). C Diagram displaying the position of 5 SNPs that showed consistent significant differences between alleles through EMSA and luciferase reporter assay; rs2297550 in promoter of IKBKE, rs906868 in intergenic region between YPEL5 and LBH, rs936394 in intron of WBP2, rs9907966 in intron of IKZF3, rs13213604 in intron of BLTP3A. The unit of chromosome position is in kilobases (Kb). A diagram of gene features including exon, intron, and UTR was generated using GSDS 2.0 (http://gsds.gao-lab.org/index.php). Source data are provided as a Source Data file.
