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EPI-2021-0215 Suppl. Data

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posted on 06.10.2021, 09:41 authored by Handan Tan, Guannan Su, Xiao Tan, Yang Qin, Lin Chen, Gangxiang Yuan, Aize Kijlstra, Peizeng Yang

Supplemental Figure 1. Differential allelic transcription factor binding activities in peripheral blood mononuclear cells (PBMCs)

This figure depicts electrophoretic mobility shift assays (EMSA) analysis meant to characterise the binding properties of the risk allele vs. non-risk allele to nuclear protein extract (NE) from PBMCs and interacting protein of NE and antibody, respectively. EMSA were performed using 5`biotinylated probes corresponding to location including rs3024490 (A, B, C, D and E), rs1518110 (F, G) and rs1554286 (H). (A), (B), (C), (D) and (E) show no special binding for the rs3024490 T-allele or G-allele with interacting protein of NE and anti-TBX21, NE and anti-TBX15, NE and anti-MGA, NE and anti-TBX4 or NE and anti-TBX5, respectively. (F) and (G) show no special binding for the rs1518110 T-allele or G-allele with interacting protein of NE and anti-LMX1A or NE and anti-LMX1B, respectively. (H) shows no binding for the rs1554286 T-allele or C-allele with interacting protein of NE and anti-NFATC3.

Supplemental Figure 2. Epigenomic profiling identifies rs3024490 and linkage disequilibrium (LD) single nucleotide polymorphisms (SNPs) as candidate functional SNPs

Associated variants rs3024490 and LD SNPs (hg19 chr1:206944233-206946634) are plotted with the ENCODE (top) and the Roadmap Epigenomics project (bottom) tracking for peripheral blood mononuclear cells. Rs3024490 and LD SNPs were annotated as “enhancer SNPs” based on a 25-state model predicted by histone-modified ChromHMM (top) and H3K27ac and H3K4Me1 enhancer-specific enrichments (bottom).

Supplemental Table 1. DNA sequence designed for primers of luciferase gene-reporter assay

Supplemental Table 2. The basic characteristics of all subjects

Supplemental Table 3. Variants linked to rs3024490 in 1000 GENOMES: phase_3: CHB

Supplemental Table 4. Variants linked to rs3024490 in 1000 GENOMES: phase_3: CHS

Supplemental Table 5. A list of TFs from JASPAR predicted to bind similar DNA motifs containing alleles

Supplemental Table 6. A list of TFs predicted to bind only a similar DNA motif containing rs3024490-G

Supplemental Table 7. A list of TFs predicted to bind only a similar DNA motif containing rs1518110-T

Supplemental Table 8. A list of TFs predicted to bind only a similar DNA motif containing rs1554286-T

Funding

Natural Science Foundation Major International (Regional) Joint Research Project (81720108009)

National Natural Science Foundation Key Program (81930023)

Chongqing Outstanding Scientists Project (2019)

Chongqing Chief Medical Scientist Project (2018)

Chongqing Key Laboratory of Ophthalmology (CSTC, 2008CA5003)

and Chongqing Science & Technology Platform and Base Construction Program (cstc2014pt-sy10002)

History