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Table 1 Top 13 CpG sites with loss of DNA methylation in KDM5C mutation cases with the lowest false discovery proportion level =0, the highest confidence level of 99.5% and delta beta ≤ −0.2

From: Multilocus loss of DNA methylation in individuals with mutations in the histone H3 Lysine 4 Demethylase KDM5C

Target ID KDM5C AVG Beta Control AVG Beta VUS AVG Beta p-value delta beta delta Z SYMBOL DISTANCE TO TSS
cg02630888 0.41 0.89 0.91 9.98E-08 −0.48 2.03 FBXL5 −807
cg03387723 0.26 0.71 0.73 9.98E-08 −0.45 2.01 SCMH1 −676
cg16743289 0.24 0.52 0.53 9.98E-08 −0.28 2.02 CACYBP −427
cg06736444 0.50 0.78 0.77 9.98E-08 −0.28 1.90 SRRM2 −861
cg22809047 0.31 0.59 0.54 9.98E-08 −0.27 1.91 RPL31 −490
cg19884658 0.55 0.77 0.74 9.98E-08 −0.23 1.98 KLHL21 −1,339
cg14719055 0.20 0.42 0.37 9.98E-08 −0.23 1.92 RBBP7 −1,218
cg16604218 0.09 0.31 0.35 9.98E-08 −0.22 1.84 EIF2B3 −349
cg20318748 0.07 0.29 0.18 9.98E-08 −0.22 1.95 NANP −564
cg03621001 0.46 0.67 0.77 9.98E-08 −0.21 1.91 RAB8A −771
cg00328227 0.08 0.28 0.30 9.98E-08 −0.2 1.95 C1orf59 −177
cg05072008 0.13 0.33 0.37 9.98E-08 −0.2 1.86 FIGNL1 −599
cg03221914 0.50 0.69 0.70 9.98E-08 −0.2 1.82 HIST1H2AJ −813
  1. VUS is p.R1546Q variant of unknown significance, AVG beta is mean beta value for each of three groups, delta beta is differences between mean of KDM5C mutations cases (N = 10) and controls (N = 19). Delta Z is delta beta divided by standard deviation of combined cases and controls data. All 13 CpG sites were located within CpG islands.