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Table 2 CpGs associated with CPO compared to CLO in the single-site EWAS analysis after filtering out age-related CpGs

From: Distinct DNA methylation profiles in subtypes of orofacial cleft

Chr CpG Regression coefficient P value Gene Relation to CpG island Relation to gene
19 cg01634146 0.19 9.80 × 10−13 NFIX S_Shelf Body
22 cg12899065 0.16 3.98 × 10−8 GP1BB;SEPT5 Island TSS1500;3′UTR
6 cg14623715 0.14 2.46 × 10−10 PDE7B   Body
10 cg02017450 −0.14 5.93 × 10−11 intergenic [SFTA1P]   
8 cg04364695 −0.13 4.27 × 10−8 ZMAT4   Body
7 cg22114489 −0.13 4.60 × 10−8 intergenic [CUX2]   
1 cg12697139 −0.13 2.23 × 10−11 intergenic [MIR205HG]   
2 cg19075787 −0.13 8.44 × 10−9 intergenic [LOC284998]   
11 cg17696044 −0.13 8.61 × 10−8 SHANK2   Body
20 cg19592472 −0.12 5.04 × 10−8 OXT Island 1stExon;5′UTR
4 cg14348967 −0.12 5.12 × 10−9 intergenic [DQ599898]   
6 cg00257775 −0.12 9.45 × 10−10 ZFAND3   Body
3 cg25938530 −0.11 2.04 × 10−8 ITIH1   TSS200;Body
11 cg12155547 −0.11 9.96 × 10−12 intergenic [NEAT1] S_Shelf  
1 cg18147098 0.11 5.44 × 10−8 intergenic [ATF3] S_Shore  
8 cg19496364 0.10 1.16 × 10−8 intergenic [LINC00535]   
7 cg27508620 0.10 3.67 × 10−8 intergenic [SP4]   
6 cg25426302 0.10 9.90 × 10−8 PPT2;PRRT1 N_Shore TSS1500
10 cg20327845 −0.10 6.66 × 10−8 PFKP   Body
3 cg05581878 −0.10 2.50 × 10−9 intergenic [AK097161]   
10 cg19220719 −0.10 7.02 × 10−9 intergenic [C10orf11]   
22 cg13251842 0.09 6.67 × 10−8 MIRLET7A3;MIRLET7B   TSS200; TSS1500
19 cg27392771 0.09 5.25 × 10−15 NFIX S_Shore Body
6 cg23279756 −0.09 7.14 × 10−8 intergenic [ARMC2]   
2 cg07644939 0.09 3.12 × 10−10 SNED1 S_Shore Body
  1. The top 25 CpGs with the largest effect sizes and P values <1 × 10−7 are shown. For intergenic regions, the closest annotated gene is shown in square brackets
  2. S_Shore South shore, S_Shelf South shelf, N_Shore North shore, TSS1500 1500 base pairs from a transcription start site; TSS200 200 base pairs from a transcription start site, UTR untranslated region