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Table 3 CpG sites showing significant differences in DNA methylation between cases with PDR and controls (FDR q <5 %, Additional file 3: Table S3), that are also nominally differentially methylated in the same direction in the converters of the prospective cohort at P <0.05

From: Genome-wide analysis of DNA methylation in subjects with type 1 diabetes identifies epigenetic modifications associated with proliferative diabetic retinopathy

   Location in relation to: DNA Methylation (%)  
Probe ID Chr Nearest gene Gene region CpG Island Controls Converters Difference P value q value
cg26703534 5 AHRR Body S Shelf 63.6 ± 2.6 59.9 ± 4.1 −3.7 9.5 × 10−4 0.17
cg05575921 5 AHRR Body N Shore 82.4 ± 6.3 75.0 ± 8.1 −7.4 2.1 × 10−3 0.18
cg07339236 20 ATP9A Body Open sea 18.0 ± 2.5 15.6 ± 1.6 −2.4 0.013 0.35
cg05026884 X BCOR 5′UTR Island 26.5 ± 11.1 22.7 ± 4.7 −3.8 4.2 × 10−3 0.21
cg01490258 X BCOR 5′UTR N Shore 13.2 ± 2.9 12.4 ± 2.0 −0.8 0.010 0.33
cg23701759 X BCOR 5′UTR Island 34.9 ± 4.9 30.9 ± 3.7 −4.0 0.014 0.35
cg10055320 X BCOR 5′UTR N Shore 42.2 ± 4.4 39.2 ± 5.1 −3.0 0.029 0.50
cg00507154 19 C19orf76 1st Exon; 5′UTR Island 70.2 ± 4.6 67.7 ± 2.6 −2.5 0.030 0.50
cg08601628 8 C8orf74 Body Open sea 82.5 ± 3.0 80.6 ± 3.2 −1.9 0.022 0.43
cg12993916 6 DTNBP1 Body Open sea 78.9 ± 3.0 76.8 ± 3.7 −2.1 0.015 0.35
cg03636183 19 F2RL3 Body N Shore 68.9 ± 4.4 65.1 ± 4.7 −3.8 9.3 × 10−3 0.32
cg02942825 19 GIPR 3′UTR S Shore 49.8 ± 3.2 48.0 ± 5.8 −1.8 0.050 0.62
cg17808910 7 GLCCI1 Body S Shelf 73.7 ± 3.9 75.5 ± 4.6 1.8 0.048 0.62
cg26567012 5 GLRA1 3′UTR Open sea 55.4 ± 3.8 52.0 ± 6.0 −3.4 0.030 0.50
cg01010839 10 NET1 TSS1500; Body N Shore 71.2 ± 4.3 70.2 ± 2.2 −1.0 0.015 0.35
cg24796663 6 PHF1 TSS1500 N Shore 12.9 ± 1.8 11.3 ± 1.9 −1.6 1.5 × 10−3 0.17
cg11224624 8 PLEC1 Body Island 2.1 ± 0.3 2.3 ± 0.3 0.2 0.033 0.52
cg22291265 19 SHANK1 Body Open sea 7.5 ± 2.3 6.9 ± 1.3 −0.6 0.050 0.62
cg06589051 2 TGFBRAP1 TSS1500 S Shore 72.4 ± 2.0 70.2 ± 4.1 −2.2 0.040 0.61
cg08597832 8 TOP1MT Body N Shore 82.1 ± 2.5 79.8 ± 2.7 −2.3 0.020 0.41
cg11166303 2 TSSC1 Body N Shore 67.8 ± 7.5 61.2 ± 8.5 −6.6 4.0 × 10−3 0.21
cg09577317 8   Intergenic N Shore 83.9 ± 1.6 81.0 ± 1.2 −2.9 1.7 × 10−4 0.058
cg07948143 14   Intergenic Open sea 75.5 ± 3.2 71.0 ± 4.6 −4.5 2.9 × 10−3 0.20
cg24058013 18   Intergenic Island 89.8 ± 1.0 87.7 ± 1.8 −2.1 5.4 × 10−3 0.24
cg03889263 3   Intergenic Open sea 20.0 ± 3.9 15.9 ± 2.6 −4.1 6.9 × 10−3 0.27
cg05546763 14   Intergenic Island 82.0 ± 2.0 80.6 ± 2.3 −1.4 0.016 0.36
cg15342087 6   Intergenic Open sea 81.1 ± 2.1 80.2 ± 2.2 −0.9 0.046 0.62
cg06126421 6   Intergenic Open sea 69.2 ± 6.2 69.0 ± 4.4 −0.2 0.050 0.62
  1. Data are presented a mean ± SD