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Table 2 Replicated DMPs associated with Braak stage

From: Epigenome-wide association study of Alzheimer’s disease replicates 22 differentially methylated positions and 30 differentially methylated regions

Name Chr Pos Gene annotation Strand Relation to Island UCSC RefGene Group This study Smith et al. meta-analysis
STG IFG ES p value Brain region
beta p value beta p value
cg15645660 1 55,247,356   + Island Body 0.09 1.03E−03 0.09 2.28E−05 0.04 2.12E−08 Prefrontal Cortex
cg15645660 1 55,247,356   + Island Body 0.09 1.03E−03 0.09 2.28E−05 0.03 4.67E−10 Cross Cortex
cg17104258 1 1.67E+08   − Island Body − 0.12 8.72E−03 − 0.22 5.99E−06 − 0.02 6.27E−11 Cross Cortex
cg17104258 1 1.67E+08   − Island Body − 0.12 8.72E−03 − 0.22 5.99E−06 − 0.03 2.60E−08 TG
cg12307200 3 1.89E+08 TPRG1;TPRG1-AS1 + N Shore   − 0.05 7.18E−04 − 0.04 8.65E−05 − 0.02 2.19E−11 Prefrontal Cortex
cg12307200 3 1.89E+08 TPRG1;TPRG1-AS1 + N Shore   − 0.05 7.18E−04 − 0.04 8.65E−05 − 0.02 2.72E−12 TG
cg12307200 3 1.89E+08 TPRG1;TPRG1-AS1 + N Shore   − 0.05 7.18E−04 − 0.04 8.65E−05 − 0.02 4.48E−16 Cross Cortex
cg11964461 5 1.8E+08 RASGEF1C − OpenSea 5′UTR 0.01 1.58E−01 0.03 1.01E−04 0.01 9.48E−08 Cross Cortex
cg00921266 7 27,153,663 HOXA3;HOXA-AS2;HOXA3 − N Shore 5′UTR;TSS200 0.11 8.39E−05 0.04 2.01E−01 0.03 8.94E−10 Prefrontal Cortex
cg00921266 7 27,153,663 HOXA3;HOXA-AS2;HOXA3 − N Shore 5′UTR;TSS200 0.11 8.39E−05 0.04 2.01E−01 0.02 9.25E−09 Cross Cortex
cg05066959 8 41,519,308 ANK1 − OpenSea TSS1500;Body 0.10 2.91E−02 0.10 2.04E−05 0.02 1.45E−12 Cross Cortex
cg05066959 8 41,519,308 ANK1 − OpenSea TSS1500;Body 0.10 2.91E−02 0.10 2.04E−05 0.04 4.58E−13 TG
cg05066959 8 41,519,308 ANK1 − OpenSea TSS1500;Body 0.10 2.91E−02 0.10 2.04E−05 0.03 7.35E−10 Prefrontal Cortex
cg05066959 8 41,519,308 ANK1 − OpenSea TSS1500;Body 0.10 2.91E−02 0.10 2.04E−05 0.06 2.93E−09 EC
cg23968456 10 73,521,631   − OpenSea Body 0.11 1.95E−02 0.09 2.37E−05 0.01 1.09E−09 Cross Cortex
cg23968456 10 73,521,631   − OpenSea Body 0.11 1.95E−02 0.09 2.37E−05 0.01 1.06E−09 TG
cg10469774 11 44,642,932   − OpenSea   0.05 2.23E−03 0.07 4.77E−05 0.01 7.26E−09 Cross Cortex
cg07883124 13 1.14E+08 MCF2L − Island Body;1stExon 0.03 3.52E−02 0.05 8.57E−06 0.02 9.10E−13 Cross Cortex
cg07883124 13 1.14E+08 MCF2L − Island Body;1stExon 0.03 3.52E−02 0.05 8.57E−06 0.02 6.40E−08 Prefrontal Cortex
cg09448088 13 1.14E+08   − Island Body 0.02 8.69E−02 0.06 3.95E−09 0.01 1.04E−08 Cross Cortex
cg26127778 15 93,617,141 RGMA − Island 1stExon;TSS1500;Body;5′UTR − 0.05 3.52E−05 − 0.03 1.88E−03 − 0.02 4.88E−08 TG
cg17400113 15 93,617,146 RGMA − Island 1stExon;TSS1500;Body;5′UTR − 0.03 1.23E−03 − 0.03 1.75E−05 − 0.01 1.15E−08 Cross Cortex
cg17400113 15 93,617,146 RGMA − Island 1stExon;TSS1500;Body;5′UTR − 0.03 1.23E−03 − 0.03 1.75E−05 − 0.02 3.75E−08 TG
cg09109520 16 57,673,258 GPR56 − OpenSea 5′UTR;1stExon 0.06 9.14E−05 0.03 1.39E−01 0.02 9.00E−11 Cross Cortex
cg09109520 16 57,673,258 GPR56 − OpenSea 5′UTR;1stExon 0.06 9.14E−05 0.03 1.39E−01 0.02 2.53E−10 Prefrontal Cortex
cg03169557 16 89,598,950 SPG7 + OpenSea Body 0.13 4.99E−02 0.21 1.33E−06 0.01 3.15E−08 Prefrontal Cortex
cg03169557 16 89,598,950 SPG7 + OpenSea Body 0.13 4.99E−02 0.21 1.33E−06 0.02 2.71E−10 TG
cg03169557 16 89,598,950 SPG7 + OpenSea Body 0.13 4.99E−02 0.21 1.33E−06 0.01 5.41E−11 Cross Cortex
cg03169557 16 89,598,950 SPG7 + OpenSea Body 0.13 4.99E−02 0.21 1.33E−06 0.02 4.41E−09 EC
cg19803550 17 1,637,391 RP11-961A15.1 + Island Body 0.14 1.91E−02 0.13 1.67E−05 0.01 1.06E−08 Cross Cortex
cg19803550 17 1,637,391 RP11-961A15.1 + Island Body 0.14 1.91E−02 0.13 1.67E−05 0.01 3.68E−08 Prefrontal Cortex
cg05810363 17 74,475,270   − Island Body 0.12 6.05E−02 0.16 6.73E−07 0.03 2.25E−11 TG
cg05810363 17 74,475,270   − Island Body 0.12 6.05E−02 0.16 6.73E−07 0.02 2.01E−10 Cross Cortex
cg13076843 17 74,475,294   + Island Body 0.07 3.13E−02 0.10 1.02E−04 0.03 7.31E−10 Prefrontal Cortex
cg13076843 17 74,475,294   + Island Body 0.07 3.13E−02 0.10 1.02E−04 0.02 7.57E−13 Cross Cortex
cg13076843 17 74,475,294   + Island Body 0.07 3.13E−02 0.10 1.02E−04 0.03 2.97E−11 TG
cg12163800 17 74,475,355 RHBDF2 + Island Body 0.08 1.92E−03 0.10 9.19E−06 0.01 5.13E−09 Cross Cortex
cg12163800 17 74,475,355 RHBDF2 + Island Body 0.08 1.92E−03 0.10 9.19E−06 0.02 2.06E−08 Prefrontal Cortex
cg12163800 17 74,475,355 RHBDF2 + Island Body 0.08 1.92E−03 0.10 9.19E−06 0.02 5.85E−09 TG
cg12309456 17 74,475,402   − Island Body 0.09 2.46E−02 0.10 7.68E−06 0.02 1.33E−08 TG
cg12309456 17 74,475,402   − Island Body 0.09 2.46E−02 0.10 7.68E−06 0.01 4.09E−08 Cross Cortex
cg08481112 19 2,544,100 GNG7 + S Shore 5′UTR 0.07 4.81E−05 0.03 7.27E−02 0.02 2.84E−08 Prefrontal Cortex
cg23449541 21 47,855,893 PCNT − Island Body 0.04 3.16E−02 0.07 8.45E−06 0.01 7.49E−08 Cross Cortex
cg23449541 21 47,855,893 PCNT − Island Body 0.04 3.16E−02 0.07 8.45E−06 0.02 9.43E−11 TG
cg00621289 21 47,855,916 PCNT − Island Body 0.04 1.43E−02 0.06 2.51E−05 0.01 4.69E−11 Cross Cortex
  1. Chr: chromosome; Pos: base pair position in reference to human genome hg19; Gene Annotation: gene annotation in reference to Gencode Basic V12; beta coefficient and p value was reported from the limma robust regression model for this study for each DMP, while the effect size (ES) and corresponding unadjusted p value from the inverse variance fixed effects meta-analysis model was shown for the Smith et al. meta-analysis. In addition, ES from the Smith et al. meta-analysis has been multiplied by six to demonstrate the difference between Braak stage 0 and Braak stage VI samples. This was not done for this study
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Clinical Epigenetics

ISSN: 1868-7083

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