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Table 1 Top 10 CpGs in sex-stratified analysis. Shown are CpGs that are highly significant in one sex (FDR < 0.05), but not significant (P-value > 0.05) in the other sex. For each CpG, annotations include the location of the CpG based on hg19/GRCh37 genomic annotation (chr, position), Illumina gene annotations, nearby genes based on GREAT, and chromatin state. The inverse-variance weighted meta-analysis regression model results include estimated effect size (estimate) where CpGs that are hyper-methylated in samples with AD neuropathology have positive values, and its associated standard error (se), P-value, and false discovery rate (FDR) for multiple comparison corrections. Bold indicates a significant association at 5% FDR

From: Sex-specific DNA methylation differences in Alzheimer’s disease pathology

cpg Annotations Female samples Males samples
chr Position Illumina GREAT (distance to TSS) chromatin state estimate se P-value FDR estimate se P-value FDR
Significant only in female samples
cg09502865 chr16 88600155 ZFPM1 ZC3H18(− 36633); ZFPM1(+ 80431) Active TSS 0.179 0.028 2.50E−10 1.15E−04 0.094 0.034 4.46E−01 9.64E−01
cg05235171 chr11 117958104 TMPRSS4 TMPRSS4(+ 10301); SCN4B(+ 65430) Quiescent/Low − 0.168 0.029 7.61E−09 6.99E−04 − 0.025 0.033 4.47E−01 9.64E−01
cg15610437 chr19 827821 AZU1 AZU1(− 4) Weak Repressed PolyComb − 0.155 0.029 5.45E−08 1.99E−03 − 0.090 0.034 9.79E−02 8.25E−01
cg13572782 chr18 74799495 MBP MBP(+ 45229); ZNF236(+ 263380) Active TSS 0.157 0.029 5.75E−08 1.99E−03 0.047 0.036 1.90E−01 8.92E−01
cg17881200 chr7 27138850   HOXA1(− 3258) Repressed PolyComb 0.152 0.029 1.41E−07 2.98E−03 0.131 0.034 6.22E−02 7.73E−01
cg22632947 chr17 64787784 PRKCA CACNG5(− 43450); PRKCA(+ 488841) Flanking Active TSS − 0.139 0.026 1.50E−07 3.00E−03 − 0.005 0.028 8.57E−01 9.95E−01
cg15467503 chr4 1727234 TACC3 TMEM129(− 4177); TACC3(+ 3969) Weak transcription − 0.146 0.028 1.81E−07 3.45E−03 − 0.083 0.034 1.33E−01 8.59E−01
cg26033526 chr6 32819858 TAP1 PSMB9(− 2079); TAP1(+ 1896) Genic enhancers 0.148 0.029 2.64E−07 4.18E−03 − 0.021 0.034 5.23E−01 9.73E−01
cg08363067 chr16 16170085 ABCC1 ABCC1(+ 126652); ABCC6(+ 147235) Weak transcription − 0.120 0.024 7.68E−07 7.32E−03 − 0.050 0.028 7.41E−02 7.94E−01
cg12926693 chr6 36665611   RAB44(− 17644); CDKN1A(+ 19125) Quiescent/Low − 0.149 0.030 8.59E−07 7.32E−03 − 0.067 0.035 5.19E−02 7.52E−01
Significant only in male samples
cg07687398 chr3 53198666 PRKCD PRKCD(+ 3531); TKT(+ 91371) Weak transcription 0.052 0.030 8.63E−02 8.19E−01 0.183 0.035 1.16E−07 9.88E−03
cg10513118 chr11 118047203 SCN2B SCN2B(+ 184) Active TSS 0.038 0.030 2.01E−01 9.17E−01 0.172 0.033 1.42E−07 9.88E−03
cg21253952 chr8 143662999   ARC(+ 33833); BAI1(+ 132209) Weak Repressed PolyComb − 0.019 0.030 5.33E−01 9.84E−01 0.169 0.034 4.44E−07 1.53E−02
cg18281939 chr5 77783895 LHFPL2 SCAMP1(+ 127557); LHFPL2(+ 160752) Weak transcription − 0.022 0.029 4.55E−01 9.76E−01 − 0.179 0.036 6.26E−07 1.79E−02
cg11809272 chr6 31409361   HLA-B(− 84398); MICB(− 56530) Quiescent/Low − 0.001 0.031 9.77E−01 1.00E + 00 0.161 0.033 9.08E−07 2.17E−02
cg15952933 chr7 1899886 MAD1L1 ELFN1(+ 172132); MAD1L1(+ 372991) Weak transcription − 0.058 0.033 7.56E−02 8.00E−01 − 0.156 0.032 9.48E−07 2.17E−02
cg11614451 chr3 160167729 TRIM59 ENSG00000248710(− 113); TRIM59(− 113) Flanking Bivalent TSS/Enh − 0.041 0.029 1.56E−01 8.92E−01 − 0.150 0.031 1.28E−06 2.44E−02
cg18942110 chr15 91072797 CRTC3 CRTC3(− 502) Active TSS 0.031 0.030 3.06E−01 9.52E−01 − 0.164 0.035 2.23E−06 3.19E−02
cg01655008 chr14 93652954 C14orf109 MOAP1(− 1687); TMEM251(+ 1597) Transcr. at gene 5′ and 3' − 0.042 0.029 1.51E−01 8.89E−01 − 0.152 0.032 2.54E−06 3.33E−02
cg02331272 chr11 66964208 KDM2A ADRBK1(− 69672); KDM2A(+ 77051) Weak transcription 0.058 0.030 1.10E−01 8.52E−01 − 0.166 0.036 2.99E−06 3.52E−02