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Table 2 Top 10 and 6 DMRs in sex-stratified analysis. Shown are DMRs that are highly significant in one sex (FDR < 0.05), but not significant (P-value > 0.05) in another sex. Only 6 DMRs satisfied these criteria in male samples. For each DMR, annotations include the location of the DMR based on hg19/GRCh37 genomic annotation (DMR), Illumina gene annotations, nearby genes based on GREAT, and chromatin state. The inverse-variance weighted meta-analysis regression models results based on coMethDMR include estimated effect size (estimate) where DMRs that are hyper-methylated in samples with AD neuropathology have positive values, its associated standard error (se), P-value, and false discovery rate (FDR) for multiple comparison corrections. Shown in bold are significant results with FDR < 0.05

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

DMR Annotations Female samples Male samples
Illumina GREAT (distance to TSS) chromatin state estimate se P-value FDR estimate se P-value FDR
Significant only in female samples
chr5:27038605-27038836 CDH9 CDH9(− 28) Active TSS;Flanking Active TSS 0.128 0.024 1.87E−07 2.30E−03 0.077 0.027 2.74E−01 8.99E−01
chr15:31621629-31621843 KLF13 KLF13(+ 2678); OTUD7A(+ 325806) Active TSS 0.115 0.023 3.30E−07 2.30E−03 0.042 0.027 1.19E−01 8.07E−01
chr18:74799495-74799572 MBP MBP(+ 45191); ZNF236(+ 263418) Active TSS 0.138 0.028 5.81E−07 2.48E−03 0.049 0.033 1.30E−01 8.13E−01
chr7:45066738-45067057 CCM2 CCM2(+ 273) Weak transcription − 0.125 0.026 2.23E−06 6.20E−03 − 0.090 0.027 5.51E−02 7.00E−01
chr13:67803895-67804060 PCDH9 PCDH9(+ 490) Active TSS − 0.088 0.019 5.04E−06 1.02E−02 − 0.017 0.022 4.40E−01 9.50E−01
chr16:66969401-66969506 CES2;FAM96B FAM96B(− 1151); CES2(+ 1091) Flanking Active TSS 0.115 0.025 5.68E−06 1.02E−02 0.052 0.028 6.52E−02 7.28E−01
chr15:40268421-40268777 EIF2AK4 EIF2AK4(+ 42245); SRP14(+ 62790) Active TSS 0.125 0.028 7.12E−06 1.16E−02 − 0.005 0.032 8.72E−01 9.94E−01
chr5:14492774-14492945 TRIO FAM105B(− 171997); TRIO(+ 349049) Strong transcription − 0.103 0.023 8.25E−06 1.24E−02 − 0.009 0.029 7.49E−01 9.85E−01
chr17:56736571-56737118 TEX14 SEPT4(− 118666); TEX14(+ 32539) Active TSS − 0.070 0.016 9.13E−06 1.26E−02 0.017 0.017 3.20E−01 9.16E−01
chr17:46651722-46651952 HOXB3 HOXB3(− 20553); HOXB4(+ 5636) Repressed PolyComb 0.113 0.025 9.24E−06 1.26E−02 0.030 0.027 2.63E−01 8.97E−01
Significant only in male samples
chr17:1173700-1173767 BHLHA9 BHLHA9(− 119) Weak Repressed PolyComb − 0.041 0.025 1.07E−01 8.23E−01 − 0.118 0.026 5.08E−06 1.59E−02
chr11:68780866-68780984 MRGPRF MRGPRF(− 48) Flanking Bivalent TSS/Enh 0.032 0.024 1.80E−01 8.93E−01 0.112 0.026 1.16E−05 2.96E−02
chr12:52437299-52437571   C12orf44(− 26320); NR4A1(+ 20819) Enhancers 0.009 0.017 5.93E−01 9.93E−01 0.075 0.017 1.38E−05 3.31E−02
chr14:89017615-89017776 PTPN21 PTPN21(+ 3381); SPATA7(+ 165822) Active TSS 0.046 0.024 6.03E−02 7.31E−01 0.102 0.024 1.46E−05 3.31E−02
chr19:17691465-17691691 GLT25D1 COLGALT1(+ 25175); UNC13A(+ 107430) Strong transcription − 0.006 0.022 8.06E−01 1.00E + 00 0.107 0.025 2.47E−05 4.16E−02
chr6:32920567-32921233 HLA-DMA ENSG00000248993(− 1); HLA− DMA(− 1) Flanking Active TSS; Active TSS; Quiescent/Low − 0.045 0.024 3.16E−01 9.56E−01 − 0.117 0.028 3.17E−05 4.78E−02