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Table 4 Differentially methylated regions in blood

From: Alzheimer’s disease-associated (hydroxy)methylomic changes in the brain and blood

GenePositionGene featurenp valueŠidák PAverage Δ% (range Δ%)
Baseline
 LDLRAD4chr18:13611370-13611825TSS; Exon; 5′UTR; Intron7 (7 up; 0 down)3.25E−112.88E−083.64 (2.54:5.14)
 ZNF154chr19:58220080-58220838TSS; Intron; 5′UTR; CDS; Exon11 (11 up; 0 down)1.16E−096.16E−073.87 (1.75:5.11)
 PRRT1chr6:32116216-32117402Intron; 3′UTR; CDS26 (24 up; 2 down)2.61E−098.85E−071.77 (− 3.1:5.37)
 SYMPK; RSPH6Achr19:46318514-46319399Intron; 3′UTR; CDS; TSS; Exon; 5′UTR7 (7 up; 0 down)6.18E−092.81E−063.2 (2.07:4.87)
 TENM3chr4:183728549-183729462Intergenic5 (5 up; 0 down)1.02E−084.48E−062.69 (− 0.67:4.25)
 GLIPR1L2; CAPS2chr12:75784617-75785296TSS; Intron; 5′UTR; CDS; Exon10 (10 up; 0 down)2.36E−071.40E−042.72 (1.85:4.5)
 GPR35chr2:241562085-241562758Intron6 (6 up; 0 down)3.16E−071.89E−043.83 (3.35:4.37)
 ZMAT2chr5:140079591-140080246TSS; Intron; 5′UTR; CDS10 (9 up; 1 down)3.86E−072.37E−041.21 (− 1.35:2.81)
 ZNF649-AS1; ZNF577chr19:52390810-52391368Exon; TSS; Intron; 5′UTR10 (10 up; 0 down)7.42E−075.35E−045.11 (2.93:6.61)
 ULK1chr12:132380696-132380904Intron3 (3 up; 0 down)3.57E−076.90E−042.1 (0.92:3.5)
 SLC44A4chr6:31846769-31847029TSS; Exon; 5′UTR8 (0 up; 8 down)4.61E−077.13E−04− 1.14 (− 3.86:2.41)
 OXTchr20:3051954-3052484TSS; Intron; 5′UTR; CDS10 (9 up; 1 down)9.41E−077.14E−043.43 (− 0.45:6.79)
 FAM222Achr12:110156245-110156460Intron; 5′UTR4 (4 up; 0 down)2.85E−065.33E−033.11 (2.66:3.43)
 CYBRD1chr2:172430723-172430817Intergenic3 (0 up; 3 down)1.83E−067.78E−03− 1.75 (− 2.7:− 0.26)
 RUNX2chr6:45391852-45391974Intron3 (3 up; 0 down)5.11E−061.67E−023.19 (0.74:4.53)
Follow-up
 GSDMDchr8:144635309-144635611TSS; Exon; 5′UTR5 (0 up; 5 down)7.08E−189.43E−15− 0.68 (− 1.53:− 0.25)
 IRGCchr19:44203583-44203914Intergenic3 (0 up; 3 down)2.40E−122.92E−090.87 (− 0.32:1.53)
 LINC01149chr6:31409319-31409758Exon12 (0 up; 12 down)3.03E−102.78E−07− 0.96 (− 2.17:− 0.12)
 RUFY1chr5:178986131-178986907TSS; Exon; 5′UTR; Intron9 (9 up; 0 down)3.77E−091.96E−062.85 (1.3:4.19)
 GLIPR1L2; CAPS2chr12:75784541-75785296TSS; Intron; 5′UTR; CDS; Exon11 (11 up; 0 down)1.30E−086.94E−061.34 (0.64:2.81)
 RAD51B; LOC100996664chr14:69095057-69095680Intron; Exon5 (5 up; 0 down)3.57E−082.31E−056.05 (4.89:7.1)
 LOC105372397; MAP4K1chr19:39086733-39087768Intron; Exon; CDS5 (4 up; 1 down)8.14E−083.17E−05− 0.28 (− 1.05:0.3)
 KHDRBS2chr6:62996022-62996703Exon; TSS; 5′UTR11 (11 up; 0 down)6.92E−084.09E−051.25 (0.69:1.89)
 STAG3L5P-PVRIG2P-PILRB; STAG3L5P; PMS2P1chr7:99933717-99933798Exon3 (3 up; 0 down)1.01E−085.02E−050.16 (− 0.01:0.45)
 ISOC2chr19:55972646-55973339TSS; Intron; Exon; 5′UTR9 (9 up; 0 down)8.68E−085.04E−051.52 (0.78:2.51)
 RARRES2chr7:150037988-150038599Intron; 5′UTR3 (0 up; 3 down)1.63E−071.07E−040.71 (− 0.64:2.19)
 LINC01169chr15:66947171-66947618Intron5 (0 up; 5 down)1.54E−071.39E−04− 2.24 (− 5.41:− 0.83)
 TRAM1L1chr4:118006405-118007226TSS; CDS11 (10 up; 1 down)9.95E−074.88E−041.14 (− 0.81:2.96)
 LDHCchr11:18433500-18434016TSS; Intron; Exon; 5′UTR7 (7 up; 0 down)6.92E−075.40E−042.76 (− 0.3:4.7)
 ZNF337-AS1; NANPchr20:25604462-25605179Intron; Exon; TSS; 5′UTR; CDS12 (12 up; 0 down)1.10E−066.18E−040.4 (− 0.27:1.36)
 IFT74; IFT74-AS1chr9:26956236-26956770Intron; 5′UTR; TSS; Exon3 (2 up; 1 down)8.65E−076.52E−040.21 (− 0.2:0.52)
 MIR3659chr1:38599626-38600200Intergenic4 (0 up; 4 down)1.34E−069.38E−04− 0.49 (− 1.35:0.64)
 LINC01983chr3:195578011-195578281Intron6 (0 up; 6 down)6.38E−079.51E−04− 0.07 (− 0.76:0.67)
 HEXDchr17:80393124-80393667Intron; CDS5 (5 up; 0 down)1.89E−061.40E−03− 0.52 (− 2.54:0.39)
 GNG7chr19:2543602-2544101Intron; 5′UTR5 (5 up; 0 down)5.29E−064.26E−031 (0.25:1.95)
 F11-AS1chr4:187422005-187422120Exon5 (5 up; 0 down)1.66E−065.81E−031.26 (0.4:1.87)
  1. Differentially methylated regions in the comparisons of Alzheimer’s disease converters and non-converters, prior to conversion at baseline (converters n = 54, non-converters n = 42), and after conversion at follow-up (converters n = 41, non-converters n = 42). Displayed for each region is the UCSC gene name, chromosomal position (genome build 37), gene feature (TSS, transcription start site; 5′UTR, 5′ untranslated region; CDS, coding sequence), number of probes in region and number of upregulated and downregulated probes (n), p value and multiple testing-corrected p (Šidák P), and average change in beta value (Alzheimer’s disease converter - control), including the range of the probe differences