ARTICLE TITLE: DNA methylation signatures of peripheral leukocytes in schizophrenia
JOURNAL NAME: NeuroMolecular Medicine
Makoto Kinoshita1,6, Shusuke Numata1,6, Atsushi Tajima2, Shinji Shimodera3, Shinji Ono4, Akira Imamura4, Jun-ichi Iga1, Shinya Watanabe1, Kumiko Kikuchi1, Hiroko Kubo1, Masahito Nakataki1, Satsuki Sumitani1, Issei Imoto2, Yuji Okazaki5, Tetsuro Ohmori1
1Department of Psychiatry, Course of Integrated Brain Sciences, Medical Informatics, Institute of Health Biosciences, The University of Tokushima Graduate School, Tokushima, Japan
2 Department of Human Genetics, Institute of Health Biosciences, The University of Tokushima Graduate School, Tokushima, Japan
3Department of Neuropsychiatry, Kochi Medical School, Kochi, Japan
4Department of Neuropsychiatry, Nagasaki University Graduate School of Biomedical Science, Nagasaki, Japan
5Tokyo Metropolitan Matsuzawa Hospital, Tokyo, Japan
6These authors contributed equally to this work.
Corresponding author: Shusuke Numata
Department of Psychiatry, Course of Integrated Brain Sciences, Medical Informatics, Institute of Health Biosciences, The University of Tokushima Graduate School
3-8-15 Kuramoto-cho Tokushima 770-8503, Japan
TEL: 81-886-33-7130,
FAX: 81-886-33-7131
E-mail address:
Supplementary table S2. The top 100-ranking of differentially methylated CpG sites in the first set of samples at FDR 5% correction. *Positions refer to Genome Research Consortium human genome build 37 (GRCh37)/UCSC human genome 19 (hg19)
Rank / Probe ID / UCSC RefGene name / Chromosome / Position* / UCSC RefGene group / Relation to UCSC CpG island / FDR corrected p-value / Mean beta difference1 / cg07637658 / PPP1R13L / 19 / 45887042 / Gene body / CGI shore / < 1.00E-11 / 0.122
2 / cg12447346 / PVRL4 / 1 / 161055663 / Gene body / Others / < 1.00E-11 / 0.079
3 / cg25354716 / CRTAP / 3 / 33159475 / Gene body / CGI shelf / 1.74E-11 / 0.112
4 / cg27021666 / HSPA1B / 6 / 31794278 / Promoter / CGI shore / 5.21E-11 / 0.113
5 / cg19788417 / DEFB123 / 20 / 30027638 / Promoter / Others / 8.34E-11 / 0.132
6 / cg19110428 / - / 20 / 30324912 / Intergenic / CGI shelf / 1.91E-10 / 0.155
7 / cg14334147 / - / X / 70291925 / Intergenic / CGI shelf / 2.68E-10 / 0.139
8 / cg13986498 / - / 13 / 24917418 / Intergenic / CGI shelf / 4.17E-10 / 0.083
9 / cg10888523 / - / 10 / 111460288 / Intergenic / Others / 6.25E-10 / 0.086
10 / cg09380357 / NUB1 / 7 / 151042072 / Promoter / CGI shelf / 7.20E-10 / 0.113
11 / cg05751616 / IFFO1 / 12 / 6652601 / Gene body / CGI shelf / 7.20E-10 / 0.100
12 / cg27105914 / DNAH17 / 17 / 76445798 / Gene body / CGI shore / 8.16E-10 / 0.099
13 / cg13086586 / PPAT / 4 / 57303149 / Promoter / CGI shore / 9.82E-10 / -0.056
14 / cg18346402 / TIGD1 / 2 / 233412831 / Promoter / CGI shelf / 9.82E-10 / 0.186
15 / cg10550471 / - / 7 / 156239550 / Intergenic / Others / 1.36E-09 / 0.111
16 / cg11992550 / - / 15 / 89533607 / Intergenic / Others / 1.36E-09 / 0.096
17 / cg17588904 / HIPK1 / 1 / 114493165 / Promoter / Others / 1.40E-09 / 0.145
18 / cg20623645 / NAGLU / 17 / 40687392 / Promoter / CGI shore / 1.40E-09 / 0.143
19 / cg25719374 / - / 19 / 3930244 / Intergenic / CGI shelf / 1.40E-09 / 0.129
20 / cg01954686 / ASB10 / 7 / 150885654 / Promoter / Others / 1.60E-09 / 0.165
21 / cg02943305 / CCDC129 / 7 / 31685368 / Gene body / Others / 1.63E-09 / 0.197
22 / cg00378007 / - / 15 / 48620603 / Intergenic / CGI shelf / 1.63E-09 / 0.113
23 / cg00053536 / CROCC / 1 / 17291209 / Gene body / CGI shore / 1.64E-09 / 0.076
24 / cg08645980 / LRP2 / 2 / 169984729 / 3'UTR / Others / 1.64E-09 / 0.110
25 / cg27258878 / RBPMS / 8 / 30407398 / Gene body / Others / 1.64E-09 / 0.085
26 / cg19544510 / CAV3 / 3 / 8786747 / Gene body / Others / 1.71E-09 / 0.150
27 / cg10456628 / - / 16 / 89302571 / Intergenic / CGI shelf / 1.71E-09 / 0.129
28 / cg19147499 / - / 6 / 16234615 / Intergenic / CGI shelf / 1.73E-09 / 0.141
29 / cg20889774 / TOX2 / 20 / 42548586 / Promoter / CGI shelf / 1.73E-09 / 0.188
30 / cg09736526 / ITGAM / 16 / 31270808 / Promoter / Others / 2.32E-09 / 0.115
31 / cg02193513 / - / 4 / 57395012 / Intergenic / CGI shore / 2.60E-09 / 0.122
32 / cg13742532 / CCBP2 / 3 / 42850848 / Promoter / Others / 2.60E-09 / 0.080
33 / cg15327998 / PLEKHA5 / 12 / 19527571 / 3'UTR / Others / 2.60E-09 / 0.097
34 / cg22732549 / - / 8 / 8820073 / Intergenic / CGI shore / 2.60E-09 / 0.103
35 / cg02427511 / - / 16 / 15524851 / Intergenic / CGI shelf / 3.17E-09 / 0.130
36 / cg02854490 / - / 7 / 144108266 / Intergenic / Others / 3.17E-09 / 0.103
37 / cg22722807 / STRA8 / 7 / 134919060 / Gene body / CGI shore / 3.17E-09 / 0.068
38 / cg22788109 / - / 1 / 225867346 / Intergenic / CGI shelf / 3.17E-09 / 0.078
39 / cg15495901 / NWD1 / 19 / 16829985 / Promoter / Others / 3.56E-09 / 0.104
40 / cg13460465 / ZNF709 / 19 / 12572864 / 3'UTR / Others / 4.21E-09 / 0.098
41 / cg26309498 / EDAR / 2 / 109607038 / Promoter / Others / 4.41E-09 / 0.067
42 / cg06424550 / CAMK1D / 10 / 12808422 / Gene body / Others / 4.64E-09 / 0.057
43 / cg04262892 / - / 19 / 50877422 / Intergenic / CGI shelf / 4.85E-09 / 0.105
44 / cg16568759 / - / 17 / 75249580 / Intergenic / CGI shelf / 4.85E-09 / 0.092
45 / cg21573263 / SLC6A9 / 1 / 44482918 / Promoter / Others / 4.85E-09 / 0.096
46 / cg05212465 / SNX9 / 6 / 158253572 / Gene body / Others / 6.52E-09 / 0.107
47 / cg21175246 / - / 14 / 95964097 / Intergenic / Others / 6.70E-09 / 0.144
48 / cg01412011 / - / 4 / 3652433 / Intergenic / Others / 7.11E-09 / 0.087
49 / cg08276543 / NCOR2 / 12 / 124856791 / Gene body / CGI / 8.48E-09 / 0.069
50 / cg13688974 / - / 2 / 62683655 / Intergenic / CGI shore / 9.39E-09 / 0.124
51 / cg11404203 / - / 12 / 42850338 / Intergenic / Others / 1.18E-08 / 0.107
52 / cg20297940 / - / 1 / 14746121 / Intergenic / Others / 1.18E-08 / 0.086
53 / cg24509398 / EYA3 / 1 / 28416532 / Promoter / CGI shore / 1.18E-08 / 0.205
54 / cg06293195 / TXN2 / 22 / 36878654 / Promoter / Others / 1.28E-08 / 0.099
55 / cg02052377 / MRVI1 / 11 / 10674182 / Promoter / Others / 1.31E-08 / 0.128
56 / cg01220720 / NOTCH4 / 6 / 32167020 / Gene body / CGI shelf / 1.37E-08 / 0.098
57 / cg18759260 / DNM3 / 1 / 171916040 / Gene body / Others / 1.37E-08 / 0.123
58 / cg22012693 / COL22A1 / 8 / 139919163 / Promoter / Others / 1.37E-08 / 0.167
59 / cg13951190 / DENND1A / 9 / 126155038 / Gene body / CGI shore / 1.41E-08 / 0.161
60 / cg12850695 / PRPSAP2 / 17 / 18761932 / Promoter / CGI shore / 1.57E-08 / -0.061
61 / cg00395990 / PDZD3 / 11 / 119054921 / Promoter / Others / 1.73E-08 / 0.141
62 / cg09510269 / HCG18 / 6 / 30292743 / Gene body / CGI shore / 1.74E-08 / 0.102
63 / cg20731100 / - / 7 / 47298162 / Intergenic / CGI shelf / 1.78E-08 / 0.089
64 / cg00703849 / ZNF611 / 19 / 53229766 / Promoter / CGI shore / 1.79E-08 / 0.118
65 / cg08363518 / - / 19 / 42905128 / Intergenic / CGI shore / 1.79E-08 / 0.100
66 / cg23248615 / - / 10 / 2005709 / Intergenic / Others / 1.84E-08 / 0.100
67 / cg01879556 / SLC37A1 / 21 / 43932043 / Promoter / CGI shore / 2.02E-08 / 0.106
68 / cg02600413 / - / 5 / 43063172 / Intergenic / CGI shelf / 2.02E-08 / 0.102
69 / cg05203949 / - / 19 / 9849151 / Intergenic / CGI shelf / 2.02E-08 / 0.115
70 / cg00291316 / RP1L1 / 8 / 10469891 / Gene body / CGI / 2.40E-08 / 0.076
71 / cg26317888 / - / 7 / 158770704 / Intergenic / CGI shelf / 2.40E-08 / 0.071
72 / cg27639249 / NCRNA00171 / 6 / 30016420 / Gene body / Others / 2.40E-08 / 0.095
73 / cg11015356 / TCEA2 / 20 / 62693102 / Promoter / CGI shore / 2.47E-08 / 0.060
74 / cg19476741 / FAM20C / 7 / 226959 / Gene body / CGI shore / 2.66E-08 / 0.098
75 / cg19863980 / - / 18 / 18517370 / Intergenic / Others / 2.66E-08 / 0.096
76 / cg19508555 / - / 21 / 11107031 / Intergenic / CGI / 2.85E-08 / 0.082
77 / cg12476455 / NASP / 1 / 46052453 / Promoter / CGI shore / 2.95E-08 / 0.301
78 / cg24641201 / SPAM1 / 7 / 123564016 / Promoter / Others / 2.95E-08 / 0.112
79 / cg15493018 / SLC25A24 / 1 / 108710337 / Gene body / Others / 3.27E-08 / 0.081
80 / cg08334022 / - / 11 / 75879348 / Intergenic / CGI shelf / 4.07E-08 / 0.104
81 / cg08941873 / DTWD2 / 5 / 118308850 / Gene body / CGI shore / 4.29E-08 / 0.147
82 / cg08961047 / RPS10 / 6 / 34395138 / Promoter / CGI shore / 4.35E-08 / 0.041
83 / cg22395811 / - / 4 / 164945455 / Promoter / Others / 4.59E-08 / 0.069
84 / cg15842208 / ABR / 17 / 1053674 / Promoter / Others / 4.59E-08 / 0.054
85 / cg05283804 / - / 16 / 86743683 / Intergenic / Others / 4.61E-08 / 0.078
86 / cg27022602 / ZNF574 / 19 / 42579074 / Promoter / CGI shore / 4.64E-08 / 0.138
87 / cg15849446 / - / 14 / 22965472 / Intergenic / Others / 4.75E-08 / 0.057
88 / cg24073418 / - / 2 / 198236150 / Intergenic / Others / 4.99E-08 / 0.114
89 / cg19811863 / HLA-DOB / 6 / 32785740 / Promoter / Others / 5.06E-08 / 0.155
90 / cg07067773 / ABRA / 8 / 107783270 / Promoter / Others / 5.17E-08 / 0.105
91 / cg04990609 / - / 13 / 46219268 / Intergenic / Others / 5.20E-08 / 0.076
92 / cg08463173 / - / 7 / 23715974 / Intergenic / CGI shelf / 5.20E-08 / 0.118
93 / cg09408023 / - / 1 / 91873278 / Intergenic / CGI shelf / 5.40E-08 / 0.099
94 / cg09456760 / RPL23AP82 / 22 / 51206645 / Gene body / Others / 5.50E-08 / 0.118
95 / cg15538009 / - / 14 / 51304083 / Intergenic / Others / 5.50E-08 / 0.098
96 / cg19165344 / AP1B1 / 22 / 29785355 / Promoter / CGI shore / 5.88E-08 / 0.072
97 / cg21240283 / FAM3C / 7 / 121032965 / Promoter / CGI shelf / 6.27E-08 / 0.099
98 / cg09404131 / - / 16 / 33730539 / Intergenic / CGI / 6.63E-08 / 0.043
99 / cg26011210 / - / 12 / 122125276 / Intergenic / CGI shore / 6.65E-08 / -0.091
100 / cg22232695 / UPK1A / 19 / 36156356 / Promoter / Others / 6.92E-08 / 0.081