Genes differentially methylated in schizophrenia

Study1
Study2

Gene	Position	Discovery set (N=1334)			Replication set (N=497)
Gene	Position	ΔBeta	P-value	FDR	ΔBeta	P-value
KIAA0125	14:106322429	-0.007	1.06e-07	0.010	-0.008	2.13e-04
RPS6KA1	1:26857284	-0.008	1.16e-07	0.010	-0.009	4.38e-05
MGRN1	16:4714733	-0.009	1.32e-07	0.010	-0.007	6.95e-05
S100A2	1:153538406	-0.007	3.26e-07	0.011	-0.005	2.77e-02
NCOR2	12:124912021	0.006	4.99e-07	0.014	0.010	3.91e-07
KIAA0355	19:34744396	0.010	5.39e-07	0.014	0.007	2.10e-02
RPTOR	17:78860076	0.013	6.70e-07	0.014	0.008	3.72e-02
RAD51B	14:68830704	0.011	6.90e-07	0.014	0.010	1.62e-02
RP11-699L21.1	3:193570256	0.011	6.94e-07	0.014	0.006	4.98e-02
C6orf136	6:30619232	0.007	9.39e-07	0.015	0.006	3.28e-03
PEAK1	15:77472416	0.010	1.02e-06	0.015	0.011	6.62e-04
MAD1L1	7:2111060	0.011	1.07e-06	0.016	0.011	2.32e-04
MAN2B1	19:12776725	-0.008	1.09e-06	0.016	-0.013	8.72e-10
TCF3	19:1630248	0.010	1.32e-06	0.017	0.007	7.92e-03
PPP1CA	11:67166104	0.008	2.45e-06	0.023	0.006	4.65e-03
AUP1	2:74753759	0.009	2.67e-06	0.023	0.006	3.72e-02
CHST12	7:2480493	0.016	2.85e-06	0.024	0.012	7.44e-03
IFITM1	11:315262	-0.007	3.02e-06	0.024	-0.006	2.27e-02
PACS2	14:105860954	0.009	3.08e-06	0.024	0.007	2.27e-02
FAM102B	1:109103731	-0.006	3.27e-06	0.025	-0.005	1.23e-03
AGO2	8:141550539	0.006	3.78e-06	0.028	0.004	4.65e-02
CARD14	17:78163268	0.007	4.89e-06	0.029	0.006	2.28e-02
SEC14L1	17:75096382	0.011	4.93e-06	0.029	0.014	1.38e-04
MIR101-1	1:65531864	-0.007	5.11e-06	0.029	-0.004	2.76e-02
PRDM11	11:45124456	-0.009	5.39e-06	0.030	-0.013	2.95e-05
GFI1	1:92947332	-0.013	5.73e-06	0.031	-0.011	1.90e-02
RPTOR	17:78854232	0.008	7.92e-06	0.038	0.009	8.35e-03
TMEM173	5:138861241	-0.005	8.39e-06	0.040	-0.003	2.49e-02
IKZF4	12:56415591	-0.006	9.06e-06	0.042	-0.004	1.69e-03
LPO	17:56316162	-0.006	9.34e-06	0.043	-0.006	1.04e-04
RNF212	4:1076247	-0.006	1.04e-05	0.045	-0.005	7.14e-04
DAZAP1	19:1423902	0.003	1.08e-05	0.045	0.004	2.61e-02
MARK4	19:45756845	-0.008	1.07e-05	0.045	-0.008	1.31e-03
AGAP1	2:236671149	-0.005	1.15e-05	0.046	-0.005	7.72e-03
ANKS3	16:4751569	0.009	1.26e-05	0.049	0.012	7.00e-05
GFI1	1:92952702	-0.008	1.30e-05	0.050	-0.008	4.99e-04
MCM3	6:52170606	-0.011	1.44e-05	0.052	-0.009	1.12e-02
SEC14L1	17:75096239	0.010	1.49e-05	0.054	0.011	4.65e-04
MIR1538	16:69564625	-0.012	1.71e-05	0.059	-0.015	7.17e-05
HES1	3:193807749	-0.005	1.73e-05	0.059	-0.004	1.47e-02
ZFPM1	16:88540241	0.004	1.89e-05	0.063	0.006	2.87e-05
NPDC1	9:139939792	-0.010	1.95e-05	0.063	-0.016	1.72e-07
MLXIP	12:122617908	0.004	1.99e-05	0.064	0.003	2.36e-02
ZFP36L2	2:43405947	-0.006	2.31e-05	0.066	-0.004	8.91e-03
NCOR2	12:124911924	0.005	2.29e-05	0.066	0.008	1.64e-04
SKI	1:2166155	-0.005	2.33e-05	0.066	-0.003	2.37e-02
SCAP	3:47460784	0.006	2.38e-05	0.067	0.005	1.94e-02
NTM	11:131618277	0.005	2.43e-05	0.067	0.002	3.22e-02
ITGA2	5:52283760	-0.006	2.50e-05	0.068	-0.005	6.13e-03
VPS52	6:33235504	0.006	2.97e-05	0.074	0.006	5.65e-03
DHCR24	1:55353706	-0.010	3.14e-05	0.076	-0.011	6.95e-03
KIFC3	16:57793728	-0.005	3.16e-05	0.076	-0.003	4.81e-02
HS6ST1	2:129231478	-0.007	3.35e-05	0.077	-0.006	1.46e-02
DDR1	6:30860887	0.011	3.78e-05	0.084	0.009	1.27e-02
POR	7:75586348	0.011	4.03e-05	0.086	0.010	2.46e-02
TGFA	2:70751721	-0.006	4.15e-05	0.088	-0.005	9.43e-04
XYLT1	16:17563300	-0.011	4.14e-05	0.088	-0.017	2.28e-05
CHD3	17:7792674	-0.004	4.38e-05	0.091	-0.003	5.23e-03
RANBP3L	5:36302349	0.009	4.39e-05	0.091	0.007	2.03e-02
GMDS	6:1629850	0.006	4.51e-05	0.093	0.006	4.58e-03
GAS7	17:9940004	-0.005	4.76e-05	0.096	-0.003	2.69e-02
CARD10	22:37921640	-0.010	4.77e-05	0.096	-0.011	1.30e-03
B3GNT7	2:232265670	0.010	4.90e-05	0.097	0.006	4.79e-02
DDR1	6:30860237	0.011	5.09e-05	0.098	0.009	4.53e-02
AQP6	12:50368110	0.005	5.22e-05	0.098	0.005	3.32e-02
PLD5	1:242687412	-0.004	5.20e-05	0.098	-0.003	3.34e-02
STK40	1:36840028	-0.007	5.27e-05	0.098	-0.012	4.95e-06
FAM60A	12:31476479	-0.005	5.36e-05	0.099	-0.005	1.33e-03
EMP2	16:10626884	-0.011	5.65e-05	0.102	-0.009	1.94e-02
VSIG8	1:159825049	0.006	5.68e-05	0.102	0.004	8.76e-03
MARCH11	5:16179633	-0.010	5.85e-05	0.103	-0.009	1.43e-02
ZFR	5:32355062	0.010	5.96e-05	0.103	0.007	2.89e-02
KLF13	15:31691214	-0.005	5.98e-05	0.103	-0.005	1.72e-02
CLNK	4:10673188	0.003	5.98e-05	0.103	0.002	4.81e-02
RPTOR	17:78860029	0.011	5.97e-05	0.103	0.017	1.03e-04
IFT122	3:129160154	-0.007	6.25e-05	0.104	-0.006	4.67e-03
FSCN1	7:5635134	-0.010	6.41e-05	0.105	-0.019	1.32e-06
MAP3K1	5:55897584	0.007	6.39e-05	0.105	0.006	1.03e-02
DYRK2	12:68044208	-0.007	6.52e-05	0.105	-0.006	1.18e-02
FBXO46	19:46224285	0.007	6.52e-05	0.105	0.009	1.87e-03
MLST8	16:2258457	0.005	6.62e-05	0.105	0.005	9.28e-03
NCOR2	12:124912049	0.006	6.70e-05	0.105	0.013	5.07e-09
SPRED3	19:38881032	0.011	6.87e-05	0.106	0.023	1.86e-06
RPS6KA4	11:64138764	0.007	7.30e-05	0.108	0.004	3.42e-02
SEC14L1	17:75096202	0.012	7.93e-05	0.112	0.021	9.21e-05
PXDC1	6:3722818	-0.009	8.02e-05	0.113	-0.008	2.65e-02
SULT4A1	22:44258132	-0.008	8.86e-05	0.118	-0.007	2.85e-02
TRAPPC9	8:141229477	0.011	9.19e-05	0.119	0.009	3.89e-02
SLC38A10	17:79235968	0.008	9.14e-05	0.119	0.008	1.03e-02
CUTA	6:33385056	-0.007	9.36e-05	0.119	-0.016	8.09e-08
RAP1GAP2	17:2886250	0.006	9.35e-05	0.119	0.007	6.06e-03
NOD2	16:50743027	-0.005	9.43e-05	0.119	-0.004	3.26e-02
SELPLG	12:109023799	-0.007	9.61e-05	0.119	-0.011	1.10e-06
GFI1	1:92952897	-0.007	9.77e-05	0.120	-0.012	3.10e-05
NCOA7	6:126110790	-0.008	1.01e-04	0.121	-0.006	4.69e-02
DDR1	6:30860300	0.015	9.97e-05	0.120	0.019	1.91e-03
CCNE1	19:30303495	-0.006	1.07e-04	0.123	-0.006	9.50e-04
RP5-1086L22.1	6:170536124	0.011	1.08e-04	0.124	0.015	1.69e-04
ZC3H12D	6:149803087	-0.007	1.09e-04	0.125	-0.007	4.55e-05
UNKL	16:1425469	0.004	1.20e-04	0.131	0.004	2.59e-02
SATB1	3:18484742	-0.013	1.22e-04	0.132	-0.010	4.03e-02
IFITM1	11:313478	-0.010	1.24e-04	0.132	-0.009	1.43e-02
PPT2	6:32123258	-0.004	1.27e-04	0.134	-0.005	9.64e-03
SLC7A5	16:87866696	0.007	1.32e-04	0.135	0.008	1.48e-02
FOXO1	13:41055491	0.007	1.36e-04	0.136	0.011	7.66e-05
PUF60	8:144906507	0.008	1.39e-04	0.136	0.007	3.72e-02
RNF212	4:1076041	-0.006	1.42e-04	0.139	-0.009	1.63e-03
AUTS2	7:70060153	0.008	1.42e-04	0.139	0.006	2.22e-02
SLC7A5	16:87866833	0.008	1.43e-04	0.139	0.014	1.76e-04
GXYLT2	3:72940510	-0.006	1.45e-04	0.139	-0.006	3.99e-03
LRFN3	19:36427721	-0.006	1.46e-04	0.139	-0.006	7.65e-03
SLC7A5	16:87866800	0.006	1.47e-04	0.139	0.006	1.49e-02
RPTOR	17:78853966	0.007	1.52e-04	0.141	0.005	3.48e-02
FDX1L	19:10420353	-0.003	1.52e-04	0.141	-0.003	3.93e-02
GET4	7:922825	0.006	1.52e-04	0.141	0.009	2.34e-03
CD177	19:43857717	0.011	1.55e-04	0.142	0.014	7.99e-03
CDC37	19:10506915	0.004	1.59e-04	0.142	0.005	1.16e-02
MRPL19	2:75888565	0.006	1.59e-04	0.142	0.007	3.19e-02
DIS3L2	2:233125062	0.005	1.62e-04	0.143	0.004	3.79e-02
DBR1	3:137892432	-0.005	1.62e-04	0.143	-0.004	4.99e-02
PSMB8	6:32810785	-0.007	1.63e-04	0.143	-0.007	7.63e-03
UNCX	7:1328627	-0.004	1.64e-04	0.143	-0.004	8.03e-03
LENG9	19:54975087	0.012	1.71e-04	0.147	0.007	1.43e-02
ENTPD8	9:140330621	-0.005	1.73e-04	0.148	-0.007	6.13e-03
KIAA0125	14:106321936	-0.008	1.77e-04	0.149	-0.010	1.86e-03
VPS37B	12:123350361	0.005	1.85e-04	0.152	0.005	1.82e-02
IGF2R	6:160409942	0.008	1.86e-04	0.152	0.008	2.42e-02
ULBP3	6:150393535	-0.008	1.88e-04	0.152	-0.007	2.63e-02
BMPR1B	4:95679381	-0.007	1.96e-04	0.155	-0.005	4.27e-02
GOLGA7	8:41258634	-0.005	1.98e-04	0.155	-0.004	1.93e-02
EEF1D	8:144672242	0.007	2.06e-04	0.158	0.007	2.96e-02
MIR143HG	5:148785408	-0.015	2.11e-04	0.159	-0.013	4.08e-02
IRS1	2:227661656	0.006	2.15e-04	0.160	0.011	1.20e-04
LOC284454	19:13947162	-0.004	2.15e-04	0.160	-0.004	9.82e-03
IFITM1	11:313527	-0.010	2.18e-04	0.160	-0.008	1.48e-02
SLC22A18AS	11:2920789	-0.005	2.27e-04	0.164	-0.005	1.22e-03
CDA	1:20914028	-0.006	2.32e-04	0.164	-0.005	1.56e-02
WNT5B	12:1702001	-0.007	2.31e-04	0.164	-0.012	1.23e-06
DDR1	6:30860136	0.007	2.31e-04	0.164	0.007	4.54e-02
FES	15:91427184	-0.005	2.33e-04	0.164	-0.003	1.26e-02
SYNJ2	6:158490013	-0.005	2.40e-04	0.167	-0.004	3.11e-02
SORL1	11:121337508	-0.005	2.49e-04	0.170	-0.006	6.97e-04
TBCD	17:80861008	0.006	2.48e-04	0.170	0.007	3.89e-03
C1orf228	1:45187551	0.009	2.55e-04	0.171	0.004	4.90e-02
CPT1A	11:68611596	0.004	2.53e-04	0.171	0.003	2.43e-02
ABHD16A	6:31669902	-0.005	2.60e-04	0.172	-0.009	3.85e-05
CRBN	3:3219781	-0.004	2.60e-04	0.172	-0.003	3.12e-02
BASP1P1	13:23499838	-0.007	2.64e-04	0.172	-0.009	9.35e-03
THBD	20:23029287	-0.007	2.68e-04	0.173	-0.006	7.17e-03
CEP72	5:619883	0.005	2.64e-04	0.172	0.004	2.20e-02
FAM46C	1:118188756	0.006	2.69e-04	0.173	0.006	1.56e-02
TTLL11	9:124854664	-0.005	2.86e-04	0.177	-0.010	3.76e-07
TAOK2	16:29987261	-0.005	2.86e-04	0.177	-0.006	1.02e-03
IKZF4	12:56414508	-0.004	2.89e-04	0.177	-0.003	1.60e-02
ACAP3	1:1234367	0.005	2.97e-04	0.179	0.004	3.88e-02
FAM83A	8:124179875	-0.004	3.10e-04	0.182	-0.004	7.12e-03
ICAM3	19:10445516	0.006	3.17e-04	0.183	0.006	2.21e-02
AP2M1	3:183899704	0.006	3.20e-04	0.184	0.007	7.39e-03
LINC00623	1:149614778	0.007	3.33e-04	0.186	0.008	1.86e-02
PIK3R1	5:67522298	0.006	3.44e-04	0.191	0.005	1.38e-02
DNAJB12	10:74076930	-0.005	3.54e-04	0.193	-0.004	2.07e-03
DIP2C	10:676740	-0.003	3.57e-04	0.193	-0.004	1.10e-02
IGF2R	6:160380572	0.006	3.60e-04	0.193	0.007	4.45e-03
PNPO	17:46018654	0.007	3.63e-04	0.193	0.006	6.19e-03
EIF2B2	14:75472643	-0.006	3.63e-04	0.193	-0.006	8.71e-03
NFATC1	18:77284509	-0.006	3.67e-04	0.193	-0.007	1.29e-03
PWWP2B	10:134225120	0.006	3.70e-04	0.193	0.005	3.33e-02
FCRL1	1:157776690	-0.004	3.69e-04	0.193	-0.005	2.31e-03
GALK1	17:73760817	0.004	3.92e-04	0.197	0.003	8.12e-04
ZC3H4	19:47610813	-0.004	3.93e-04	0.197	-0.004	1.58e-03
ASPRV1	2:70188605	0.007	3.98e-04	0.198	0.006	2.97e-02
PRRT1	6:32119874	-0.006	4.04e-04	0.198	-0.005	4.71e-03
Gene	Position	ΔBeta	P-value	FDR	ΔBeta	P-value

Note:

Data source: Montano et al. Association of DNA methylation differences with schizophrenia in an epigenome-wide association study.
JAMA psychiatry, 73(5): 506-14(2016).

Gene	Gene	Gene	Gene	Gene	Gene
ACSL1	AFF3	ARHGAP15	ARHGAP26	ARL3	ARNT
AUH	BRD4	BRP44L	BTBD10	CHFR	CHN2
CREB1	CSDE1	CSPP1	CXCR4	DAAM1	ETS2
FAM63B	FCAR	FCGR2B	FCGR2C	FNDC3B	FOXN3
FOXP1	FRZB	GDI2	GNB4	INPP5D	IPO11
KDM3A	MAN1A1	MAPKAP1	MBD6	MLL3	MTHFD1L
MYT1L	NAALADL2	NDFIP2	NSUN7	NUS1	PELI2
PHLPP1	PIK3R3	PPARA	PPM1D	PRKD2	RASSF2
RBMS3	RCOR1	RHOH	RPS15A	RUNX2	RUNX3
SATB1	SMAD3	SS18L1	TBC1D22A	TCF12	TIAM1
TMEM131	TRAPPC6B	TRERF1	UCK2	UPP2
Gene	Gene	Gene	Gene	Gene	Gene

Note:

Data source: Aberg et al. Methylome-wide association study of schizophrenia identifying blood biomarker signatures of environmental insults.
JAMA Psychiatry, 71(3): 255-264(2014).