Table 3.

Differentially methylated regions (DMRs) in MRS, Army STARRS, and PRISMO

Chr: start-stop	No. of probes	Gene	Region	MRS		Army STARRS		Stage 1: MRS and Army STARRS		Stage 1: replication in PRISMO		Stage 2: meta-analysis of 3 cohorts
				NES	p value	NES	p value	Z	p value	NES	p value	Z	p value
6: 33043976-33054001	56	HLA-DPB1	Body	− 2.08	3.45E−05	− 1.98	8.06E−05	− 5.69	1.25E−08	− 1.05	3.51E−01	− 5.43	5.46E−08
6: 33048416-33048814	17	HLA-DBP1	Island	− 2.04	6.96E−05	− 2.25	1.62E−04	− 5.46	4.80E−08	− 1.16	2.15E−01	− 5.38	7.49E−08
21: 35831697-35832365	10	KCNE1	Island	− 1.93	1.32E−04	− 2.16	1.72E−04	− 5.33	9.99E−08	− 1.27	1.58E−01	− 5.34	8.93E−08
21: 35827824-35884508	23	KCNE1	Promoter	− 1.93	9.45E−05	− 2.00	3.42E−04	− 5.28	1.27E−07	− 1.22	1.91E−01	− 5.26	1.46E−07
6: 32547019-32557404	34	HLA-DRB1	Body	− 1.23	2.00E−01	− 2.48	1.67E−05	− 3.67	2.43E−04	− 2.58	2.62E−05	− 5.24	1.58E−07
7: 1885033-1885402	3	MAD1L1	Island	− 2.22	1.81E−05	− 2.12	1.72E−04	− 5.69	1.25E−08	− 0.81	7.38E−01	− 5.15	2.65E−07
7: 27169572-27170638	10	HOXA4	Island	− 2.21	1.73E−05	− 1.98	3.26E−04	− 5.60	2.15E−08	− 0.84	7.46E−01	− 5.06	4.20E−07
8: 125461772-125464547	9	TRMT12	Promoter	− 2.20	1.85E−05	− 1.14	2.98E−01	− 4.01	6.11E−05	− 1.93	1.55E−03	− 5.03	4.69E−07
6: 32551851-32552331	13	HLA-DRB1	Island	− 1.25	1.79E−01	− 2.49	1.68E−04	− 3.38	7.17E−04	− 2.52	2.59E−05	− 4.99	5.92E−07
7: 27169740-27171528	24	HOXA4	Promoter	− 2.31	1.78E−05	− 1.97	3.41E−04	− 5.59	2.31E−08	− 0.68	9.18E−01	− 4.94	7.71E−07
6: 25882327-25882560	4	SLC17A3	Island	− 1.96	9.39E−05	− 1.50	4.91E−02	− 4.29	1.81E−05	− 1.63	3.04E−02	− 4.80	1.60E−06
1: 156814881-156815792	5	NTRK1	Island	− 1.51	5.29E−02	− 1.78	3.74E−03	− 3.31	9.20E−04	− 2.12	1.16E−04	− 4.76	1.90E−06
16: 1561036-1652552	121	IFT140	Body	− 1.67	7.56E−04	− 1.82	5.99E−05	− 5.12	2.92E−07	− 0.83	8.80E−01	− 4.57	4.96E−06
17: 8700574-8703341	12	MFSD6L	Promoter	− 2.33	1.84E−05	− 1.82	3.56E−03	− 5.17	2.36E−07	1.03	4.10E−01	− 4.52	6.33E−06
16: 1583809-1584641	8	IFI140	Island	− 2.46	1.81E−05	− 1.79	2.75E−03	− 5.22	1.78E−07	0.69	8.80E−01	− 4.50	6.79E−06
5: 191792-192544	5	LRRC14B	Island	− 2.19	1.81E−05	− 1.57	2.34E−02	− 4.77	1.83E−06	− 0.93	5.50E−01	− 4.47	7.96E−06
6: 168433191-1.68E+08	18	KIF25	Body	− 2.13	5.45E−05	− 1.79	4.11E−03	− 4.94	7.59E−07	− 0.62	9.50E−01	− 4.36	1.30E−05
10: 530713-531099	5	DIP2C	Island	− 2.22	3.54E−05	− 1.98	5.05E−04	− 5.40	6.63E−08	1.148	2.60E−01	− 4.19	2.78E−05
1: 2986362-3349982	608	PRDM16	Body	− 1.73	1.34E−05	− 1.43	2.06E−04	− 5.71	1.09E−08	1.168	8.00E−02	− 4.15	3.25E−05
17: 8702342-8702824	7	MFSD6L	Island	− 2.19	1.84E−05	− 1.82	2.42E−03	− 5.24	1.59E−07	0.684	8.70E−01	− 4.13	3.57E−05
12: 9217328-9217715	6	LINC00612	Island	− 2.27	1.84E−05	− 2.36	1.75E−04	− 5.69	1.30E−08	1.465	6.00E−02	− 4.09	4.31E−05
12: 9217079-9217769	9	LOC144571	Promoter	− 2.27	1.85E−05	− 2.16	1.81E−04	− 5.68	1.34E−08	1.530	4.00E−02	− 4.00	6.46E−05
11: 70672834-70673055	6	SHANK2	Island	− 2.56	1.83E−05	− 2.32	1.73E−04	− 5.69	1.28E−08	1.752	6.00E−03	− 3.67	2.45E−04
17: 76037074-76037323	3	TNRC63	Island	− 2.03	9.29E−05	− 2.05	1.78E−04	− 5.39	7.07E−08	1.693	1.10E−02	− 3.49	4.82E−04

Chr chromosome, NES normalized effect score. All positions and regions were in reference to GRCh37/hg19. Significance is indicated in italics. The p values for MRS, Army STARRS, and the combined analyses are Bonferroni-corrected for ~ 26K DMRs. In stage 1, MRS and Army STARRS were combined and PRISMO was used to replicate significant findings. In stage 2, all three studies were combined. The table is organized based on significances of the DMRs in the stage 2 meta-analysis