Table 3.

Top 50 DhMRs associated with quantitative NFTs in human postmortem brain (N=30)

Chromosome	Start (bp)	End (bp)	Distance to TSS (bp) of nearest gene	Nearest gene	Effect size*	P-value*	q-value†
1	16490000	16500000	6292	CDK11A	0.2579	6.87× 10−11	8.03×10−7
9	131920000	131930000	87064	MPDZ	0.2350	1.47× 10−10	8.57×10−7
16	3360000	3370000	3381	PDIA2	−0.1322	3.62× 10−10	1.41×10−6
9	79400000	79410000	−140700	TMEM261	0.1143	6.30× 10−10	1.84×10−6
7	105090000	105100000	470314	NDUFA4	−0.4217	1.42× 10−9	3.33×10−6
22	39410000	39420000	−12220567	BMS1P17	−0.4868	1.93× 10−9	3.76×10−6
3	39330000	39340000	92378	LRRN1	0.1198	3.29× 10−9	5.49×10−6
14	55520000	55530000	−13825095	OR11H12	−0.3974	4.14× 10−9	6.05×10−6
16	68960000	68970000	72689	RBFOX1	0.1142	1.60× 10−8	2.08×10−5
11	62200000	62210000	45	OR52W1	0.1312	2.05× 10−8	2.39×10−5
2	101040000	101050000	12707	GRHL1	0.0958	2.34× 10−8	2.49×10−5
10	105400000	105410000	−36187	LOC101928322	0.0677	2.75× 10−8	2.68×10−5
12	12620000	12630000	125585	ERC1	0.1227	2.99× 10−8	2.69×10−5
10	99380000	99390000	−162186	LOC101928298	0.2970	5.93× 10−8	4.95×10−5
22	37930000	37940000	−12368567	BMS1P17	0.1362	7.53× 10−8	5.87×10−5
16	72910000	72920000	−91252	RBFOX1	0.0806	8.49× 10−8	6.20×10−5
16	70610000	70620000	237689	RBFOX1	0.1096	9.82× 10−8	6.75×10−5
3	171010000	171020000	126811	MIR3714	−0.5098	1.20× 10−7	7.76×10−5
17	57950000	57960000	119945	LOC339166	−0.2200	1.49× 10−7	9.17×10−5
13	52980000	52990000	14015740	LINC00417	0.0757	2.07× 10−7	1.21×10−4
10	123250000	123260000	−66084	CAMK1D	0.2151	2.26× 10−7	1.26×10−4
12	121210000	121220000	−42392	RNU6-19P	0.1551	3.43× 10−7	1.82×10−4
1	117610000	117620000	9718	DRAXIN	0.2147	3.92× 10−7	1.99×10−4
2	198390000	198400000	−229116	LINC00954	0.0826	4.25× 10−7	2.07×10−4
3	72980000	72990000	278472	GRM7-AS1	−0.0571	4.78× 10−7	2.23×10−4
14	105970000	105980000	−8780095	OR11H12	0.1601	5.75× 10−7	2.59×10−4
14	58890000	58900000	−13488095	OR11H12	0.0832	1.18× 10−6	5.11×10−4
8	2250000	2260000	42949	ZNF596	0.0922	1.84× 10−6	7.7×10−4
4	7380000	7390000	37137	LOC100129917	0.1447	2.21× 10−6	8.91×10−4
6	3770000	3780000	−14240	IRF4	−0.0850	2.38× 10−6	9.28×10−4
13	49890000	49900000	14324740	LINC00417	0.0853	2.78× 10−6	1.05×10−3
1	1460000	1470000	−5933	LOC729737	−0.0401	4.59× 10−6	1.67×10−3
16	87810000	87820000	13055	ABAT	0.0724	6.32× 10−6	2.24×10−3
9	131730000	131740000	106064	MPDZ	0.0576	6.92× 10−6	2.38×10−3
4	83310000	83320000	60007	HTRA3	−0.3446	7.61× 10−6	2.54×10−3
17	57500000	57510000	74945	LOC339166	0.0973	8.58× 10−6	2.78×10−3
8	6450000	6460000	35727	ERICH1	0.1302	1.02× 10−5	3.22×10−3
17	41910000	41920000	−16310	LOC103021295	0.1064	1.26× 10−5	3.86×10−3
3	179080000	179090000	−95565	LOC339862	−0.1694	1.29× 10−5	3.86×10−3
22	24060000	24070000	−13755567	BMS1P17	0.1000	1.32× 10−5	3.87×10−3
8	1400000	1410000	−23475	OR4F21	−0.0197	1.61× 10−5	4.50×10−3
14	102410000	102420000	−9136095	OR11H12	0.0694	1.82× 10−5	5.06×10−3
19	56660000	56670000	−14277	HSD11B1L	−0.0424	1.91× 10−5	5.18×10−3
20	11520000	11530000	12618	TMEM74B	−0.2219	2.13× 10−5	5.67×10−3
4	187210000	187220000	−698016	LCORL	−0.0566	2.32× 10−5	6.02×10−3
1	93200000	93210000	20596	H6PD	−0.0479	2.84× 10−5	7.21×10−3
17	64440000	64450000	15378	PITPNM3	−0.1952	2.91× 10−5	7.23×10−3
1	2220000	2230000	−81933	LOC729737	0.0403	3.22× 10−5	7.84×10−3
16	910000	920000	12133	POLR3K	−0.0652	3.55× 10−5	8.46×10−3
8	19490000	19500000	27455	KBTBD11	−0.0337	3.71×10−5	8.67×10−3

^*Obtained from zero-inflated negative binomial regression, adjusting for age at death, sex, education, neuronal proportions and the first 3 PCs derived from GWAS;

^†Adjusting for a total number of 18,767 10-kb bins.