Table 3.

Top 50 most significant variably methylated probes (VMPs) associated with tangles (q<0.05)

CpG probe	Chr	Position (bps)	Genomic features	p-value	q-value	Gene*	Direction†
cg21406811	1	51,271,043	introns	4.08×10−12	1.63×10−6	FAF1	↑
cg23067228	15	70,881,206	intergenic	7.37×10−12	1.63×10−6		↑
cg22895202	14	21,238,166	promoters	3.11×10−11	4.58×10−6	EDDM3B	↑
cg09183598	19	57,679,015	promoters	5.26×10−11	5.81×10−6	DUXA	↑
cg12308275	15	43,558,855	promoters	1.54×10−10	1.37×10−5	TGM5	↑
cg16008918	4	78,740,080	intergenic	2.03×10−10	1.49×10−5		↑
cg13689497	19	3,201,528	intergenic	2.82×10−9	1.78×10−4		↑
cg17678740	7	53,254,947	intergenic	4.36×10−9	2.41×10−4		↓
cg23524184	17	48,129,754	intergenic	2.75×10−8	1.25×10−3	ITGA3	↑
cg22661129	8	35,580,715	promoters	3.11×10−8	1.25×10−3	UNC5D	↑
cg25868285	7	134,455,275	intergenic	3.12×10−8	1.25×10−3		↑
cg04559604	8	22,031,763	intergenic	5.34×10−8	1.97×10−3		↑
cg01363574	3	40,354,920	intergenic	1.03×10−7	3.31×10−3	EIF1B-AS1	↑
cg16353628	2	85,239,916	introns	1.05×10−7	3.31×10−3	KCMF1	↑
cg09352908	3	37,017,749	intergenic	1.23×10−7	3.63×10−3		↓
cg14115740	9	98,054,883	intergenic	2.16×10−7	5.97×10−3		↓
cg04212651	6	112,671,523	promoters	2.30×10−7	5.98×10−3	RFPL4B	↑
cg02745683	4	3,513,990	exons	2.60×10−7	6.28×10−3	LRPAP1	↑
cg20376421	12	56,546,193	promoters	2.70×10−7	6.28×10−3	MYL6B	↓
cg26227935	18	77,682,412	intergenic	3.13×10−7	6.91×10−3		↑
cg19729949	5	142,514,108	intergenic	4.11×10−7	8.66×10−3		↑
cg01869224	12	53,356,063	intergenic	4.79×10−7	9.13×10−3		↑
cg05929056	21	43,274,690	intergenic	4.81×10−7	9.13×10−3		↑
cg12538597	11	85,906,334	intergenic	5.13×10−7	9.13×10−3		↓
cg20660860	2	122,095,855	exons	5.27×10−7	9.13×10−3	CLASP1	↑
cg24663683	5	39,721,720	intergenic	5.26×10−7	9.13×10−3		↓
cg09537031	8	19,171,706	intergenic	5.87×10−7	9.13×10−3		↑
cg09828625	20	23,331,259	promoters	5.97×10−7	9.13×10−3	NXT1	↑
cg08866589	5	141,303,260	promoters	6.02×10−7	9.13×10−3	KIAA0141	↑
cg20208633	4	55,405,888	intergenic	6.19×10−7	9.13×10−3		↑
cg07252851	5	74,063,056	promoters	6.55×10−7	9.29×10−3	GFM2	↓
cg10690677	1	87,019,175	introns	6.73×10−7	9.29×10−3	CLCA4	↓
cg12550816	19	47,163,979	promoters	7.07×10−7	9.46×10−3	DACT3-AS1	↓
cg06159435	11	118,966,351	promoters	7.31×10−7	9.46×10−3	H2AFX	↓
cg13838599	9	128,989,097	intergenic	7.49×10−7	9.46×10−3		↑
cg06459913	16	11,361,823	introns	7.93×10−7	9.59×10−3	RMI2	↑
cg18803079	1	64,014,643	promoters	8.03×10−7	9.59×10−3	EFCAB7	↓
cg14559409	10	65,930,703	intergenic	8.87×10−7	1.03×10−2		↓
cg21962918	5	134,094,454	intergenic	1.00×10−6	1.11×10−2		↓
cg02738677	3	133,265,129	intergenic	1.01×10−6	1.11×10−2		↓
cg10269358	19	17,728,585	exons	1.03×10−6	1.11×10−2	UNC13A	↑
cg22331096	8	128,749,328	introns	1.16×10−6	1.21×10−2	MYC	↓
cg01778384	13	27,236,961	introns	1.20×10−6	1.21×10−2	WASF3	↑
cg02746684	3	197,347,276	introns	1.23×10−6	1.21×10−2	LOC220729	↑
cg08450091	3	82,857,215	intergenic	1.24×10−6	1.21×10−2		↓
cg04005938	7	148,334,417	intergenic	1.27×10−6	1.21×10−2		↓
cg27618483	2	155,433,424	intergenic	1.31×10−6	1.21×10−2		↓
cg17095167	13	21,833,918	intergenic	1.31×10−6	1.21×10−2		↓
cg01757206	17	7,183,913	intergenic	1.46×10−6	1.32×10−2	SLC2A4	↓
cg26342398	1	85,156,326	promoters	1.61×10−6	1.42×10−2	SSX2IP	↓

^*The nearest annotated gene within ±5kb of the CpG probe

^†↑ indicates hypervariable (increased variability in subjects with higher neuropathological burden as compared to those with lower burden), and ↓ indicates hypovariable (decreased variability in subjects with higher neuropathological burden as compared to those with lower burden).