Table 2.

Top 50 most significant variably methylated probes (VMPs) associated with amyloid-β (q<0.05).

CpG probe	Chr	Position (bps)	Genomic feature	p-value	q-value	Gene*	Direction†
cg01624068	13	113,137,799	intergenic	1.35×10−9	2.68×10−4	TUBGCP3	↑
cg10506070	5	114,502,492	intergenic	1.60×10−9	2.68×10−4		↑
cg00391025	3	100,427,239	intergenic	2.13×10−9	2.68×10−4		↑
cg19734937	2	63,855,048	intergenic	2.58×10−9	2.68×10−4		↑
cg25871696	13	81,914,087	intergenic	3.03×10−9	2.68×10−4		↑
cg26102082	17	47,590,272	exons	7.70×10−9	5.67×10−4	NGFR	↓
cg06060962	6	32,515,150	introns	1.01×10−8	5.75×10−4	HLA-DRB5	↑
cg02226953	7	150,525,449	intergenic	1.04×10−8	5.75×10−4		↑
cg03660952	11	2,644,418	exons	1.21×10−8	5.93×10−4	KCNQ1OT1	↑
cg23968456	10	73,521,631	exons	1.87×10−8	8.25×10−4	C10orf54	↓
cg14313916	8	8,640,017	intergenic	2.61×10−8	1.00×10−3		↑
cg15948245	7	104,581,746	promoters	2.72×10−8	1.00×10−3		↑
cg21110873	12	131,712,414	intergenic	3.66×10−8	1.24×10−3		↑
cg19550439	5	64,470,134	introns	4.64×10−8	1.47×10−3	ADAMTS6	↑
cg23493751	3	46,204,787	promoters	5.86×10−8	1.65×10−3	CCR3	↑
cg25814432	19	54,620,431	introns	5.97×10−8	1.65×10−3	PRPF31	↑
cg17917920	7	93,220,788	intergenic	7.00×10−8	1.82×10−3		↑
cg13501912	3	87,424,518	intergenic	7.72×10−8	1.90×10−3		↑
cg06890950	4	81,382,711	introns	8.28×10−8	1.93×10−3	C4orf22	↑
cg08041573	21	33,651,723	intergenic	8.72×10−8	1.93×10−3		↑
cg03043928	11	2,085,203	intergenic	9.28×10−8	1.95×10−3		↑
cg21002735	11	77,350,306	intergenic	9.85×10−8	1.98×10−3	CLNS1A	↑
cg07725198	1	27,229,130	intergenic	1.13×10−7	2.00×10−3	GPATCH3	↑
cg09609314	2	174,147,631	intergenic	1.20×10−7	2.00×10−3		↑
cg18677996	5	17,031,869	intergenic	1.25×10−7	2.00×10−3		↑
cg10655371	7	91,749,682	introns	1.29×10−7	2.00×10−3	CYP51A1	↑
cg20996620	7	20,623,878	intergenic	1.30×10−7	2.00×10−3		↑
cg06931905	8	42,036,940	intergenic	1.35×10−7	2.00×10−3		↑
cg00689014	17	39,869,138	introns	1.38×10−7	2.00×10−3	JUP	↑
cg13290719	4	58,063,449	introns	1.43×10−7	2.00×10−3	IGFBP7-AS1	↑
cg10575940	17	75,365,389	intergenic	1.44×10−7	2.00×10−3		↑
cg07561890	2	133,036,548	intergenic	1.45×10−7	2.00×10−3		↑
cg16608672	5	30,346,809	intergenic	1.86×10−7	2.49×10−3		↑
cg14446166	7	148,934,349	intergenic	2.05×10−7	2.60×10−3		↑
cg27340958	4	7,755,730	promoters	2.19×10−7	2.60×10−3	AFAP1-AS1	↑
cg26529712	19	35,399,253	intergenic	2.20×10−7	2.60×10−3		↑
cg26879538	6	30,014,916	introns	2.21×10−7	2.60×10−3	ZNRD1ASP	↑
cg03318222	19	56,847,740	introns	2.24×10−7	2.60×10−3	ZSCAN5A	↑
cg21512370	13	48,990,327	introns	2.34×10−7	2.65×10−3	LPAR6	↑
cg12447346	1	161,055,663	introns	2.45×10−7	2.70×10−3	NECTIN4	↑
cg27616595	7	146,484,518	intergenic	2.77×10−7	2.98×10−3		↑
cg01481116	11	93,867,992	introns	3.11×10−7	3.27×10−3	PANX1	↑
cg14519534	7	102,082,149	introns	3.32×10−7	3.36×10−3	ORAI2	↑
cg24620463	7	95,917,902	intergenic	3.35×10−7	3.36×10−3		↑
cg20185525	17	41,278,712	introns	3.54×10−7	3.48×10−3	BRCA1	↑
cg21775279	1	28,285,385	exons	3.71×10−7	3.56×10−3	SMPDL3B	↓
cg03169557	16	89,598,950	exons	4.05×10−7	3.80×10−3	SPG7	↓
cg02180296	14	24,404,306	intergenic	4.24×10−7	3.90×10−3	DHRS4-AS1	↑
cg02312525	22	50,525,778	intergenic	4.48×10−7	4.04×10−3	MLC1	↑
cg19988798	5	175,511,300	intergenic	4.58×10−7	4.05×10−3		↑

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

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