Table 2.

Genes with at least one differentially methylated CpG in the discovery cohort (absolute delta-beta ≥ 5%, adj. p < 0.05) and with additional CpGs differentially methylated in the MSA mixed replication cohort and/or MSA OPCA (absolute delta-beta ≥ 5%, gene-wide significant)

CpG	Delta beta discovery MSA mixed	Delta beta replication MSA mixed	P.Val replication MSA mixed	Delta beta MSA OPCA	P.Val MSA OPCA	Delta beta MSA SND	P.Val MSA SND	Chr	Map (GRCh37)	Gene symbol	Gene name	Feature
(a) Gene-wide significant changes in the MSA mixed replication cohort and occasionally in MSA OPCA [cross-region significance threshold p < 9.00E−04 (0.05/54 genes) or cerebellum-specific threshold p < 1.90E − 03 (0.05/27 genes)]
cg15271829***	− 0.03	− 0.06	4.04E−04	− 0.22	7.91E−05	− 0.04	5.40E−01	2	28789262	PLB1	Phospholipase B1	Body-shore
cg08313420*	− 0.01	− 0.07	8.90E−04	− 0.25	3.37E−03	− 0.08	2.32E−02	7	6476110	DAGLB	Diacylglycerol lipase beta	Body-opensea
cg00282245*	0.05	0.09	5.27E−04	− 0.06	4.74E−02	0.01	2.36E−01	7	51130590	COBL	Cordon-bleu WH2 repeat protein	Body-opensea
cg14212951***	− 0.02	− 0.07	3.32E−04	0.03	7.90E−02	− 0.03	3.64E−02	7	137139878	DGKI	Diacylglycerol kinase iota	Body-opensea
cg05540100***	− 0.03	− 0.12	5.38E−06	− 0.0003	1.72E−03	− 0.02	2.39E−02	7	137367050	DGKI	Diacylglycerol kinase iota	Body-opensea
cg02113214***	− 0.01	− 0.06	9.34E−05	− 0.01	1.84E−03	− 0.02	4.78E−02	7	137410625	DGKI	diacylglycerol kinase iota	Body-opensea
cg10264318*	− 0.02	− 0.07	5.93E−04	0.05	4.09E−01	− 0.02	1.35E−01	7	154633168	DPP6	Dipeptidyl peptidase like 6	Body-opensea
cg12499572***	0.06	0.09	8.26E−04	0.28	7.62E−05	0.07	3.52E−01	10	134462831	INPP5A	Inositol polyphosphate-5-phosphatase A	Body-shelf
cg22343263*	− 0.03	− 0.05	1.00E−04	0.002	3.48E−02	− 0.001	1.06E−01	12	50466510	ASIC1	Acid sensing ion channel subunit 1	TSS1500-opensea
cg18498263***	0.03	0.05	1.19E−03	− 0.06	8.36E−03	0.002	1.55E−01	14	91034963	TTC7B	Tetratricopeptide repeat domain 7B	Body-opensea
(b) Gene-wide significant in OPCA only [cross-region significance threshold p < 9.00E−04 (0.05/54 genes) or cerebellum-specific threshold p < 1.90E−03 (0.05/27genes)]
cg16729794*	0.06	0.09	0.016	0.28	1.83E−05	0.08	2.22E−01	3	39509195	MOBP	Myelin-associated oligodendrocyte basic protein	5′UTR-opensea
cg24602838*	0.09	0.10	0.003	0.33	3.86E−04	0.08	4.90E−01	3	39527173	MOBP	Myelin-associated oligodendrocyte basic protein	5′UTR-opensea
cg05317077*	0.08	0.08	1.34E−02	0.26	7.22E−04	0.09	1.48E−01	3	39542991	MOBP	Myelin-associated oligodendrocyte basic Protein	TSS1500-shore
cg06277657***	− 0.03	− 0.01	0.318	− 0.08	1.06E−03	− 0.03	5.78E−02	7	137532374	DGKI	Diacylglycerol kinase iota	TSS1500-island
cg10947146**	− 0.02	− 0.02	0.006	− 0.06	2.73E−04	− 0.02	2.94E−02	8	11058710	XKR6	XK related 6	1st exon-island
cg02881186***	− 0.004	− 0.02	0.012	− 0.22	6.51E−05	− 0.03	4.17E−01	8	140892009	TRAPPC9	Trafficking protein particle complex 9	Body-opensea
cg10445361***	0.08	0.06	0.027	0.24	1.05E−03	0.05	5.85E−01	10	134461611	INPP5A	Inositol polyphosphate-5-phosphatase A	Body-shore
cg13582959***	0.05	0.08	0.004	0.26	4.28E−04	0.05	9.95E−01	10	134462849	INPP5A	Inositol polyphosphate-5-phosphatase A	Body-shelf
cg02240936***	0.05	0.04	0.687	0.09	1.53E−03	0.02	8.32E−01	10	134584660	INPP5A	Inositol polyphosphate-5-phosphatase A	Body-shore
cg03237845***	0.11	0.08	0.033	0.25	4.13E−04	0.05	9.36E−01	15	57377660	TCF12	Transcription factor 12	Body-opensea

*Gene with significant CpG(s) in the cross-region analysis only; **gene with significant CpG(s) in cerebellum-specific analysis only; ***with significant CpG(s) in both cerebellum-specific and cross-region analyses; bold highlights CpGs showing absolute delta beta values > 5% and gene-wide significant p values