Table 3.

CpG sites showing significant (P < 0.05) differences between T2DM and control pools following multiple hypothesis testing (q < 0.05). Average methylation levels, number of aligned sequence reads and absolute methylation differences are shown

Chromosome	Position (hg18)	Nearest gene	Gene relation	Control methylation (%)	T2DM methylation (%)	Control reads	T2DM reads	Methylation difference	P-value	q-value
2	43590864	THADA	Intron	95.64	94.41	3947	3957	1.23	0.0120	0.0464
7	28143482	JAZF1	Intron	94.54	92.94	4305	3555	1.60	0.0034	0.0188
8	118257326	SLC30A8	3′-UTR	85.61	83.43	5159	4888	2.18	0.0025	0.0188
8	118257358	SLC30A8	3′-UTR	96.12	95.07	5130	4845	1.05	0.0102	0.0428
8	118258573	SLC30A8	Down	61.78	65.43	3370	2930	3.65	0.0027	0.0188
10	114734658	TCF7L2	Intron	88.76	86.41	4618	3755	2.34	0.0012	0.0116
10	114739401	TCF7L2	Intron	99.25	98.53	4642	1768	0.72	0.0079	0.0361
10	114743601	TCF7L2	Intron	94.52	92.59	3542	4777	1.93	0.0004	0.0055
10	114743664	TCF7L2	Intron	98.23	96.91	3551	4788	1.32	0.0001	0.0025
11	2805916	KCNQ1	Intron	90.23	92.20	2979	4180	1.97	0.0033	0.0188
11	2806049	KCNQ1	Intron	88.06	90.97	2981	4187	2.92	0.0001	0.0015
11	2806079	KCNQ1	Intron	93.43	95.03	2968	4168	1.60	0.0038	0.0192
16	52366732	FTO	Intron	30.15	27.53	12180	11013	2.61	1e−5	0.0006