DNA methylation differences within INS, PTPN22 and IL2RA promoters in lymphocyte subsets in children with type 1 diabetes and controls

Figures & data

Figure 2. CpG sites where DNA methylation is associated with rs689 and rs12722495 genotypes.

Table 1. Association between SNP markers and CpG site methylation: p values statistically significant before correcting for multiple comparisons, and the corrected p values.

SNP	Cell subset	Gene	CpG site	p value	Corrected p value (BH)
rs689	Bcell	INS	−234	4.00E-06	3.52E-05
	Bcell	INS	−206	6.22E-07	1.05E-05
	Bcell	INS	−102	0.014	5.13E-02
	CD4+	INS	−234	7.18E-07	1.05E-05
	CD4+	INS	−206	3.39E-07	1.05E-05
	CD4+	INS	−102	0.003	0.012
	CD4+	INS	−69	0.001	4.89E-03
	CD8+	INS	−234	2.00E-06	2.20E-05
	CD8+	INS	−206	1.06E-04	7.77E-04
	CD8+	INS	−180	0.042	1.41E-01
	CD8+	INS	−102	0.001	4.89E-03
	CD8+	INS	−69	0.045	1.41E-01
rs12722495	Bcell	IL2RA	−373	0.002	8.80E-03
	Bcell	IL2RA	−356	0.001	4.89E-03

Table 2. DNA methylation levels (%) in T1D patients and controls: results with significant p-values before correction, and their p values after correcting for multiple comparisons.

Cell subset	Gene	CpG site	T1D patients	Controls	p-value	Corrected p values (BH)
CD4+	INS	−234	81.2 ± 8.0	76.1 ± 6.2	0.047	0.228
CD8+	INS	−234	79.0 ± 4.7	75.6 ± 5.7	0.046	0.228
CD8+	INS	−206	87.0 ± 4.0	83.5 ± 5.7	0.032	0.218
CD8+	INS	−180	69.5 ± 7.6	62.1 ± 8.9	0.017	0.145
CD8+	INS	−135	87.3 ± 7.2	78.8 ± 8.9	0.001	0.034
CD8+	INS	−102	53.6 ± 5.4	47.6 ± 7.5	0.003	0.051
CD8+	INS	−69	74.8 ± 4.6	69.2 ± 7.2	0.009	0.102

Data availability statement

The datasets used and/or analyzed in the present study are not readily available due to data privacy regulations. Requests to access the datasets should be directed to DIPP Steering Committee, [email protected].