Table 1. Average Methylation in Association SNP LD blocks by Genotype.

					Average Methylation
Chr	LD Block		Genotyped SNP	Gene/Locus	11	12	22	p-value
1	120236149	120398430	rs2934381	NOTCH2	0.496	0.495	0.502	0.187
2	43529937	43617946	rs7578597	THADA	0.492	0.512	0.504	0.564
3	12298413	12372392	rs1801282	PPARG	0.512	0.509	0.511	0.640
3	64673853	64705161	rs4607103	ADAMTS9	0.477	0.472	0.481	0.760
3	186971576	187031377	rs4402960	IGF2BP2	0.502	0.493	0.502	0.016
4	6317902	6363877	rs10010131	WFS1	0.581	0.604	0.590	0.982
7	28147081	28175361	rs864745	JAZF1	0.501	0.492	0.494	0.317
8	118252732	118254914	rs13266634	SLC30A8	0.333	0.350	0.303	0.865
9	22122209	22126489	rs10811661	CDKN2A/CDKN2B	0.543	0.512	0.512	0.389
10	12367941	12368040	rs12779790	CDC123/CAMK1D	0.611	0.590	0.671	0.913
10	94426831	94467199	rs1111875	HHEX/IDE	0.480	0.483	0.483	0.369
11	17350649	17365206	rs5219	KCNJ11	0.501	0.502	0.498	0.540
12	69942990	69949369	rs7961581	TSPAN8	0.457	0.461	0.470	0.289
16	52357008	52402988	rs8050136	FTO	0.497	0.510	0.531	9.397′10−4
17	33170413	33182480	rs757210	HNF1B	0.423	0.430	0.427	0.382

P-values are calculated by Linear Regression and are shown uncorrected (11 – homozygote common, 12 – heterozygote, 22 – homozygote rare allele).

a) r² = 1 with rs10923931,

b) Not in LD block – single BATMAN window of 100 bp utilised,

c) LD block of associated SNP rs5215 used as rs5219 not typed in HapMap, r² = 0.995 with rs5219. Methylation is given as average BATMAN scores across regions (0 =  unmethylated, 1 =  fully methylated).