Population-specificity of human DNA methylation

Table 1 High-confidence mSNPs in CEU

Gene	Chromosome	CpG position	mSNP	Perccentage CEU variance explained	Perccentage YRI variance explained	CEU h ²	YRI h ²	Brain mSNP?
TTC13	1	229182620	rs7545429	71.3	49.0	0.41	0.64	No
MGC3207	19	13736014	rs371671	68.8	27.2	0.60	0.35	Yes
PPP4R2	3	73128376	rs9816164	66.7	43.2	0.51	0.23	Yes
LDHC	11	18390591	rs11601413	65.4	86.5	0.55	0.68	Yes
RNF186	1	20015084	rs3806308	65.1	68.3	0.41	0.50	No
FLJ32569	1	204085874	rs823080	58.5	4.5	0.28	0.05	Yes
NDUFAF2	5	60275337	rs162244	57.4	62.6	0.26	0.49	No
PCGF3	4	689950	rs2242234	57.2	19.9	0.47	-0.10	No
LTA	6	31648435	rs2516390	55.9	40.5	0.48	0.24	No
IGSF2	1	117345939	rs12130298	52.6	10.0	0.96	-0.19	No
GSTM5	1	110056139	rs4970776	52.4	12.1	0.55	0.14	Yes
FLJ32569	1	204085802	rs823080	50.4	3.7	0.49	0.08	Yes
ASCIZ	16	79627243	rs16954698	47.8	9.6	0.24	-0.12	No
TACSTD2	1	58815787	rs1109896	42.2	50.4	0.29	0.49	No
HLA-C	6	31347299	rs6457375	42.1	44.0	0.24	0.61	Yes
HLA-DRB5	6	32606582	rs9271586	42.0	28.2	0.32	0.42	No
LYCAT	2	30523367	rs829650	40.8	52.4	0.75	0.64	Yes
PARK2	6	163069159	rs13218900	40.4	41.6	0.21	0.03	No
ITPR1	3	4510075	rs304075	39.4	7.6	0.21	-0.07	No
PSMD5	9	122644335	rs12343516	39.4	35.1	0.53	0.11	Yes
BTN3A2	6	26472772	rs2393667	38.1	14.9	0.22	0.31	Yes
RAPGEF3	12	46439111	rs3759407	37.2	6.8	0.71	-0.17	No
FAM83A	8	124264314	rs16898095	36.3	76.5	0.27	0.71	No
CRIP2	14	105011436	rs4983346	36.1	3.6	0.46	0.04	No

The 24 mSNP-CpG site pairs where > 36% of the variance in CEU methylation is explained by the mSNP genotype, and h ² > 0.2. When more than one SNP was tied for the strongest association (due to perfect LD), one was chosen randomly. The YRI association strength is for the top local (within 100 kb) mSNP association for the same CpG site. In bold are YRI associations that explain < 20% of the variance in YRI methylation, indicating a high-confidence set of CEU-specific associations. For brain mSNPs, the intersection of cis-acting mSNP lists used by the authors of each original study [11, 12] was used. YRI mSNPs are listed in Table S2 in Additional file 1.

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