Genetic analysis of DNA methylation and gene expression levels in whole blood of healthy human subjects

Table 2 Distribution of results over CpG islands and shores

Location	Illumina Human Methylation 27		Methylation & expression *cis*		Methylation & expression *trans*		Methylation & expression & SNP *cis*
Island	11,582	42%	70	13.5%, p <2.2e-16↓	269	38.2%, p=0.04	11	15.1%, p =1.1e-06↓
Island shore (2kb)	8,718	32%	184	35.6%, p=0.056	172	24.4%, p =3.9e-05↓	39	53.4%, p =1.3e-04↑
Outside island/shore	7,278	26%	263	50.9%, p <2.2e-16↑	264	37.4%, p =2.5e-10↑	23	31.5%, ns
Total	27,578		517		705		73

Methylation probes were classified into three categories according to UCSC browser (http://genome.ucsc.edu/); CpG islands, CGI shores (up to 2kb around an island) and outside islands or shores. Differences compared to Illumina Human Methylation 27K array were tested using Fisher’s Exact for count data (Bonferroni threshold p:0.05/9=0.006). A downward arrow indicates significantly lower percentage of probes while an upward arrow indicates significantly higher percentage of observations compared to the overall probe distribution on the Illumina array.