Table 2 Chromatin marks are enriched on meQTL SNPs.

From: Characterizing the genetic basis of methylome diversity in histologically normal human lung tissue

Cell line

Mark

Control proportion (%)

cis only

trans only

cis+trans

   

Proportion (%)

Fold change

Proportion (%)

Fold change

Proportion (%)

Fold change

SAEC

CTCF

11.8

35.3

3.0

29.6

2.5

45.4

3.8

 

DnaseI

25.4

54.0

2.1

45.8

1.8

59.6

2.3

 

H3K27me3

20.4

34.1

1.7

25.4

1.2

42.9

2.1

 

H3K4me3

4.8

29.7

6.2

18.0

3.8

39.9

8.3

 

H3K36m3

13.4

36.8

2.7

22.8

1.7

45.4

3.4

hAEC

H3K27me3

17.5

25.3

1.4

15.6

0.9

33.2

1.9

 

H3K4me3

7.6

37.0

4.9

25.0

3.3

54.9

7.2

 

H3K9-14Ac

17.3

47.6

2.8

32.3

1.9

65.3

3.8

  1. meQTL SNPs were enriched in chromatin marks, including CTCF binding sites, DNaseI hypersensitive sites and histone marks from SAEC from ENCODE and hAEC from our laboratory. A SNP is determined to be related with a regulatory region if the SNP or any LD-related SNP (r2≥0.8) resides in the ChIP-Seq peaks of the regulatory regions. Enrichment for cis-meQTL SNPs without trans effects (‘cis only’), trans-meQTL SNPs without cis effects (‘trans only’) and SNPs with both trans and cis effects (‘cis+trans’). The baseline proportion (control set) was calculated based on SNPs not associated with meQTLs and with minor allele frequencies and local CpG probe-density matching to the meQTL SNPs. The fold changes were calculated using the control set as baseline.
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