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. 2019 Mar 14;14(2):171–184. doi: 10.1080/15592294.2019.1581589

Table 3.

Genomic features of the 22 significant sites.

CpG Nearest genea Chr CGI regionb Promoterb Gene bodyb Enhancerb DHSb
cg00030047 RNF207 1 N_Shore   TRUE TRUE TRUE
cg21494776 ICAM4 19 Island       TRUE
cg16638540 ZNF135 19 Island TRUE   TRUE TRUE
cg08675664 ALDH7A1 5 Island        
cg10549973 TOMM20L 14 Island   TRUE TRUE  
cg03533058 NR4A1 12          
cg04597449 GPR150 5 N_Shore TRUE      
cg03760483 ALOX12 17 Island TRUE   TRUE TRUE
cg11668923 ADAM12 10 Island       TRUE
cg21303386 RGS7 1 Island       TRUE
cg11323198 CDH8 16 Island        
cg03026462 FOXA1 14 Island TRUE      
cg15731815 RNF207 1 Island   TRUE TRUE TRUE
cg23984434 GUCY1A2 11 Island       TRUE
cg18133966 PLA2G1B 12   TRUE      
cg02590345 LPPR1 9 Island TRUE   TRUE  
cg17457560 NRG1 8 Island   TRUE   TRUE
cg19502744 SRD5A2 2 Island     TRUE  
cg17906786 C13orf36 13 N_Shore TRUE      
cg12262564 IQGAP3 1 Island   TRUE    
cg03554552 PPP1R13L; CD3EAP 19 Island TRUE
(for CD3EAP)		      
cg19764436
 RTDR1;GNAZ
 22
 Island
  
 TRUE
(for RTDR1)
  
  
Enrichment
p valuec 		- - p1= 9.4E-05
p2= 0.049		 0.97 0.31 0.015 0.001

aThe nearest gene(s) around the CpG, according to Illumina annotation and the UCSC Genome Browser.

bGenomic features are based on Illumina annotation and the UCSC Genome Browser. CGI region: CpG island as well as flanking shores and shelves; ‘Island’ represents being within a CGI; ‘N_Shore’ represents being 0–2 kb upstream from a CGI. Promoter: located within 1.5 kb before the transcription start site of any transcript of the associated gene. DHS: DNAse hypersensitivity sites.

cOne-sided Fisher’s exact test was used to examine enrichment in specific genomic regions. For the enrichment analysis on CGI region, p1 indicates enrichment for CGI, and p2 indicates enrichment in broader CGI regions (including flanking CGI shores and shelves).