Table 3.

Summary of temporal trend (β-scale) in CpG site methylation, by genomic location and probe typea

Nonsex chromosomesX chromosome
Percentage of loci with significant trendPercentage of loci with significant trend
Location/probe typeNNegative trendPositive trendNNegative trendPositive trend
All CpG loci472,6651.861.5411,2151.841.64
Enhancer101,6631.831.796291.751.91
Known DMR36,0531.911.291,2311.541.62
Location with respect to CpG island
 CpG Island145,5711.911.314,2722.011.17
 Shoreb108,8391.931.502,8371.971.55
 Shelfb45,7901.861.701,1381.851.76
Functional location
 TSS150081,2671.941.442,7772.021.76
 TSS20060,0051.881.382,4412.171.11
 5′UTR62,9751.881.422,4012.251.71
 1st Exon37,6561.931.341,6352.321.59
 Body172,0681.861.582,8931.691.56
 3′UTR19,1741.831.605131.953.31
Location by probe type
 Infinium I132,0391.551.593,0421.941.15
 Infinium II340,6261.991.528,1731.801.82
  • aAll estimates are adjusted for cell-type composition.

  • bShores, up to 2 kb from CpG islands; shelves, from 2 to 4 kb from CpG islands.