Table 1.

Summary of ICCs (β-scale) of CpG locus methylation, by genomic location and probe-type, nonsex chromosomesa

Δβ < 0.10.1 ≤ Δβ < 0.2Δβ ≥ 0.2
ICCPercentage of loci by ICC rangePercentage of loci by ICC rangePercentage of loci by ICC rangePercentage of loci by ICC range
Location/probe typeNMedianIQR0–0.50.5–0.80.8–1N0–0.50.5–0.80.8–1N0–0.50.5–0.80.8–1N0–0.50.5–0.80.8–1
All CpG loci472,6650.360.130.6364.123.012.9446,67767.824.18.120,8510.25.694.25,1370.00.499.5
Enhancer101,6630.390.150.6661.124.414.595,36465.125.79.25,1100.25.794.11,1890.00.499.6
Known DMR36,0530.490.240.7251.531.816.733,80254.933.611.51,9650.15.494.52860.00.799.3
Location with respect to CpG island
 CpG Island145,5710.340.120.5967.621.810.6139,25470.722.76.65,1570.23.096.81,1600.00.699.4
 Shoreb108,8390.430.180.7157.225.417.4101,09161.626.911.56,6230.26.293.61,1250.00.499.6
 Shelfb45,7900.340.120.5967.122.110.743,61470.522.96.61,5910.48.790.95850.00.0100.0
Functional location
 TSS150081,2670.360.130.6264.523.112.477,26567.824.08.23,4330.27.092.85690.00.599.5
 TSS20060,0050.290.090.5373.019.17.858,23575.319.65.21,4640.26.193.73060.01.398.7
 5′UTR62,9750.320.110.5669.521.68.960,82072.022.25.91,7940.16.493.63610.00.699.4
 1st Exon37,6560.330.110.5769.421.49.236,40671.822.06.21,0790.23.696.21710.00.699.4
 Body172,0680.350.130.6065.822.411.8163,30969.323.37.36,8130.25.494.31,9460.10.499.6
 3′UTR19,1740.320.100.5669.420.89.818,38172.421.56.26030.87.192.01900.00.0100.0
Location by probe type
 Infinium I132,0390.370.130.6264.024.711.3124,89267.625.86.65,6400.46.992.71,5070.10.999.1
 Infinium II340,6260.360.130.6364.122.313.5321,78567.923.48.715,2110.25.194.73,6300.00.399.7
  • aAll estimates are adjusted for cell-type composition. Δβ is estimated as twice the between-person SE (β-scale).

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