Table 2.

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

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 loci11,2150.800.600.8918.531.849.79,01423.038.438.62,1610.15.095.0400.02.597.5
Enhancer6290.840.710.919.931.558.747813.040.246.91490.04.096.020.00.0100.0
Known DMR1,2310.850.720.9110.627.861.693614.034.951.12900.05.294.850.00.0100.0
Location with respect to CpG island
 CpG Island4,2720.820.670.9013.232.054.83,39116.638.944.48670.05.294.8140.00.0100.0
 Shoreb2,8370.820.630.9017.329.753.02,17622.537.240.36490.35.194.6120.00.0100.0
 Shelfb1,1380.710.460.8528.036.335.71,00331.840.427.81300.06.293.850.00.0100.0
Functional location
 TSS15002,7770.800.600.9018.531.350.22,21123.238.438.45550.03.496.6110.00.0100.0
 TSS2002,4410.820.670.9013.531.455.11,86617.539.343.25640.45.993.8110.09.190.9
 5′UTR2,4010.820.670.9013.232.154.71,87316.939.643.55220.05.694.460.00.0100.0
 1st Exon1,6350.830.670.9012.332.954.81,29315.540.743.83400.03.596.520.00.0100.0
 Body2,8930.760.520.8823.332.544.22,40728.038.333.74810.03.796.350.00.0100.0
 3′UTR5130.710.440.8428.737.433.946631.540.128.3460.010.989.110.00.0100.0
Location by probe type
 Infinium I3,0420.780.600.8716.838.344.82,44420.945.733.45830.28.491.4150.06.793.3
 Infinium II8,1730.810.600.9019.129.451.56,57023.735.740.61,5780.13.796.3250.00.0100.0
  • 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.