Table 2

Significantly differentially methylated CpG sites when comparing baseline and follow-up samples from new recruits (with q value <0.05 and absolute difference >5%)

Probe IDGenomic location*Gene nameEstimate (SE)†P valueq value
Decreased methylation at follow-up
 cg11835347chr1: 113248232 RHOC −0.054 (0.011)1.09E-050.035
 cg16265542chr1: 152814831 LCE6A −0.058 (0.012)8.23E-060.032
 cg21721331chr1: 157670877 FCRL3 −0.061 (0.013)2.13E-050.043
 cg02928345chr1: 224411698NA−0.065 (0.014)8.08E-060.032
 cg15591386chr1: 76265299 MSH4 −0.054 (0.012)2.67E-050.044
 cg03740864chr10: 120660492NA−0.054 (0.01)8.46E-070.023
 cg02884943chr10: 72725905NA−0.059 (0.013)1.71E-050.040
 cg10967759chr10: 73555025 CDH23 −0.071 (0.015)7.81E-060.032
 cg23024158chr10: 78011952 C10orf11 −0.051 (0.011)2.36E-050.043
 cg03762984chr11: 29355671NA−0.081 (0.016)4.70E-060.027
 cg01078446chr12: 115113212 TBX3 −0.05 (0.01)1.31E-050.037
 cg18956104chr12: 119621039 HSPB8 −0.059 (0.012)3.68E-060.026
 cg12248652chr12: 132703589 GALNT9 −0.056 (0.011)3.64E-060.026
 cg02121135chr14: 24858912NA−0.073 (0.015)4.82E-060.027
 cg02938807chr14: 63785523 GPHB5 −0.069 (0.015)2.72E-050.044
 cg02428178chr15: 49104237 CEP152 −0.053 (0.011)9.69E-060.034
 cg04245616chr15: 59543693 MYO1E −0.072 (0.017)4.20E-050.048
 cg06297541chr16: 22384949 CDR2 −0.053 (0.011)1.35E-050.037
 cg12891543chr16: 53958626 FTO −0.052 (0.012)3.09E-050.045
 cg07280206chr16: 56554249 BBS2 −0.063 (0.01)1.61E-070.016
 cg03432196chr18: 9643805NA−0.063 (0.013)6.43E-060.029
 cg19995259chr19: 53795827 BIRC8 −0.056 (0.013)3.53E-050.046
 cg16903817chr2: 114655480 ACTR3 −0.09 (0.019)7.62E-060.031
 cg16262572chr2: 122479703 NIFK-AS1 −0.052 (0.01)2.53E-060.026
 cg25296103chr2: 145268533 ZEB2 −0.06 (0.012)5.25E-060.028
 cg00441550chr20: 29955998 DEFB118 −0.06 (0.013)2.21E-050.043
 cg16145176chr21: 25596030NA−0.06 (0.013)2.32E-050.043
 cg17885233chr3: 132450221 NPHP3-AS1 −0.051 (0.011)1.84E-050.041
 cg13166622chr3: 150904863 MED12L −0.081 (0.016)1.64E-060.025
 cg03520471chr3: 97753623 GABRR3 −0.054 (0.012)2.30E-050.043
 cg16350196chr4: 137426420NA−0.052 (0.011)2.36E-050.043
 cg20300412chr4: 65749341NA−0.064 (0.014)3.07E-050.045
 cg21359538chr4: 76440740 RCHY1 −0.062 (0.014)3.05E-050.045
 cg03498271chr5: 38427885 EGFLAM −0.055 (0.012)1.12E-050.036
 cg06887251chr5: 67576008 PIK3R1 −0.054 (0.012)2.83E-050.045
 cg10874300chr5: 67588385 PIK3R1 −0.066 (0.011)4.36E-080.014
 cg04708601chr6: 101880078 GRIK2 −0.051 (0.011)2.19E-050.043
 cg24105728chr6: 13007033 PHACTR1 −0.054 (0.011)6.61E-060.029
 cg18742528chr6: 13053520 PHACTR1 −0.055 (0.011)5.83E-060.029
 cg27509293chr6: 14919597NA−0.057 (0.013)3.36E-050.046
 cg08188318chr6: 34984953 ANKS1A −0.093 (0.02)1.24E-050.037
 cg10420626chr6: 43741154 VEGFA −0.057 (0.013)2.72E-050.044
 cg00325383chr6: 85404488 LOC102724201 −0.057 (0.012)9.43E-060.034
 cg19989663chr7: 115981565NA−0.056 (0.013)4.46E-050.050
 cg03083251chr7: 135408513 SLC13A4 −0.076 (0.016)6.70E-060.029
 cg12018852chr7: 138777233 ZC3HAV1 −0.052 (0.01)4.63E-060.027
 cg05753918chr7: 14899040NA−0.065 (0.013)2.32E-060.026
 cg04946588chr7: 86271783 GRM3 −0.052 (0.011)1.66E-050.040
 cg21637741chr8: 69834365 LINC01592 −0.052 (0.011)2.40E-050.043
 cg15728672chr8: 89189971 MMP16 −0.059 (0.011)1.64E-060.025
 cg01761595chr8: 9821723NA−0.069 (0.015)1.70E-050.040
 cg14611112chr9: 139643351 LCN6 −0.053 (0.011)6.49E-060.029
 cg03779244chrX: 56771607 LINC01420 −0.085 (0.016)1.60E-060.025
Increased methylation at follow-up
 cg19190900chr2: 37553621NA0.053 (0.012)2.23E-050.043
 cg25229577chr3: 58367583 PXK 0.062 (0.013)6.81E-060.029
 cg00367499chr5: 170634447 RANBP17 0.062 (0.014)3.81E-050.048
 cg14396995chr7: 42278089 GLI3 0.06 (0.013)1.86E-050.041
 cg21156439chr9: 94716496NA0.051 (0.011)1.57E-050.039
 cg00625110chr16: 53741731 FTO 0.069 (0.014)3.35E-060.026
 cg01154210chr21: 27493310 APP 0.102 (0.022)1.63E-050.039
  • NA means the CpG site is not within a gene or within a known feature (eg, promoter) of a specific gene.

  • *Genomic location is according to genome build GRCh37/hg19.

  • †Effect estimates represent the proportion of methylation difference at follow-up compared with baseline, adjusted for batch, cell type estimates, Hispanic ethnicity, estimated smoking pack-years and a random intercept for individual to account for the repeated sampling design.