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. 2019 Jan 5;11:1. doi: 10.1186/s13148-018-0606-9

Table 1.

Results from the discovery and secondary epigenome-wide association analyses of serum cotinine levels in current smokers

CpG Chr Nearest gene Discovery analysis Secondary analysis References
Beta SE P value P FDR Beta SE P value P FDR
cg25189904 1 GNG12 − 0.000135 0.000026 5.6E−07 9.0E−03 − 0.000134 0.000028 1.8E−06 3.1E−02 [2–13, 52]
cg21033965 1 CLEC20A − 0.000096 0.000020 4.0E−06 3.7E−02 ** [2]
cg26687670 1 OPN3 − 0.000025 0.000005 6.5E−06 4.4E−02 ** Novel
cg27241845 2 ALPP − 0.000083 0.000016 3.3E−07 6.2E−03 − 0.000082 0.000016 8.8E−07 1.7E−02 [2–10]
cg03329539 2 ALPPL2 − 0.000070 0.000012 2.7E−08 6.6E−04 − 0.000069 0.000013 1.3E−07 3.0E−03 [2–10, 12, 52]
cg06644428 2 ALPPL2 − 0.000054 0.000012 5.5E−06 4.3E−02 ** [2–11, 19, 52]
cg05951221 2 ALPPL2 − 0.000178 0.000021 1.9E−15 2.0E−10 − 0.000171 0.000022 1.4E−13 1.5E−08 [2–13, 19, 20, 52]
cg21566642 2 ALPPL2 − 0.000210 0.000026 1.1E−14 8.8E−10 − 0.000205 0.000027 4.2E−13 3.4E−08 [2–12, 19, 20, 52]
cg01940273 2 ALPPL2 − 0.000134 0.000017 9.8E−14 6.3E−09 − 0.000129 0.000018 3.4E−12 2.2E−07 [2–13, 20, 52]
cg13193840 2 ALPPL2 − 0.000045 0.000010 3.6E−06 3.4E−02 − 0.000048 0.000010 2.5E−06 3.3E−02 [2–7, 9, 10]
cg02306995 3 SEMA5B * 0.000047 0.000010 4.4E−06 4.8E−02 Novel ***
cg04776445 4 MSX1 * 0.000085 0.000018 4.3E−06 4.8E−02 Novel ***
cg13740236 4 LSM6 − 0.000053 0.000009 2.9E−08 6.7E−04 − 0.000057 0.000010 1.0E−08 3.0E−04 Novel
cg11902777 5 AHRR − 0.000071 0.000011 1.1E−09 3.2E−05 − 0.000068 0.000012 2.1E−08 5.6E−04 [3–7, 9]
cg01899089 5 AHRR − 0.000063 0.000014 6.1E−06 4.4E−02 ** [2–8]
cg05575921 5 AHRR − 0.000359 0.000039 3.3E−18 1.1E−12 − 0.000351 0.000041 4.4E−16 1.1E−10 [2–13, 16, 18–20, 51, 52]
cg26703534 5 AHRR − 0.000086 0.000013 5.8E−10 1.9E−05 − 0.000084 0.000014 6.2E−09 2.0E−04 [2–8, 12, 18, 51, 52]
cg14817490 5 AHRR − 0.000099 0.000021 2.4E−06 2.9E−02 ** [2–10, 12, 13, 18, 52]
cg25648203 5 AHRR − 0.000091 0.000015 4.3E−09 1.1E−04 − 0.000086 0.000016 1.1E−07 2.8E−03 [2–13, 52]
cg21161138 5 AHRR − 0.000142 0.000016 1.8E−17 2.9E−12 − 0.000141 0.000017 6.6E−16 1.1E−10 [2–12, 18, 51, 52]
cg24090911 5 AHRR − 0.000076 0.000015 4.3E−07 7.4E−03 − 0.000074 0.000015 2.5E−06 3.3E−02 [2–7, 10]
cg10961758 5 EDIL3 * − 0.000069 0.000014 2.5E−06 3.3E−02 Novel***
cg16179182 5 VTRNA1–1 0.000048 0.000010 5.7E−06 4.3E−02 ** Novel
cg14580211 5 SMIM3 − 0.000062 0.000013 1.7E−06 2.2E−02 ** [2–9, 52]
cg06126421 6 IER3 − 0.000132 0.000020 1.1E−10 4.3E−06 − 0.000132 0.000021 6.9E−10 2.8E−05 [2–12, 20, 52]
cg14753356 6 IER3 − 0.000072 0.000015 3.1E−06 3.4E−02 ** [2–9]
cg22856972 6 TBPL1 0.000066 0.000014 3.0E−06 3.4E−02 0.000073 0.000014 9.1E−07 1.7E−02 Novel
cg05469934 7 PDGFA 0.000038 0.000008 3.6E−06 3.4E−02 ** Novel
cg09022230 7 TNRC18 − 0.000079 0.000014 4.1E−08 8.8E−04 − 0.000070 0.000014 2.4E−06 3.3E−02 [2–6, 8]
cg21322436 7 CNTNAP2 − 0.000055 0.000012 5.6E−06 4.3E−02 ** [2–7, 9]
cg25949550 7 CNTNAP2 − 0.000045 0.000009 1.4E−06 1.9E−02 ** [2–9, 11, 52]
cg09267815 8 YTHDF3 − 0.000080 0.000016 7.2E−07 1.1E−02 ** Novel
cg22288066 8 NOV 0.000033 0.000007 6.8E−06 4.4E−02 ** Novel
cg24838345 8 MTSS1 − 0.000088 0.000017 2.6E−07 5.3E−03 − 0.000084 0.000017 2.3E−06 3.3E−02 [2–6, 8, 9]
cg25305703 8 CASC8 − 0.000088 0.000018 1.7E−06 2.2E−02 ** [2–7]
cg01692968 9 SLC44A1 − 0.000075 0.000016 3.3E−06 3.4E−02 − 0.000079 0.000017 2.7E−06 3.3E−02 [2–9]
cg14120703 9 NOTCH1 − 0.000043 0.000009 4.3E−06 3.8E−02 − 0.000045 0.000010 4.3E−06 4.8E−02 [2, 4]
cg05992400 10 CYP2C18 − 0.000050 0.000011 4.9E−06 4.1E−02 ** Novel
cg16421726 10 ZRANB1 0.000056 0.000012 2.7E−06 3.1E−02 ** Novel
cg05335388 11 ABTB2 * 0.000035 0.000007 1.6E−06 2.9E−02 Novel***
cg19254163 11 PTGDR2 − 0.000042 0.000009 6.4E−06 4.4E−02 ** [2–7]
cg21611682 11 LRP5 −  0.000071 0.000010 1.2E−12 6.7E−08 − 0.000067 0.000010 8.2E−11 3.8E−06 [2–11, 52]
cg14624207 11 LRP5 − 0.000063 0.000010 2.6E−10 9.2E−06 − 0.000063 0.000010 1.4E−09 5.1E−05 [2–7, 9]
cg10788371 11 LRRC32 − 0.000064 0.000013 1.3E−06 1.8E−02 − 0.000067 0.000013 8.6E−07 1.7E−02 [2–6]
cg11491407 12 CACNA2D4 − 0.000095 0.000020 5.7E−06 4.3E−02 ** Novel
cg18443392 12 LRP1 0.000027 0.000006 4.2E−06 3.8E−02 ** Novel
cg04524475 13 RNY1P5 − 0.000053 0.000012 6.2E−06 4.4E−02 ** Novel
cg26589665 15 THSD4 − 0.000042 0.000008 3.8E−07 6.9E−03 − 0.000041 0.000008 2.1E−06 3.3E−02 Novel
cg05361530 16 GNG13 0.000044 0.000009 4.8E−06 4.1E−02 ** Novel
cg07991586 16 ADCY7 − 0.000042 0.000009 6.6E−06 4.4E−02 ** Novel
cg05460226 17 PIK3R5 − 0.000072 0.000015 3.4E−06 3.4E−02 ** [2–4]
cg05396243 17 TMEM220-AS1 − 0.000036 0.000007 1.0E−06 1.5E−02 ** Novel
cg07658936 17 ARHGAP44 0.000029 0.000006 6.8E−06 4.4E−02 ** Novel
cg03636183 19 F2RL3 − 0.000151 0.000022 1.9E−11 8.7E−07 − 0.000155 0.000022 2.8E−11 1.5E−06 [2–15, 17, 18, 20–22, 52]
cg12817959 22 SSTR3 * 0.000034 0.000007 4.3E−06 4.8E−02 Novel***

*CpG not genome-wide significant in discovery analysis

**CpG not genome-wide significant in secondary analysis

***Novel hits identified in secondary analysis