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Table 3 Differentially methylated regions in blood DNA in relation to current smoking compared to never smoking (multiple-testing corrected p < 0.01 at DMRcate and comb-p, ordered by chromosomal location)

From: DNA methylation and smoking in Korean adults: epigenome-wide association study

Chra Gene Distance to geneb DMRcate Comb-p Minimum P i
Start (bpc) End (bp) FDRd #CpGse Start (bp) End (bp) Sidak Pf #CpGs
1 MXRA8 −812 1286917 1287259 0.002 2(2)    0.002   2.2E−04
CASZ1 −600 10695686 10696066 8.7E−04 2(2)    0.009   1.5E−05
AHDC1   27929092 27929260 2.2E−04 2(2)    0.006   1.5E−04
NT5C1A   40137636g 40138402 3.2E−06 6(3)    0.001   5.5E−06
ACOT11 h −58,441 54954187 54955366 0.002 7(4) 54953632   0.009 8(4) 6.1E−04
GNG12 h   68298816g 68299511 7.0E−07 7(5) 68299057   0.001 6(5) 1.4E−06
GFI1 h   92946700 92947961 1.1E−04 6(4)    1.2E−04   8.1E−05
SPAG17   118727658g 118728226 1.3E−04 10(2)    0.005   7.1E−06
ZNF697   120173989 120174570 0.006 4(4)   120174873 0.006 6(4) 0.002
GALNT2   230415343 230416101 0.002 6(3) 230414987 230417096 1.2E−04 12(4) 0.005
SCCPDH −26,962 246859889 246860416 7.0E−04 5(4)    2.6E−04   0.002
2 PAX8   113992762 113993313 0.005 8(6)    0.004   0.011
ALPPL2 h 11,458 233283010g 233285607 8.0E−15 8(5)    1.5E−13   8.4E−09
SNED1 h   241975756 241976244 1.9E−06 4(4)    3.8E−06   1.4E−04
3 KRBOX1 11 42977777 42978180 9.7E−04 7(5)    0.003   4.1E−04
GPR15 h   98250723g 98251294 6.2E−07 2(1) 98249859   6.2E−04 4(2) 1.0E−07
ZBTB38   141086820 141087363 0.006 6(4)    0.005   0.005
LPP h   187870621 187871538 1.5E−05 11(5)    0.001   1.1E−04
C3orf43 21,882 196255632 196256223 9.7E−04 5(3)    0.004   1.8E−04
4 PCGF3   737005 738199 0.002 8(2) 736328   0.001 12(4) 2.5E−05
FGFRL1 −1776 1003208 1003834 1.5E−04 3(2)    0.002   2.0E−04
PRDM8   81117647g 81119473 6.7E−13 11(10)    2.9E−13   6.7E−06
NHEDC1   103940711 103941300 6.8E−14 11(10)    2.7E−10   6.2E−05
CFI   110724358 110724834 0.006 2(2)    0.009   4.4E−04
5 AHRR h   373378g 374425 4.6E−17 5(2)   373887 4.8E−05 2(1) 6.5E−13
392920g 393366 5.8E−08 3(3)    3.9E−08   4.7E−06
LPCAT1   1494980 1495356 0.001 5(4)    0.003   0.001
LINC01019 −236,319 3180918 3180947 0.006 2(2)   3182108 6.0E−04 5(4) 5.7E−04
FLJ44606   126408756 126409553 7.0E−07 13(11)    1.9E−06   0.001
ADAMTS2   178548229 178548700 0.002 3(3)    0.003   8.5E−04
6 IER3 h 9104 30720080 30720491 1.2E−06 8(4)    0.002   1.7E−05
LY6G6E   31683051 31683352 5.4E−05 6(5)    1.2E−04   0.002
HLA-DPB1   33047944 33049505 2.5E−09 20(15)    4.8E−08   0.002
SYNGAP1 h   33400477 33401542 6.9E−06 9(7) 33400021   2.2E−05 10(7) 2.7E−04
CRISP2   49681178 49681774 5.5E−06 9(8)    5.5E−06   1.8E−04
UTRN −4373 144607399 144608500 0.004 7(4) 144607074   0.010 8(4) 2.6E−04
ZC3H12D h   149805995 149806732 2.3E−15 10(10)    1.9E−14   8.7E−05
TIAM2 h   155537595 155538155 1.6E−05 8(5)    3.7E−05   7.6E−04
THBS2   169653612 169654719 9.5E−04 11(4)   169654842 7.0E−04 12(4) 5.3E−04
7 GNA12 h   2768988 2770410 4.7E−06 5(5) 2769253   7.4E−05 4(4) 3.0E−05
TRG-AS1 h −29,710 38350464 38351468 2.0E−06 7(6)    1.1E−05   1.7E−04
MYO1G h   45001765g 45002919 5.5E−14 6(5)    5.7E−09   2.7E−06
INSIG1 61,195 155150681 155151427 0.007 4(3)    0.002   0.003
8 DEFA4   6795162 6796618 2.0E−04 4(4) 6794872   1.7E−05 5(4) 4.0E−05
EPB49 h   21915184 21915510 0.004 2(2) 21914287 21916853 5.3E−05 11(6) 0.002
TRAPPC9   141057285 141057827 3.7E−06 5(5)    2.1E−06   2.0E−04
GLI4   144358043 144359316 0.001 5(5)    1.5E−05   0.002
9 CD72   35609853 35610380 0.002 2(2)    0.007   1.1E−04
CIZ1   130955135 130956057 0.001 4(3)   130955436 0.004 3(3) 0.001
10 SNCG   88717926 88718393 5.5E−04 5(5)    3.8E−04   0.003
SLC16A12 h   91296252 91296457 1.6E−04 3(3)    0.004   4.4E−04
LGI1   95517382 95517895 6.3E−04 7(4)    0.002   5.6E−04
NKX2-3 −4844 101287381g 101287846 8.2E−06 5(3)    1.3E−04   7.4E−06
GRK5   121171859 121172898 6.4E−04 5(4)    2.4E−04   4.1E−04
11 C11orf21 h   2321770 2322674 1.2E−05 18(7)   2323938 1.3E−04 33(8) 5.9E−04
C11orf41   33562503 33563377 7.0E−04 4(4)   33563946 2.3E−04 5(4) 5.4E−04
NEAT1 h 4664 65194933 65196227 2.2E−05 7(7)   65196696 3.0E−05 10(7) 4.9E−04
ACY3   67418045 67418405 1.1E−09 12(11)    8.7E−08   1.3E−04
CCND1   69462660g 69463323 2.4E−06 6(3)    1.7E−04   7.5E−07
AMICA1 h   118084920 118085736 0.005 4(4)    0.002   0.003
12 IFFO1   6657744 6658945 2.7E−04 10(5)   6659524 2.2E−04 12(5) 8.1E−05
MGP   15038440 15039432 9.5E−04 4(3)    3.5E−05   9.3E−05
KRT7   52638005 52638592 0.002 3(2)    0.005   1.5E−04
ZNF385A   54778312 54779175 0.002 4(3)    0.008   0.001
RP11-474D1.3 36,620 130554977 130555091 1.8E−04 3(3)    9.4E−04   1.7E−04
STX2 −73,033 131199848 131201112 7.2E−04 10(4) 131198873 131201268 0.008 12(5) 6.5E−05
14 LGMN   93170710 93170970 0.002 3(3)    0.008   6.6E−05
EVL   100610071 100610667 9.8E−05 6(4)    1.9E−04   4.0E−04
RIN3   92981121 92981666 1.6E−05 3(3)    2.1E−05   1.8E−04
15 CALML4   68498251g 68499367 2.6E−06 5(2) 68497992   0.002 6(2) 2.9E−07
16 PRR25   854168 854640 0.002 4(3)   855449 0.002 6(4) 7.7E−04
BCL7C   30906810 30907246 0.001 2(2)   30907560 8.0E−04 3(3) 9.0E−04
17 ALOX15B   7942137 7942743 1.1E−04 6(5)    2.4E−04   3.9E−04
NTN1   9018806 9019336 2.0E−05 5(4)    5.5E−04   5.3E−04
SLFN12L −13,916 33787402 33788026 0.003 4(4)    0.001   8.8E−04
CYB561   61511069 61511829 4.9E−04 4(4)    9.3E−05   5.2E−04
CCDC57   80076338 80076378 1.1E−04 2(2)    0.002   2.2E−05
FOXK2   80545020g 80545869 8.1E−08 11(6)    2.6E−04   5.5E−06
TBCD   80870107 80870923 0.001 5(3)   80871405 0.002 7(4) 1.8E−04
18 C18orf1   13611370 13611824 0.007 6(4)    0.009   0.003
19 GNG7   2543602 2544100 0.008 5(2) 2542837   0.002 6(3) 6.4E−04
MAN2B1   12758416 12759546 0.004 7(4)    0.001   0.002
LAIR1   54876446 54876795 1.8E−04 5(4)    8.1E−04   2.3E−04
20 C20orf27   3745817 3746315 0.002 2(2)    0.004   8.8E−05
22 SYNGR1   39759864g 39760267 1.2E−07 5(5)    1.2E−06   2.5E−06
SHISA8 −978 42304331 42304580 1.4E−04 2(2)    6.9E−04   2.3E−05
ODF3B   50970943 50971140 4.2E−04 3(3)    0.002   1.6E−04
  1. Empty cells in “Start,” “End,” and “#CpGs” for comb-p represent the same regional information compare to results in DMRcate. DMRs ordered by p values can be found in Additional file 11
  2. aChromosome
  3. bMinimum distance to transcription start site of the mapped gene (basepair)
  4. cPhysical position (basepair, National Center for Biotechnology Information human reference genome assembly Build 37.3)
  5. dFalse discovery rate
  6. eNumber of probes in the region (number of CpGs of nominal statistical significance)
  7. f P of Sidak multiple-testing correction
  8. gRegion including significant (FDR <0.05) differentially methylated probes from our epigenome-wide association study (EWAS)
  9. hGene identified in previous EWASs of smoking
  10. iMinimum p values among unadjusted p values of CpGs in each region