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. 2021 Dec 2;11:23292. doi: 10.1038/s41598-021-01324-0

Table 3.

Most significant meQTLs and eQTLs exhibiting disease-dependent genetic effects.

CpG Gene SNP SNP Position (hg38 Chr:bp) Discovery cohort Replication cohort
βINT PINT βSS.meQTL PSS.meQTL βCTRL.meQTL PCTRL.meQTL βINT PINT
A. SS-dependent meQTLs
cg08818207 TAP1 rs113547322 6:32,238,742 0.058 1.5 × 10−05 0.048 0.0004 NA  > 0.05 0.059 0.0091
cg14392283 LY6E rs13273708 8:143,002,764  − 0.018 1.6 × 10−04  − 0.016 0.0006 NA  > 0.05  − 0.020 0.0061
cg01309328 PSMB8 rs3134951 6:32,147,308  − 0.040 4.0 × 10−04  − 0.024 0.0124 NA  > 0.05  − 0.040 0.0023
cg14951497 STAT1 rs4853645 2:191,839,218  − 0.029 5.5 × 10−04  − 0.024 0.0012 NA  > 0.05  − 0.038 0.0418
cg12906975 Intergenic (LY6E) rs55937049 8:143,033,566  − 0.013 0.0018  − 0.011 0.0087 NA  > 0.05  − 0.017 0.0410
cg23387863 SGK269 rs1079396 15:78,137,720  − 0.024 0.0022  − 0.017 0.0119 NA  > 0.05  − 0.028 0.0141
cg10734665 ATP10A rs7169481 15:25,712,123  − 0.022 0.0031 0.018 0.0047 NA  > 0.05 0.030 0.0138
cg08099136 PSMB8 rs3129943 6:32,370,868  − 0.030 0.0038  − 0.027 0.0050 NA  > 0.05  − 0.035 0.0108
Gene ID Gene SNP SNP Position (hg38 Chr:bp) Discovery cohort Replication cohort
βINT PINT βSS.eQTL PSS.eQTL βCTRL.eQTL PCTRL.eQTL βINT PINT
B.SS-dependent eQTLs
ENSG00000183486 MX2 rs9305702 21:40,755,922  − 0.300 1.8 × 10−04  − 0.302 1.8 × 10−04 NA  > 0.05  − 0.315 0.0172
ENSG00000198785 GRIN3A rs2417310 9:101,964,703 0.251 4.5 × 10−04 0.235 7.0 × 10−04 NA  > 0.05 0.262 0.0092
ENSG00000185885 IFITM1 rs12364973 11:1,116,140 0.386 6.9 × 10−04 0.280 0.0130 NA  > 0.05 0.430 0.0476
ENSG00000013374 NUB1 rs77466830 7:151,831,985  − 0.143 7.7 × 10−04  − 0.151 3.5 × 10−04 NA  > 0.05  − 0.158 0.0345
ENSG00000133106 EPSTI1 rs9525846 13:43,816,621  − 0.607 8.8 × 10−04  − 0.577 2.4 × 10−03 NA  > 0.05  − 0.651 0.0199
ENSG00000188313 PLSCR1 rs56077428 3:146,981,084 0.471 0.0010 0.357 0.0208 NA  > 0.05 0.600 0.0185
ENSG00000157601 MX1 rs9305702 21:40,755,922  − 0.602 0.0012  − 0.496 0.0083 NA  > 0.05  − 0.779 0.0085
ENSG00000247317 LY6E − DT rs902834 8:142,111,410 0.167 0.0038 0.129 0.0149 NA  > 0.05 0.149 0.0469
ENSG00000108691 CCL2 rs1490922 17:33,725,536 0.351 0.0044 0.307 0.0159 NA  > 0.05 0.367 0.0252
ENSG00000187210 GCNT1 rs2377425 9:75,947,610 0.132 0.0047 0.083 0.0452 NA  > 0.05 0.210 0.0068

β INT represents the interaction effect between a given SNP and SS status in DNA methylation level.

P INT represents the P-value obtained for the β INT in a linear regression model that adjusts for SNP, SS status, age, sex, batch effects, estimated cell proportions and the first principal genetic component.

β SS.meQTL represents the DNA methylation change with the increased in dosage of the minor allele in SS population for a given SNP.

P SS.meQTL corresponds to the P value from the linear regression model that regresses out the number of minor alleles for a given SNP to DNA methylation levels adjusting by age, sex, batch effects, estimated cell proportions, disease status and first genetic component in SS population.

β CTRL.meQTL represents the DNA methylation change with the increased in dosage of the minor allele in the healthy control population for a given SNP.

P CTRL.meQTL corresponds to the P value from the linear regression model that regresses out the number of minor alleles for a given SNP to DNA methylation levels adjusting by age, sex, batch effects, estimated cell proportions, disease status and first genetic component in the healthy control population.

NA represents effects that are non significant (P > 0.05).