Table 5.
Genetic effects of MCTD-meQTLs in MCTD and other related SADs.
| CpG site | CpG location | CpG Gene | SNP | SNP location | SNP Gene | Alleles | AF | meQTL | EWAS β (P) | MCTD OR (P) | SAD (OR,P) |
|---|---|---|---|---|---|---|---|---|---|---|---|
| MCTD/CTRL | β (P) | ||||||||||
| cg15331332 | chr6:29692111 | HLA-F | rs3130251 | chr6:29629344 | MOG | CT | 0.24/0.15 | −0.03 | −0.06 | 1.86 (0.0014) | SLE(1.63, 2 x 10−05) |
| (9.8 x 10−08) | (2.9 x 10−08) | SjS (1.94, 4 x 10−08) | |||||||||
| cg23892836 | chr6:29692085 | HLA-F | rs2251892 | chr6:29833128 | HLA-H/HLA-G | TC | 0.43/0.33 | −0.02 | −0.06 | 1.59 (0.004) | SLE (1.23,0.03) |
| (8.8 x 10−09) | (1.4 x 10−09) | SjS (1.53, 2 x 10−05) | |||||||||
| cg17114584 | chr11:613792 | IRF7 | rs3740648 | chr11:596672 | PHRF1 | TG | 0.14/0.08 | −0.08 | −0.14 | 1.98 (0.007) | – |
| (4.0 × 10−15) | (1.7 × 10−22) | ||||||||||
| cg07878065 | chr18:2641871 | intergenic | rs73936737 | chr18:2635566 | intergenic (chr18) | GA | 0.15/0.26 | 0.01 | −0.03 | 0.57 (0.007) | SLE (0.75, 0.007) |
| (9.9 × 10−08) | (5.0 × 10−09) | ||||||||||
| cg14880222 | chr1:79143979 | intergenic | rs1051047 | chr1:79129694 | IFI44 | GA | 0.50/0.60 | 0.03 | −0.04 | 0.40 (0.017) | SLE (0.72, 0.05), |
| (1.7 × 10−09) | (4.3 × 10−09) | SjS (0.72, 0.06) | |||||||||
| cg04268125 | chr1:154579384 | ADAR | rs11264235 | chr1:154631081 | intergenic (chr1) | TC | 0.40/0.28 | −0.04 | −0.2 | 1.43 (0.036) | – |
| (4.7 × 10−08) | (2.0 × 10−23) | ||||||||||
| cg00272009 | chr3:122398855 | PARP14 | rs16834903 | chr3:122379614 | intergenic (chr3) | AG | 0.40/0.36 | −0.04 | −0.09 | 1.37 (0.048) | – |
| (5.7 × 10−14) | (1.9 × 10−11) | ||||||||||
| cg26882438 | chr3:122399120 | PARP14 | rs16834903 | chr3:122379614 | intergenic (chr3) | AG | 0.40/0.36 | −0.03 | −0.14 | 1.37 (0.048) | – |
| (1.7 × 10−10) | (2.6 × 10−20) |
Alleles represent the allele tested in first place followed by the non-tested allele for each SNP. Tested allele frequency is given in parenthesis.
AF corresponds to the allele frequency of the tested allele in cases and controls.
meQTL β (P) represents the DNAm change in the addition of one tested allele together with the corresponding P value from the linear regression model adjusted by age, sex, batch effects, estimated cell proportions, disease status and first genetic component.
EWAS β (P) represents DNAm difference between controls and MCTD cases from epigenome-wide association study together with the P value obtained in the linear regression model adjusted by age, sex, batch effects and estimated cell proportions.
MCTD (OR,P) represents the Odd Ratio obtained from genetic association testing based on logistic regression model adjusted by age, sex, batch effects, estimated cell proportions and first genetic component and its corresponding P value.
SAD (OR, P) represents the odd ratio and P value obtained for other diseases.
Genomic positions are based on the hg19 human reference sequence build (GRCh37).