Table 2.
Top 10 CpG sites associated with common single nucleotide polymorphisms (cis-mQTLs).
| CpG | chr | stat | snp | pvalue | FDR | Gene symbol | island | − dist(SNP, CpG) | dist(CpG, TSS) | Minor allele | flag |
|---|---|---|---|---|---|---|---|---|---|---|---|
| cg18771300 | 14 | −23.68 | rs4902214 | 7.41E-35 | 3.73E-29 | RHOJ | TRUE | −834 | 592 | T | 0 |
| cg17829936 | 6 | −22.39 | rs3813355 | 2.31E-33 | 5.80E-28 | TAAR5 | FALSE | −69 | 144 | G | 1 |
| cg08634464 | 19 | −21.05 | rs4807358 | 9.60E-32 | 1.21E-26 | LOC126295 | TRUE | −629 | 183 | C | 0 |
| cg08634464 | 19 | −21.05 | rs8100809 | 9.60E-32 | 1.21E-26 | LOC126295 | TRUE | −4329 | 183 | C | 0 |
| cg10536916 | 6 | 18.96 | rs7748520 | 4.52E-29 | 4.56E-24 | HIST1H4L | FALSE | 23043 | 576 | C | 0 |
| cg08634464 | 19 | −17.82 | rs10410539 | 1.59E-27 | 1.33E-22 | LOC126295 | TRUE | 16465 | 183 | T | 0 |
| cg05740244 | 11 | −17.6 | rs4757662 | 3.21E-27 | 2.31E-22 | LDHC | TRUE | 5723 | 162 | A | 1 |
| cg08634464 | 19 | −17.38 | rs11084971 | 1.02E-26 | 6.39E-22 | LOC126295 | TRUE | 4766 | 183 | G | 0 |
| cg16474696 | 19 | 16.43 | rs371671 | 2.29E-25 | 1.26E-20 | MGC3207 | TRUE | −4861 | 332 | A | 0 |
| cg19766460 | 21 | 16.28 | rs1571737 | 2.50E-25 | 1.26E-20 | C21orf128 | FALSE | 2466 | 353 | C | 1 |
Stat is the test statistic; island indicates if a CpG site is from a CpG island; dist(SNP, CpG) is the distance from the SNP to the CpG site; dist(CpG, TSS) is the distance from the CpG site to the gene's transcription starting site. Minor allele was determined based on the 85 subjects in this study; flag indicates if a CpG site has SNPs with MAF<0 .05 within 5 base pairs.