Table 2.
Functional annotation for ten CpG-SNPs showing significant effects in meQTL, eQTL, and metaQTL
| rsID | GENCODE genes | Traits | meQTL (p) | eQTL hits | metaQTL (metabolites) | Promoter histone marks | Enhancer histone marks | DNAse | Proteins bound | Motifs changed |
|---|---|---|---|---|---|---|---|---|---|---|
| rs579459 | ABO | Pleiotropic | 1.45E–09 | Five hits | ADp | BLD | Gl | Four tissues | NFYA, POL2 | Hmx, Nkx2 |
| rsl 1172113 | LRP1 | CAD | 1.43E–07 | Four hits | SM C18:1 | Eight tissues | 15 tissues | 17 tissues | FOX Al | AP-2, Hiel, PU.l |
| rs3105748 | SLC22A3 | CAD | 7.67E–13 | Four hits | Succinylcarnitine | 6 tissues | Four altered motifs | |||
| rsl 0786044 | AL161652.1 | T2D | 9.93E–05 | Whole blood | 2-Hydroxypalmi- tate |
Five tissues | RAPI, ZNF263 | HNF6, ZEB1 | ||
| rs2066612 | DLEU1 | T2D | 4.06E–07 | Whole blood | X-11847 | BHLHE40, Foxa, HEY1 | ||||
| rs6770420 | EIF5A2 | T2D | 1.04E–08 | Whole blood | Ursodeoxycholate | Hsf, SIX5 | ||||
| rs7004862 | 1NTS8 | T2D | ≤ 1.00E–50 | 23 hits | SM C24:0 | BLD | HDAC2,Mef2 | |||
| rs7094128 | LRRC20 | T2D | 5.05E–08 | Fiboblast, bood | 1-Methylxanthine | BLD | IPSC, ADRL | AP-4, HEN1, Lmo2-complex | ||
| rs7723 | TMED4 | T2D | 2.14E–47 | 9 hits | 1-Oleoylglycero | Four tissues | Four tissues | Four altered motifs | ||
| rs7732628 | CTC-564N23.3 | T2D | 6.41E–05 | Heart artery | X-12206 | FAT, PANC | 15 tissues | CFOS | AP-1, ERalpha-a |
meQTL methylation quantitative trait locus (including associated SNPs with an LD r2≥0.8, Table S3), eQTL expression quantitative trait locus, metaQTL metabòlic quantitative trait locus, DNAse deoxyribonuclease, Adp ADpSGEGDFXAEGGGVR, 1 -oleoylglycero 1-oleoylglycerophosphocholine