Table 1.
Conjunction cFDR for 18 pleiotropic CpG-SNPs in T2D and CAD (ccFDR ≤ 0.05)
| rsID | Chr | Pos | Allele | Gene | Location | eQTL/meQTL/metaQTL | SNP type | Gene type | cFDR_CAD | cFDR_T2D | ccFDR |
|---|---|---|---|---|---|---|---|---|---|---|---|
| rs7604944 | 2 | 65319288 | C/T | SPRED2 | Intronic | Novel | Novel | 4.70E–02 | 2.57E–02 | 4.70E–02 | |
| rs2252641 | 2 | 145043894 | T/C | TEX41 | Non-coding intronic | CAD | Novel | 3.24E–02 | 2.46E–03 | 3.24E–02 | |
| rsl515114 | 2 | 226233671 | A/G | AC062015.1 | 48.3 kb upstream | eQTL (adipose) | Novel | Novel | 4.64E–39 | 7.20E–04 | 7.20E–04 |
| rs1428387 | 5 | 123369550 | C/T | CEP120 | Intronic | Novel | Novel | 3.55E–03 | 3.20E–04 | 3.55E–03 | |
| rs1262557 | 6 | 126733443 | C/T | RPS4XP9 | 49.6 kb upstream | Novel | Novel | 9.10E–03 | 2.60E–13 | 9.10E–03 | |
| rs17405606 | 7 | 107630918 | C/T | WBP1LP2 | 1.4 kb upstream | Novel | Novel | 9.40E–30 | 7.40E–04 | 7.40E–04 | |
| rs7049105 | 9 | 22028802 | A/G | AL359922.1, CDKN2B-AS1 | Intronic, non-coding intronic | eQTL (blood), meQTL (LD tors 10120688) | CAD | Novel, confirmed | 4.58E–02 | 1.20E–02 | 4.58E–02 |
| rs1333050 | 9 | 22125914 | C/T | CDKN2B-AS1 | 4.8 kb upstream | CAD | Confirmed | 2.96E–09 | 7.65E–06 | 7.65E–06 | |
| rs7045889 | 9 | 22133252 | G/A | CDKN2B-AS1 | 12.2 kb upstream | Novel | Confirmed | 9.39E–03 | 1.19E–02 | 1.19E–02 | |
| rs7018475 | 9 | 22137686 | T/G | CDKN2B-AS1 | 16.6 kb upstream | T2D | Confirmed | 2.16E–02 | 8.90E–03 | 2.16E–02 | |
| rs579459 | 9 | 133278724 | T/C | ABO | 3.5 kb upstream | eQTL (5 hits), meQTL, metaQTL | CAD | Novel | 1.51E–02 | 8.23E–03 | 1.51E–02 |
| rs7904519 | 10 | 113014168 | A/G | TCF7L2 | Intronic | eQTL (artery), meQTL (LD to rs7077247) | T2D | Novel | 3.78E–02 | 2.97E–02 | 3.78E–02 |
| rs1169302 | 12 | 120994499 | T/G | HNF1A | Intronic | eQTL (3 hits), meQTL (LD to rs2259816) | Novel | Novel | 2.55E–02 | 2.53E–19 | 2.55E–02 |
| rs9940128 | 16 | 53766842 | G/A | FTO | Intronic | Novel | Novel | 3.58E–02 | 4.50E–02 | 4.50E–02 | |
| rs2291725 | 17 | 48961770 | T/C | GIP | Coding nonsyn | eQTL (29 hits), meQTL (LD to rs3895874) | Novel | Novel | 6.73E–05 | 2.66E–03 | 2.66E–03 |
| rs521663 | 18 | 60155007 | T/C | AC090771.2 | Non-coding intronic | Novel | Novel | 7.05E–03 | 7.20E–03 | 7.20E–03 | |
| rs10408179 | 19 | 45653746 | T/C | RN7SL836P | 1.9 kb upstream | eQTL (blood), meQTL (LD tors 10406431) | Novel | Novel | 1.14E–02 | 4.05E–35 | 1.14E–02 |
| rs4823044 | 22 | 29528836 | T/C | THOC5,AC005529.1 | Intronic, non-coding intronic | eQTL (33 hits), meQTL (LD to rs9614006) | Novel | Novel | 2.76E–02 | 4.44E–03 | 2.76E–02 |
The allele was exhibited as reference allele/alter allele; SNP type and gene type means whether identified CpG-SNPs and genes have been reponed in previous GWAS or in our previous related cFDR studies
chr chromosome, Pos chromosomal position (GRCh38/hg38), eQTL expression quantitative trait locus, meQTL methylation quantitative trait locus (including associated SNPs with an LD r2≥0.8, Table S3), metaQTL metabolic quantitative trait locus, T2D type 2 diabetes, CAD coronary artery disease, cFDR conditional false discovery rate, ccFDR conjunctional conditional false discovery rate