Table 1.
Genomic regions showing co-localisation with lipid species and coronary artery disease.
| # | rsID | Positiona | EA/ OA | Co-localised lipid classes | Number of lipids co-localised | Strongest co-localisation | Minimum CAD P-value in region | Nearby genesb |
|---|---|---|---|---|---|---|---|---|
| 1 | rs11591147 | 1:55505647 | G/T | CE, DE, Hex2Cer, Hex3Cer, PC(P), SHexCer, SM, TG(O) | 32 | CE(18:1) | 1.86 × 10−22 | PCSK9, USP24, BSND |
| 2 | rs602633 | 1:109821511 | G/T | HexCer | 2 | HexCer(d18:1/24:1) | 3.63 × 10−58 | PSRC1, CELSR2, MYBPHL |
| 3 | rs2281719 | 1:230297659 | C/T | DG, PI, TG [NL] | 5 | DG(18:0_18:1) | 6.41 × 10−07 | GALNT2, PGBD5, COG2 |
| 4 | rs10779835 | 1:230299949 | C/T | DG, TG [NL] | 4 | TG(54:2) [NL-18:0] | 6.41 × 10−07 | GALNT2, PGBD5, COG2 |
| 5 | rs515135 | 2:21286057 | C/T | CE, PC | 4 | PC(16:0_18:0) | 5.74 × 10−17 | APOB, TDRD15, LDAH |
| 6 | rs6713865 | 2:23899807 | A/G | AC | 2 | AC(16:0) | 2.86 × 10−05 | KLHL29, ATAD2B, UBXN2A |
| 7 | rs6544713 | 2:44073881 | C/T | CE | 6 | CE(20:1) | 1.84 × 10−18 | ABCG8, ABCG5, DYNC2LI1 |
| 8 | rs2736177 | 6:31586094 | C/T | TG [NL] | 2 | TG(50:2) [NL-18:2] | 4.86 × 10−09 | AIF1, PRRC2A, BAG6 |
| 9 | rs41279633 | 7:44580876 | G/T | CE | 1 | CE(18:0) | 1.72 × 10−06 | NPC1L1, DDX56, TMED4 |
| 10 | rs6982502 | 8:126479362 | C/T | SM | 1 | SM(d18:0/22:0) | 7.67 × 10−23 | TRIB1, NSMCE2, WASHC5 |
| 11 | rs2980869 | 8:126488250 | C/T | PC | 1 | PC(36:0) | 7.67 × 10−23 | TRIB1, NSMCE2, WASHC5 |
| 12 | rs35093463 | 9:107586238 | A/C | Hex3Cer | 2 | Hex3Cer(d18:1/22:0) | 4.00 × 10−07 | ABCA1, NIPSNAP3B, NIPSNAP3A |
| 13 | rs1800978 | 9:107665978 | C/G | Hex3Cer | 1 | Hex3Cer(d18:1/24:1) | 4.00 × 10−07 | ABCA1, NIPSNAP3B, NIPSNAP3A |
| 14 | 9:136141870 | 9:136141870 | C/T | CE | 1 | CE(18:0) | 2.03 × 10−14 | ABO, SURF6, OBP2B |
| 15 | rs603424 | 10:102075479 | A/G | AC, CE, DG, Hex2Cer, LPC, PC, PC(P), TG [NL] | 24 | LPC(16:1) [sn2] | 7.41 × 10−07 | PKD2L1, BLOC1S2, SCD |
| 16 | rs7350481 | 11:116586283 | C/T | CE, DG | 2 | DG(18:1_18:2) | 5.64 × 10−07 | BUD13, ZPR1, APOA5 |
| 17 | rs6589563 | 11:116590787 | A/G | CE, DG, TG [NL] | 4 | DG(18:0_18:1) | 5.64 × 10−07 | BUD13, ZPR1, APOA5 |
| 18 | rs1558861 | 11:116607437 | C/T | CE, DG, PI, TG [NL] | 25 | TG(54:4) [NL-18:2] | 5.64 × 10−07 | BUD13, ZPR1, APOA5 |
| 19 | rs964184 | 11:116648917 | C/G | CE, DE, DG, LPI, PC, PE, PG, PI, TG [NL] | 64 | TG(54:2) [NL-18:0] | 7.03 × 10−13 | ZPR1, BUD13, APOA5 |
| 20 | rs651821 | 11:116662579 | C/T | CE, PE | 3 | CE(22:0) | 7.03 × 10−13 | APOA5, ZPR1, BUD13 |
| 21 | rs1169288 | 12:121416650 | A/C | Cer(d), PC, SM | 6 | PC(36:0) | 1.26 × 10−18 | HNF1A, C12orf43, OASL |
| 22 | rs2244608 | 12:121416988 | A/G | SM | 1 | SM(d18:0/22:0) | 1.26 × 10−18 | HNF1A, C12orf43, OASL |
| 23 | rs2043085 | 15:58680954 | C/T | PE | 1 | PE(18:0_18:1) | 7.24 × 10−06 | ALDH1A2, LIPC, AQP9 |
| 24 | rs1532085 | 15:58683366 | A/G | PE, PG | 16 | PE(18:1_18:2) | 7.24 × 10−06 | ALDH1A2, LIPC, ADAM10 |
| 25 | rs1077835 | 15:58723426 | A/G | PE | 7 | PE(15-MHDA_22:6) | 7.24 × 10−06 | ALDH1A2, LIPC, ADAM10 |
| 26 | rs1800588 | 15:58723675 | C/T | DG, LPE, PE, PE(O), PG, TG(O) | 19 | LPE(20:4) [sn1] | 7.24 × 10−06 | ALDH1A2, LIPC, ADAM10 |
| 27 | rs2070895 | 15:58723939 | A/G | CE, PE, PG, PS | 16 | PG(34:2) | 7.24 × 10−06 | ALDH1A2, LIPC, ADAM10 |
| 28 | rs588136 | 15:58730498 | C/T | DG, PC, PC(P), PS, TG(O) | 10 | Total PC | 7.24 × 10−06 | ALDH1A2, LIPC, ADAM10 |
| 29 | rs261342 | 15:58731153 | C/G | LPE, TG [NL] | 3 | LPE(20:4) [sn1] | 7.24 × 10−06 | ALDH1A2, LIPC, ADAM10 |
| 30 | rs12446515 | 16:56987015 | C/T | PC, PC(O) | 3 | PC(16:0_16:0) | 1.19 × 10−09 | CETP, HERPUD1, NLRC5 |
| 31 | rs56156922 | 16:56987369 | C/T | Hex3Cer, PC, PC(O), PC(P), PE(P) | 22 | PC(P-16:0/16:1) | 1.19 × 10−09 | CETP, HERPUD1, NLRC5 |
| 32 | rs56228609 | 16:56987765 | C/T | CE, PC(O), PE(O), PI, TG(O) | 6 | CE(18:0) | 1.19 × 10−09 | CETP, HERPUD1, NLRC5 |
| 33 | rs247616 | 16:56989590 | C/T | PC | 1 | PC(16:0_18:3) (a) | 1.19 × 10−09 | CETP, HERPUD1, NLRC5 |
| 34 | rs12149545 | 16:56993161 | A/G | PC(O), PC(P), PE(O), PI, TG(O) | 11 | TG(O-50:1) [NL-16:0] | 1.19 × 10−09 | CETP, HERPUD1, NLRC5 |
| 35 | rs3764261 | 16:56993324 | A/C | PC | 1 | PC(18:2_18:2) | 1.19 × 10−09 | CETP, HERPUD1, NLRC5 |
| 36 | rs17231506 | 16:56994528 | C/T | Hex2Cer, Hex3Cer, PC, PC(O), PC(P), PE(P), TG(O) | 40 | TG(O-50:1) [NL-16:0] | 1.19 × 10−09 | CETP, HERPUD1, NLRC5 |
| 37 | rs56289821 | 19:11188247 | A/G | CE, Cer(d), COH, GM3, Hex2Cer, Hex3Cer, HexCer, PC, PC(O), PC(P), SHexCer, SM | 60 | SM(35:2) (b) | 1.93 × 10−36 | LDLR, SMARCA4, SPC24 |
| 38 | rs72999033 | 19:19366632 | C/T | Cer(d) | 1 | Cer(d16:1/24:1) | 3.18 × 10−07 | HAPLN4, NCAN, TM6SF2 |
| 39 | rs58542926 | 19:19379549 | C/T | LPC, PC | 2 | LPC(20:3) [sn1] | 3.18 × 10−07 | TM6SF2, HAPLN4, SUGP1 |
| 40 | rs10401969 | 19:19407718 | C/T | Cer(d), DG, LPC, PC, PE, TG [NL] | 38 | DG(18:1_20:4) | 3.18 × 10−07 | SUGP1, TM6SF2, MAU2 |
| 41 | rs73001065 | 19:19460541 | C/G | Cer(d), TG [NL] | 3 | Cer(d18:1/24:0) | 3.18 × 10−07 | MAU2, SUGP1, GATAD2A |
| 42 | rs150268548 | 19:19494483 | A/G | Cer(d) | 3 | Total Cer | 3.18 × 10−07 | GATAD2A, MAU2, SUGP1 |
| 43 | rs7412 | 19:45412079 | C/T | CE, Cer(d), COH, DE, DG, GM1, GM3, Hex2Cer, Hex3Cer, HexCer, LPC, LPC(O), LPC(P), LPE(P), PC, PC(O), PC(P), PE(P), SHexCer, SM, TG [NL], TG(O) | 184 | CE(16:0) | 2.14 × 10−35 | APOE, TOMM40, APOC1 |
Co-localisation analyses performed using coronary artery disease in UK Biobank and CARDIoGRAMplusC4D. Minimum CAD P-values were obtained from the meta-analysis performed in van der Harst & Verweij 2018.
CAD coronary artery disease, EA effect allele, OA other allele.
aGenomic position based on Genome Reference Consortium Human Build 37 (GRCh37).
bClosest three protein coding genes to causal variant.