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. 2011 Jul 26;3(7):230–247. doi: 10.4330/wjc.v3.i7.230

Table 3.

Single nucleotide polymorphisms associated with high-density lipoprotein cholesterol identified through genome-wide association studie

Chromosome Strongest SNP Chromosome position Sample size MAF (average) Change in HDLc/β Pvalue Proximal gene Ref.
1 rs2144300 228 361 539 8656 40 -  6.6 × 10-7 GALNT2 [20]
rs4846914 228 362 314 19 794 40 -0.05 SD  4.0 × 10-8 [30]
1 rs4660293 39 800 767 > 100 000 23 -0.48  4.0 × 10-10 PABPC4 [28]
1 rs1689800 180 435 508 > 100 000 35 -0.47  3.0 × 10-10 ZNF648 [28]
2 rs1260326 27 584 444 16 682 41 0.93% < 5 × 10-8 GCKR [31]
2 rs6754295 21 059 688 17 915 25 2.63 (z-sc)1  4.4 × 10-8 APOB [27]
2 rs2972146 226 808 942 > 100 000 37 0.46  3.0 × 10-9 IRS1 [28]
2 rs10490964 51 926 908 18 245 12 1.35 mg/dL  3.9 × 10-9 COBLL1, GRB14 [26]
rs12328675 165 249 046 > 100 000 13 0.68  3.0 × 10-10 COBLL1 [28]
4 rs13107325 103 407 732 > 100 000 7 -0.84  7.0 × 10-11 SLC39A8 [28]
5 rs6450176 53 333 782 > 100 000 26 -0.49  5.0 × 10-8 ARL15 [28]
6 rs2814944 34 660 775 > 100 000 16 -0.49  4.0 × 10-9 C6orf106 [28]
6 rs605066 139 871 359 > 100 000 42 -0.39  3.0 × 10-8 CITED2 [28]
6 rs1084651 161 009 807 > 100 000 16 1.95  3.0 × 10-8 LPA [28]
7 rs4731702 130 083 924 > 100 000 48 0.59  1.0 × 10-15 KLF14 [28]
8 rs2083637 19 909 455 17 922 26 4.14 (z-sc)1  5.5 × 10-18 LPL [27]
rs10503669 19 891 970 8656 10  3.2 × 10-10 [20]
rs331 19 864 685 6382 28 1.5 mg/dL  9.1 × 10-7 [32]
rs17482753 19 876 926 8180 -  2.8 × 10-11 [33]
rs326 19 863 719 10 536 22-30  1.8 × 10-8 [35]
rs331 19 864 685 6382 28 1.5 mg/dL  9.1 × 10-7 [32]
rs12678919 19 888 502 19 794 10 0.23 SD  2.0 × 10-34 [30]
rs301 19 861 214 5592 25 0.04  9.3 × 10-11 [36]
8 rs3916027 19 869 148 5592 27 0.04  5.4 × 10-10 SLC18A1 [36]
8 rs331 19 864 685 16 809 27 0.43% < 5 × 10-8 Intergenic, PPP1R3B, LPL [31]
rs9987289 9 220 768 > 100 000 9 -1.21  6.0 × 10-25 PPP1R3B [25]
8 rs2293889 116 668 374 > 100 000 0.41 -0.44  6.0 × 10-11 TRPS1 [28]
9 r1323432 103 402 758 8656 12 1.93 mg/dL  2.5 × 10-8 GRIN3A [20]
9 rs3905000 106 696 891 17 913 14 -4.37 (z-sc)1  8.6 × 10-13 ABCA1 [27]
rs4149268 106 687 041 8656 36  3.3 × 10-7 [20]
rs3890182 106 687 476 21 312 -  3.0 × 10-10 [29]
rs9282541 106 660 656 10 536 0-9  4.8 × 10-8 [35]
rs2515614 106 724 139 16 798 34 0.20% < 5 × 10-8 [31]
rs1883025 106 704 122 19 371 26 -0.08 SD  1.0 × 10-9 [30]
9 rs471364 15 279 578 40 414 12 -0.08 SD  3.0 × 10-10 TTC39B [29]
rs581080 15 295 378 > 100 000 18 -0.65  3.0 × 10-12 [28]
9 rs1883025 106 704 122 > 100 000 25 -0.94  2.0 × 10-33 ABCA1 [28]
11 rs12225230 116 233 840 6382 18 1.5 mg/dL  5.3 × 10-5 APOA1/C3/A4/A5 [32]
rs618923 116 159 369 12 111 25 0.30% < 5 × 10-8 [31]
rs964184 116 154 127 19 794 14 -0.17 SD  1.0 × 10-12 [30
rs7350481 116 091 493 8993 28 0.62%  8.8 × 10-10 [36]
rs7350481 116 091 493 18 245  2.8 × 10-12 [26]
11 rs2923084 10 345 358 > 100 000 17 -0.41  5.0 × 10-8 AMPD3 [28]
11 rs3136441 46 699 823 > 100 000 15 0.78  3.0 × 10-18 LRP4 [28]
11 rs7395662 17 917 39 2.82 (z-sc)1  6.0 × 10-11 MADD-FOLH1 [27]
11 rs174547 61 327 359 40 330 33 -0.09 SD  2.0 × 10-12 FADS1-S3 [30]
11 rs6589565 116 145 447 5592 -0.05  4.4 × 10-7 BUD13 [36]
11 rs2075290 116 158 506 5592 7 -0.05  4.2 × 10-7 ZNF259 [36]
12 rs2338104 108 379 551 8656 45  1.9 × 10-6 MVK/MMAB [20]
rs2338104 108 379 551 19 793 45 -0.07 SD  1.0 × 10-10 [30]
rs7134594 108 484 574 > 100 000 47 -0.44  7.0 × 10-15 [28]
12 rs7134375 20 365 025 > 100 000 42 0.40  4.0 × 10-8 PDE3A [28]
12 rs4759375 122 362 191 > 100 000 6 0.86  7.0 × 10-9 SBNO1 [28]
12 rs4765127 123 026 120 > 100 000 34 0.44  3.0 × 10-10 ZNF664 [28]
12 rs838880 123 827 546 > 100 000 31 0.61  3.0 × 10-14 SCARB1 [28]
12 rs1818702 102 047 685 16 844 29 0.22% < 5 × 10-8 Intergenic, ASCL1, PAH [31]
15 rs1532085 56 470 658 19 736 41 5.03 (z-sc)1  9.7 × 10-36 LIPC [27]
rs4115041 121 186 681 8656 33  2.8 × 10-9 [20]
rs1532085 56 470 658 6382 37 1.8 mg/dL  1.3 × 10-10 [32]
rs1800588 56 510 967 21 312 -  2.0 × 10-32 [29]
rs11858164 56 530 023 10 536 27-55  7.0 × 10-8 [35]
rs1532085 56 470 658 6382 37 1.8 mg/dL  1.3 × 10-10 [32]
rs1800588 56 510 967 16 811 22 0.60% < 5 × 10-8 [31]
rs10468017 56 465 804 19 794 30 0.10 SD  8.0 × 10-23 [30]
rs1077834 56 510 771 5987 49 1.00%  1.3 × 10-14 [36]
rs1077834 56 510 771 18 245  1.4 × 10-23 [26]
rs261342 56 518 445 5592 22 0.03  6.3 × 10-8 [36]
rs1532085 56 470 658 > 100 000 39 1.45  3.0 × 10-96 [28]
15 rs2652834 61 183 920 > 100 000 20 -0.39  9.0 × 10-9 LACTB [28]
16 rs1800775 55 552 737 2623 47  2.5 × 10-13 CETP [28]
rs1532624 55 562 980 19 674 43 8.24 (z-sc)1  9.4 × 10-94 [27]
rs3764261 55 550 825 8656 31 2.42 mg/dL  2.8 × 10-19 [20]
rs3764261 55 550 825 6382 31 4.0 mg/dL  1.0 × 10-41 [32]
rs1800775 55 552 737 2758 49 2.6 mg/dL  3.0 × 10-13 [29]
rs1800775 55 552 737 1643 47 3.99 mg/dL  6.1 × 10-15 [33]
rs9989419 55 542 640 8216 -  8.5 × 10-27 [33]
rs7205804 55 562 390 10 536 37-50  4.7 × 10-47 [36]
rs3764261 55 550 825 6382 31 4.0 mg/dL  1.0 × 10-41 [32]
rs1800775 55 552 737 16 779 49 2.50% < 5 × 10-8 [31]
rs3764261 55 550 825 322 - 6.2 mg/dL  3.4 × 10-12 [39]
rs3764261 55 550 825 18 245  3.7 × 10-93 [26]
rs173539 55 545 545 19 794 32 0.25 SD  4.0 × 10-75 [30]
rs3764261 55 550 825 5987 21 2.11%  4.8 × 10-29 [37]
rs3764261 55 550 825 18 245 30-48  3.7 × 10-93 [27]
rs17231506 55 552 029 5592 32 0.07  2.3 × 10-36 [36]
rs3764261 55 550 825 > 100 000 32 3.39   7.0 × 10-380 [28]
16 rs255052 66 582 496 8656 17  1.5 × 10-6 LCAT [20]
rs255052 66 582 496 8656 + 4534 -  1.2 × 10-7 [20]
rs2271293 66 459 571 31 946 11 0.07 SD  9.0 × 10-13 [30]
rs16942887 66 485 543 > 100 000 12 1.27  8.0 × 10-33 [28]
16 rs2271293 66 459 571 17 910 13 4.99 (z-sc)1  8.3 × 10-16 CTCF-PRMT8 [27]
16 rs289743 55 575 29 5592 31 0.03  8.6 × 10-9 NLRC5 [36]
16 rs2925979 80 092 291 > 100 000 30 -0.45  2.0 × 10-11 CMIP [28]
17 rs11869286 35 067 382 > 100 000 34 -0.48  1.0 × 10-13 STARD3 [28]
17 rs4148008 64 386 889 > 100 000 32 -0.42  2.0 × 10-10 ABCA8 [28]
17 rs4129767 73 915 579 > 100 000 49 -0.39  8.0 × 10-9 PGS1 [28]
18 rs4939883 45 421 212 16 258 17 -3.98 (z-sc)1  1.6 × 10-11 LIPG [27]
rs2156552 45 435 666 8656 16  8.4 × 10-7 [20]
rs2156552 45 435 666 21 312 -  2.0 × 10-7 [29]
rs4939883 45 421 212 16 648 16 0.22% < 5 × 10-8 [31]
rs4939883 45 421 212 19 785 17 -0.14 SD  7.0 × 10-15 [30]
rs4939883 45 421 212 18 245  1.4 × 10-9 [26]
rs7241918 45 414 951 > 100 000 17 -1.31  3.0 × 10-49 [28]
18 rs12967135 56 000 003 > 100 000 23 -0.42  7.0 × 10-9 MC4R [28]
19 rs769449 50 101 842 16 728 12 0.30% < 5 × 10-8 APOC1-APOE [31]
18 245  2.6 × 10-11 [26]
19 rs2967605 8 375 738 35 151 16 -0.12 SD  1.0 × 10-8 ANGPTL3 [30]
rs7255436 8 339 196 > 100 000 47 -0.45  3.0 × 10-8 [28]
19 rs737337 11 208 493 > 100 000 8 -0.64  3.0 × 10-9 LOC55908 [28]
19 rs386000 59 484 573 > 100 000 20 0.83  4.0 × 10-16 LILRA3 [28]
20 rs6065906 43 987 422 16 810 48 0.40% < 5 × 10-8 PLTP [31]
18 245  1.9 × 10-14 [26]
20 rs1800961 42 475 778 30 714 3 -0.19 SD  8.0 × 10-10 HNF4A [30]
rs1800961 42 475 778 > 100 000 3 -1.88  1.0 × 10-15 [28]
20 rs7679 44 009 909 40 248 19 -0.07 SD  4.0 × 10-9 PLTP [30]
rs6065906 43 987 422 > 100 000 18 -0.93  2.0 × 10-22 [28]
22 rs181362 20 262 068 > 100 000 20 -0.46  1.0 × 10-8 UBE2L3 [28]

1z-sc: the ENGAGE consortium provided the effect size on the z-scale. GALNT2: N-acetylgalactosaminyltransferase 2; PABPC4: Poly(A) binding protein, cytoplasmic 4 (inducible form); ZNF648: Zinc finger protein 648; GCKR: Glucokinase (hexokinase 4) regulator; APOB: Apolipoprotein B; IRS1: Insulin receptor substrate 1; COBLL1: COBL-like 1; GRB14: Growth factor receptor-bound protein 14; SLC39A8: Solute carrier family 39 (zinc transporter) member 8; ARL15: ADP-ribosylation factor-like 15; C6orf106: Chromosome 6 open reading frame 106; CITED2: Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain 2; LPA: Lipoprotein, Lp(a); KLF14: Kruppel-like factor 14; LPL: Lipoprotein lipase; SLC18A1: Solute carrier family 18 (vesicular monoamine) member 1; PPP1R3B: Protein phosphatase 1, regulatory (inhibitor) subunit 3B; TRPS1: Trichorhinophalangeal syndrome 1; GRIN3A: Glutamate receptor, ionotropic, N-methyl-D-aspartate 3A; ABCA1: ATP-binding cassette, sub-family A (ABC1) member 1; TTC39B: Tetratricopeptide repeat domain 39B; ABCA1: ATP-binding cassette, sub-family A (ABC1) member 1; APOA1: Apolipoprotein A-I; AMPD3: Adenosine monophosphate deaminase 3; LRP4: Low density lipoprotein receptor-related protein 4; MADD-FOLH1: MAP-kinase activating death domain- folate hydrolase (prostate-specific membrane antigen) 1; FADS1-S3: Fatty acid desaturase 1; BUD13: BUD13 homolog; ZNF259: Zinc finger protein 259; MVK: Mevalonate kinase; MMAB: Methylmalonic aciduria (cobalamin deficiency) cblB type; PDE3A: Phosphodiesterase 3A; SBNO1: Strawberry notch homolog 1; ZNF664: Zinc finger protein 664; SCARB1: Scavenger receptor class B member 1; ASCL1: Achaete-scute complex homolog 1; PAH: Phenylalanine hydroxylase; LIPC: Hepatic lipase; LACTB: Lactamase β; CETP: Cholesteryl ester transfer protein plasma; LCAT: Lecithin-cholesterol acyltransferase; CTCF: CCCTC-binding factor (zinc finger protein); PRMT8: Protein arginine methyltransferase 8; NLRC5: NLR family CARD domain containing 5; STARD3: StAR-related lipid transfer (START) domain containing 3; ABCA8: ATP-binding cassette; sub-family A (ABC1) member 8; PGS1: Phosphatidylglycerophosphate synthase 1; LIPG: Lipase endothelial; MC4R: Melanocortin 4 receptor; APOC1: Apolipoprotein C-I; APOE: Apolipoprotien E; ANGPTL3: Angiopoietin-like 3; LILRA3: Leukocyte immunoglobulin-like receptor, subfamily A (without TM domain) member 3; PLTP: Phospholipid transfer protein; HNF4A: Hepatocyte nuclear factor 4 α; PLTP: Phospholipid transfer protein; UBE2L3: Ubiquitin-conjugating enzyme E2L 3; SNP: Single nucleotide polymorphisms; MAF: Minor allele frequency. HDLc: high-density lipoprotein cholesterol.