Table 1 Genomic regions showing co-localisation with lipid species and coronary artery disease.

From: Comprehensive genetic analysis of the human lipidome identifies loci associated with lipid homeostasis with links to coronary artery disease

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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

  1. 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.
  2. CAD coronary artery disease, EA effect allele, OA other allele.
  3. aGenomic position based on Genome Reference Consortium Human Build 37 (GRCh37).
  4. bClosest three protein coding genes to causal variant.
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