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Table 2 HDL-associated SNPs included in the genetic risk scores (GRS)

From: Impact of HDL genetic risk scores on coronary artery calcified plaque and mortality in individuals with type 2 diabetes from the Diabetes Heart Study

 

SNPs in risk scores 1a and 1b

SNP

Chr

Position

Gene(s)

Source

Alleles (Major/Minor)

Effect Allele

Effect Allele Frequency DHS

Effect (βvalue) in mmol/L

rs1689800

1

182168885

GLUL, ZNF648

Exome Chip

A/G

A

0.628

0.01

rs13107325

4

103188709

SLC39A8

Exome Chip

C/T

C

0.925

0.02

rs2293889

8

116599199

TRPS1

Sequenom

G/T

G

0.554

0.01

rs2923084

11

10388782

AMPD3

Exome Chip

A/G

A

0.815

0.01

rs7134594

12

110000193

MMAB

Exome Chip

T/C

T

0.520

0.01

rs4759375

12

123796238

SBNO1

Imputed data

C/T

T

0.092

0.02

rs838880

12

125261593

SCARB1

Exome Chip

T/C

C

0.337

0.02

rs16942887

16

67928042

PSKH1

Exome Chip

G/A

A

0.115

0.03

rs881844

17

37810218

STARD3

Imputed data

G/C

G

0.652

0.01

rs4082919

17

76377482

PGS1

Sequenom

G/T

T

0.483

0.01

rs7255436

19

8433196

ANGPTL4

Exome Chip

A/C

A

0.506

0.01

rs737337

19

11347493

DOCK6

Exome Chip

T/C

T

0.900

0.02

rs181362

22

21932068

UBE2L3

Sequenom

C/T

C

0.813

0.01

 

SNPs in risk scores 2a and 2b

rs4846914

1

230295691

GALNT2

Sequenom

A/G

A

0.606

0.02

rs17145738

7

72982874

TBL2, BCL7B

Exome Chip

C/T

T

0.124

0.03

rs17482753

8

19832646

LPL

Exome Chip

G/T

T

0.095

0.08

rs17321515

8

126486409

TRIB1

GWAS

A/G

G

0.465

0.02

rs471364

9

15289578

TTC39B

Exome Chip

T/C

T

0.896

0.03

rs3890182

9

107647655

ABCA1

Exome Chip

G/A

G

0.890

0.03

rs174547

11

61570783

FADS1

Exome Chip

T/C

T

0.668

0.03

rs6589566

11

116652423

ZNF259, APOA5

GWAS

A/G

A

0.924

0.05

rs2338104

12

109895168

KCTD10

Exome Chip

G/C

G

0.520

0.03

rs1800588

15

58723675

LIPC

Exome Chip

C/T

T

0.207

0.05

rs3764261

16

56993324

CETP

Exome Chip

C/A

A

0.331

0.1

rs2271293

16

67902070

NUTF2

Exome Chip

G/A

A

0.113

0.03

rs61755018

18

47109955

LIPG

Imputed data

A/G

G

0.007

0.14

rs2967605

19

8469738

RAB11B

Exome Chip

C/T

C

0.812

0.05

rs16988929

20

42904315

GDAP1L1

Imputed data

C/T

T

0.002

0.01

  1. SNPs in Risk Score 1a (unweighted) and Risk Score 1b (weighted) have effects on HDL levels only, while SNPs in Risk Score 2a (unweighted) and Risk Score 2b (weighted) have effects on HDL levels as well as some pleiotropic effects on LDL and triglyceride levels. Allele frequencies in the DHS are provided along with the effect size estimates (β value) reported by Voight et al.