Table 1 Characteristics of SNPs considered for use in Mendelian randomization analysis of the effect of T2D on CHD risk.

From: A Mendelian randomization study of the effect of type-2 diabetes on coronary heart disease

Locus

SNP

EA

NEA

OR T2D

P value T2D

OR CHD

P value CHD

Pleiotropic effect

Physiologic cluster

ADCY5

rs11717195

T

C

1.11

6.5E−14

1.00

8.3E−01

No

BC

CDKAL1

rs7756992

G

A

1.17

7.0E−35

1.02

7.2E−02

No

BC

CDKN2A/B

rs10811661

T

C

1.18

3.7E−27

1.00

6.8E−01

No

BC

DGKB

rs17168486

T

C

1.11

5.9E−11

1.00

6.6E−01

No

BC

HHEX/IDE

rs1111875

C

T

1.11

2.0E−19

1.02

1.3E−02

No

BC

PROX1

rs2075423

G

T

1.07

8.1E−09

1.00

7.1E−01

No

BC

SLC30A8

rs3802177

G

A

1.14

1.3E−21

1.01

3.3E−01

No

BC

THADA

rs10203174

C

T

1.14

9.5E−12

1.01

5.9E−01

No

BC

MTNR1B

rs10830963

G

C

1.10

5.3E−13

1.01

2.6E−01

No

HG

ANK1

rs516946

C

T

1.09

2.5E−10

1.01

2.8E−01

No

NA

BCAR1

rs7202877

T

G

1.12

3.5E−08

1.07

2.7E−05

No

NA

HMG20A

rs7177055

A

G

1.08

4.6E−09

1.01

2.1E−01

No

NA

KLHDC5

rs10842994

C

T

1.10

6.1E−10

0.99

2.4E−01

No

NA

TLE1

rs2796441

G

A

1.07

5.4E−09

1.02

9.5E−02

No

NA

UBE2E2

rs1496653

A

G

1.09

3.6E−09

1.01

5.8E−01

No

NA

ZMIZ1

rs12571751

A

G

1.08

1.0E−10

0.99

5.2E−01

No

NA

ARAP1 (CENTD2)

rs1552224

A

C

1.11

1.8E−10

0.99

3.4E−01

No

PI

BCL11A

rs243088

T

A

1.07

1.8E−08

1.02

3.8E−02

No

UC

HMGA2

rs2261181

T

C

1.13

1.2E−09

1.01

4.0E−01

No

UC

IGF2BP2

rs4402960

T

G

1.13

2.4E−23

1.02

1.5E−02

No

UC

JAZF1

rs849135

G

A

1.11

3.1E−17

1.02

5.8E−03

No

UC

KCNQ1

rs163184

G

T

1.09

1.2E−11

1.02

2.2E−02

No

UC

PRC1

rs12899811

G

A

1.08

6.3E−09

1.01

1.4E−01

No

UC

TSPAN8/LGR5

rs7955901

C

T

1.07

6.5E−09

0.99

4.6E−01

No

UC

WFS1

rs4458523

G

T

1.10

2.0E−15

1.01

4.6E−01

No

UC

ZBED3

rs6878122

G

A

1.10

5.0E−11

1.02

3.8E−01

No

UC

TCF7L2

rs7903146

T

C

1.39

1.2E−139

1.03

5.7E−03

Yes

BC

IRS1

rs2943640

C

A

1.10

2.7E−14

1.03

5.2E−04

Yes

IR

PPARG

rs1801282

C

G

1.13

1.1E−12

1.00

7.8E−01

Yes

IR

ANKRD55

rs459193

G

A

1.08

6.0E−09

1.02

2.5E−02

Yes

NA

CILP2

rs10401969

C

T

1.13

7.0E−09

0.93

7.3E−05

Yes

NA

FTO

rs9936385

C

T

1.13

2.6E−23

1.03

4.2E−03

Yes

NA

GRB14

rs13389219

C

T

1.07

1.0E−08

1.02

7.2E−02

Yes

NA

MC4R

rs12970134

A

G

1.08

1.2E−08

1.03

1.8E−03

Yes

NA

SPRY2

rs1359790

G

A

1.08

1.4E−08

0.99

4.7E−01

Yes

NA

ADAMTS9

rs6795735

C

T

1.08

7.4E−11

0.98

1.8E−02

Yes

UC

KCNJ11

rs5215

C

T

1.07

8.5E−10

1.02

1.8E−02

Yes

UC

  1. BC, beta-cell dysfunction; CHD, coronary heart disease; CPMA, cross-phenotype meta-analysis; EA, effect allele; HG, hyperglycemic; IR, insulin resistance; NA, not available; NEA, non-effect allele; OR, odds ratio; PI, pro-insulin; SNP, single nucleotide polymorphism; T2D, type-2 diabetes; UC, unclassified.
  2. Pleiotropic effect: ‘Yes’ indicates that the SNP was associated with at least one confounding trait in the CPMA analysis. See Supplementary Table 2 for a full description of these pleiotropic associations. Physiologic Clusters: UC, IR, BC, PI, HG and NA. Note that the OR for CHD is not weighted for the effect of each SNP on T2D or fasting glucose. Figures report the OR for CHD weighted by their effect on T2D.
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