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Table 4 Replication of rare SNPs showing statistically significant effect at genome-wide significance levels (1.2 × 10 -7 ) for CAD

From: Cohen’s h for detection of disease association with rare genetic variants

Chr

ES

SNP

Nearest gene or SNP

Location

MAF in controls

MAF in cases

OR

P-value

RD

P-value

Cohen’s h

P-value

Exact test P-valueb

Association of SNP or proxy with other cardiovascular phenotypes

Genes

within

associated

interval

           

3

All

rs17042882

PLCL2

3p24.3

0.028

0.061

2.255

4.88 × 10-15

0.033

1.11 × 10-15

0.163

4.00 × 10-15

---

Heart failure, Arthritis

3

h

rs16827563

VEPH1

3q24-q25

0.005

0

NA

NA

-0.005

2.18 × 10-5

-0.119

1.02 × 10-8

7.3 × 10-7

Carotid artery disease, Diabetes Mellitus

7

RD

rs17146094

EIF4H

7q11.23

0.017

0.034

2.036

1.27 × 10-7

0.017

7.15 × 10-8

0.109

1.32 × 10-7

---

CAD

8

All

rs16891338

SAMD12-AS1

8q24.12

0.023

0.043

1.908

4.11 × 10-8

0.02

2.50 × 10-8

0.113

4.66 × 10-8

---

Blood Pressure

8

All

rs16908145

FLJ45872

8q24.23

0.022

0.043

1.998

6.54 × 10-9

0.021

3.46 × 10-9

0.12

7.08 × 10-9

---

 

15

RD, h

rs7163007

MAP2K5

15q23

0.002

0.011

5.551

2.13 × 10-7

0.009

5.33 × 10-9

0.121

5.85 × 10-9

---

BMI, Diabetes Mellitus

16

All

rs16955238

GAN

16q24.1

0.022

0.046

2.143

8.91 × 10-11

0.024

3.41 × 10-11

0.135

8.53 × 10-11

---

Cholesterol

16

h

rs7197337

ANKRD26P1

16q11.2

0.006

0

NA

NA

-0.006

2.88 × 10-6

-0.132

1.76 × 10-10

2.3 × 10-8

 

19

All

rs11671119

MEF2B MEF2NB

19p13.11

0.033

0.071

2.239

0

0.038

0

0.174

0

---

Diabetes Mellitus

SNPs near associated SNPs within 500 kb

           

1

RD, h

rs6674781

rs6671793

2a

0.002

0.011

5.55

2.13 × 10-7

0.009

5.33 × 10-9

0.121

5.85 × 10-9

---

Coronary disease

3

h

rs17064749

rs7615788

10a

0.008

0.001

0.124

8.36 × 10-5

-0.007

2.84 × 10-6

-0.116

2.28 × 10-8

4.2 × 10-7

Cholesterol

3

h

rs10510375

rs1450097

400a

0.009

0.001

0.11

2.97 × 10-5

-0.008

4.03 × 10-7

-0.127

9.67 × 10-10

2.2 × 10-8

Cholesterol, HDL

3

h

rs6805861

rs10510197

250a

0.007

0

NA

NA

-0.007

3.84 × 10-7

-0.145

2.92 × 10-12

1.2 × 10-9

Cholesterol, HDL

4

All

rs890447

rs97669522

25a

0.043

0.078

1.883

6.49 × 10-13

0.035

3.09 × 10-13

0.148

8.35 × 10-13

---

CAD

5

All

rs159171

rs10520872

500a

0.025

0.055

2.27

6.88 × 10-14

0.03

1.62 × 10-14

0.156

5.51 × 10-14

---

Cholesterol, LDL

5

h

rs41349146

rs2431337

500a

0.007

0

NA

NA

-0.007

3.84 × 10-7

-0.145

2.92 × 10-12

1.2 × 10-9

Arteries

6

h

rs41518850

rs12190287

300a

0.006

0

NA

NA

-0.006

2.88 × 10-6

-0.132

1.76 × 10-10

2.3 × 10-8

CAD

6

h

rs4398751

rs9397922

150a

0.005

0

NA

NA

-0.005

2.18 × 10-5

-0.119

1.02 × 10-8

7.3 × 10-7

Lipoprotein

8

All

rs16883114

rs10503973

200a

0.021

0.041

1.993

1.57 × 10-8

0.02

8.57 × 10-9

0.117

1.69 × 10-8

---

Cholesterol, LDL

9

RD, h

rs12343115

rs2149998

300a

0.009

0

NA

NA

-0.009

6.97 × 10-9

-0.167

6.66 × 10-16

3.6 × 10-12

Myocardial Infarction

18

All

rs41477147

rs10502528

150a

0.028

0.065

2.413

0

0.037

0

0.179

0

---

Arteries

(rs1595963)

 

21

h

rs7276641

rs2829644

300a

0.01

0.002

0.198

2.50 × 10-5

-0.008

2.81 × 10-6

-0.111

8.91 × 10-8

---

Coronary disease

  1. adenotes the physical distance (in kb) to the nearest validated SNP. bFisher’s exact test is only required when the asymptotic assumption does not hold. NA: not available; Chr., chromosome; MAF, minor allele frequency; location according to NCBI Build 37.5; Association of SNP or proxy with other cardiovascular phenotypes was based on the HuGE Navigator database (http://hugenavigator.net/HuGENavigator/startPagePubLit.do), dbSNP (NCBI website: http://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/projects/SNP/) and MalaCards (http://www.malacards.org/pages/whatsmalacards).