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Table 3 Pleiotropic GWAS loci of NCDs

From: Biobanking across the phenome - at the center of chronic disease research

Locus, gene

dbSNP ID

NCD entity associated with SNP

P-value

Risk allele frequency

PubMed ID

Cancer linked NCDs cluster

5p15.33, TERT

rs2736100

Glioma

2.00E-17

0.49

19578367

 

rs2736100

Glioma

1.00E-14

NR

21531791

 

rs2736100

Glioma

7.00E-09

NR

21827660

 

rs2736100

Hematological and biochemical traits

3.00E-08

0.4

20139978

 

rs2736100

Idiopathic pulmonary fibrosis

3.00E-08

0.41

18835860

 

rs2736100

Lung adenocarcinoma

2.00E-22

0.39

20700438

 

rs2736100

Lung adenocarcinoma

3.00E-11

0.39

20871597

 

rs2736100

Lung cancer

1.00E-27

0.41

21725308

 

rs2736100

Testicular germ cell cancer

8.00E-15

0.49

20543847

5p15.33, TERT, CLPTM1L

rs401681

Bladder cancer

5.00E-07

0.54

20972438

 

rs401681

Lung cancer

8.00E-09

NR

18978787

 

rs401681

Melanoma

3.00E-08

0.46

21983787

 

rs401681

Pancreatic cancer

7.00E-07

0.45

20101243

 

rs401681

Serum prostate-specific antigen levels

1.00E-10

0.55

21160077

8q24.21, Intergenic

rs6983267

Colorectal cancer

1.00E-14

0.49

17618284

 

rs6983267

Colorectal cancer

7.00E-11

0.48

18372905

 

rs6983267

Colorectal cancer

2.00E-08

0.34

21242260

 

rs6983267

Prostate cancer

9.00E-13

0.5

17401363

 

rs6983267

Prostate cancer

9.00E-13

0.49

18264097

 

rs6983267

Prostate cancer

7.00E-12

0.53

18264096

 

rs6983267

Prostate cancer

9.00E-06

NR

21743057

9p21.3, CDKN2A, CDKN2B

rs4977756

Glaucoma

1.00E-14

0.6

21532571

 

rs4977756

Glioma

7.00E-15

0.6

19578367

Inflammatory trait linked NCDs cluster

1p31.3, IL23R

rs11209026

Ankylosing spondylitis

2.00E-17

0.93

21743469

 

rs11209026

Ankylosing spondylitis

9.00E-14

0.94

20062062

 

rs11209026

Crohn’s disease

1.00E-64

0.93

21102463

 

rs11209026

Crohn’s disease

4.00E-21

NR

22293688

 

rs11209026

Crohn’s disease

2.00E-18

0.92

17447842

 

rs11209026

Inflammatory bowel disease

4.00E-11

0.93

17068223

 

rs11209026

Inflammatory bowel disease

7.00E-11

0.94

18758464

 

rs11209026

Psoriasis

7.00E-07

NR

20953190

 

rs11209026

Ulcerative colitis

5.00E-28

0.94

21297633

 

rs11209026

Ulcerative colitis

3.00E-10

NR

19915572

 

rs11209026

Ulcerative colitis

1.00E-08

0.93

19122664

1p13.2, PTPN22

rs2476601

Crohn’s disease

1.00E-08

0.9

18587394

 

rs2476601

Rheumatoid arthritis

9.00E-74

0.1

20453842

 

rs2476601

Rheumatoid arthritis

2.00E-21

NR

19503088

 

rs2476601

Rheumatoid arthritis

2.00E-11

0.1

17804836

 

rs2476601

Type 1 diabetes

9.00E-85

NR

19430480

 

rs2476601

Type 1 diabetes

2.00E-80

0.09

17554260

 

rs2476601

Type 1 diabetes

1.00E-07

0.09

17632545

 

rs2476601

Type 1 diabetes autoantibodies

2.00E-111

NR

21829393

 

rs2476601

Vitiligo

1.00E-07

0.1

20410501

7q32.1, IRF5,TNPO3

rs10488631

Primary biliary cirrhosis

3.00E-10

0.11

20639880

 

rs10488631

Primary biliary cirrhosis

2.00E-07

NR

19458352

 

rs10488631

Rheumatoid arthritis

4.00E-11

0.11

20453842

 

rs10488631

Systemic lupus erythematosus

7.00E-18

0.11

21408207

 

rs10488631

Systemic lupus erythematosus

2.00E-11

0.12

18204098

 

rs10488631

Systemic sclerosis

2.00E-13

NR

20383147

 

rs10488631

Systemic sclerosis

2.00E-10

NR

21779181

 

rs10488631

Systemic sclerosis

2.00E-07

NR

21779181

 

rs10488631

Systemic sclerosis

4.00E-07

0.09

21750679

18p11.21, PTPN2

rs2542151

Crohn’s disease

5.00E-17

0.15

18587394

 

rs2542151

Crohn’s disease

3.00E-08

0.18

17554261

 

rs2542151

Crohn’s disease

2.00E-07

0.16

17554300

 

rs2542151

Type 1 diabetes

1.00E-14

0.16

17554260

 

rs2542151

Type 1 diabetes

9.00E-08

NR

18978792

 

rs2542151

Type 1 diabetes autoantibodies

4.00E-13

NR

21829393

18p11.21, PTPN2

rs1893217

Celiac disease

3.00E-10

0.17

20190752

 

rs1893217

Celiac disease and Rheumatoid arthritis

5.00E-12

NR

21383967

 

rs1893217

Type 1 diabetes

4.00E-15

NR

19430480

Cardiovascular trait linked NCDs cluster

2p23.3, GCKR

rs1260326

Cardiovascular disease risk factors

2.00E-08

0.4

21943158

 

rs1260326

Cholesterol, total

7.00E-27

0.41

20686565

 

rs1260326

Chronic kidney disease

3.00E-14

0.41

20383146

 

rs1260326

C-reactive protein

5.00E-40

NR

21300955

 

rs1260326

Hematological and biochemical traits

4.00E-09

0.44

20139978

 

rs1260326

Hypertriglyceridemia

7.00E-09

0.41

20657596

 

rs1260326

Liver enzyme levels (gamma-glutamyl transferase)

4.00E-13

0.38

22001757

 

rs1260326

Metabolic traits

4.00E-10

0.35

19060910

 

rs1260326

Platelet counts

9.00E-10

NR

22139419

 

rs1260326

Serum metabolites

3.00E-18

NR

22286219

 

rs1260326

Triglycerides

6.00E-133

0.41

20686565

 

rs1260326

Triglycerides

2.00E-31

0.45

19060906

 

rs1260326

Two-hour glucose challenge

3.00E-10

NR

20081857

 

rs1260326

Waist circumference and related phenotypes

4.00E-08

NR

18454146

11q12.2, FADS1, FADS2

rs174547

HDL cholesterol

2.00E-12

0.33

19060906

 

rs174547

Lipid metabolism phenotypes

8.00E-262

NR

22286219

 

rs174547

Metabolic traits

9.00E-116

0.32

21886157

 

rs174547

Phospholipid levels (plasma)

4.00E-154

NR

21829377

 

rs174547

Phospholipid levels (plasma)

3.00E-64

NR

21829377

 

rs174547

Resting heart rate

2.00E-09

0.33

20639392

 

rs174547

Serum metabolites

7.00E-179

0.3

20037589

 

rs174547

Triglycerides

2.00E-14

0.33

19060906

11q14.3, MTNR1B

rs1387153

Fasting plasma glucose

2.00E-36

0.29

19060909

 

rs1387153

Glycated hemoglobin levels

4.00E-11

0.28

20858683

 

rs1387153

Metabolic syndrome (bivariate traits)

2.00E-09

NR

21386085

 

rs1387153

Metabolic syndrome (bivariate traits)

8.00E-09

NR

21386085

 

rs1387153

Type 2 diabetes

8.00E-15

NR

20581827

12q24.12, ALDH2, BRAP

rs671

Coronary heart disease

2.00E-34

0.23

21971053

 

rs671

Drinking behavior

4.00E-211

0.75

21372407

 

rs671

Esophageal cancer

3.00E-24

NR

19698717

 

rs671

Hematological and biochemical traits

7.00E-10

0.26

20139978

 

rs671

Hematological and biochemical traits

5.00E-09

0.26

20139978

 

rs671

Intracranial aneurysm

3.00E-06

0.75

22286173

 

rs671

Triglycerides

2.00E-06

NR

22171074

16q13, CETP

rs3764261

Age-related macular degeneration

7.00E-09

0.33

21665990

 

rs3764261

Age-related macular degeneration

7.00E-07

0.32

20385819

 

rs3764261

Cholesterol, total

7.00E-14

0.32

20686565

 

rs3764261

HDL cholesterol

2.00E-57

0.31

18193043

 

rs3764261

HDL cholesterol

7.00E-29

0.28

19060910

 

rs3764261

HDL cholesterol

3.00E-12

0.2

19359809

 

rs3764261

HDL cholesterol

7E-380

0.32

20686565

 

rs3764261

LDL cholesterol

9.00E-13

0.32

20686565

 

rs3764261

Lipid metabolism phenotypes

1.00E-36

NR

22286219

 

rs3764261

Metabolic syndrome

1.00E-48

0.36

20694148

 

rs3764261

Metabolic syndrome

3.00E-13

NR

21386085

 

rs3764261

Triglycerides

1.00E-12

0.45

20686565

 

rs3764261

Waist circumference

1.00E-27

NR

18454146

19p13.2, LDLR

rs6511720

Cardiovascular disease risk factors

5.00E-11

0.11

21943158

 

rs6511720

Carotid intima media thickness

1.00E-07

NR

21909108

 

rs6511720

Cholesterol, total

7.00E-97

0.11

20686565

 

rs6511720

LDL cholesterol

4.00E-117

0.11

20686565

 

rs6511720

LDL cholesterol

2.00E-51

0.1

18193044

 

rs6511720

LDL cholesterol

2.00E-26

0.1

19060906

 

rs6511720

LDL cholesterol

4.00E-26

0.9

18193043

 

rs6511720

Lp-PLA2 activity and mass

3.00E-11

0.1

22003152

19q13.32, APOE, APOC1

rs4420638

Alzheimer’s disease

2.00E-44

NR

17998437

 

rs4420638

Alzheimer’s disease

1.00E-39

NR

17975299

 

rs4420638

Alzheimer’s disease (age of onset)

1.00E-12

NR

22005931

 

rs4420638

Alzheimer’s disease (late onset)

1.00E-39

NR

17474819

 

rs4420638

Cholesterol, total

5.00E-111

0.17

20686565

 

rs4420638

Cognitive decline

4.00E-27

NR

22054870

 

rs4420638

C-reactive protein

9.00E-139

NR

21300955

 

rs4420638

C-reactive protein

5.00E-27

NR

19567438

 

rs4420638

C-reactive protein

3.00E-07

0.9

21196492

 

rs4420638

HDL cholesterol

4.00E-21

0.17

20686565

 

rs4420638

LDL cholesterol

9.00E-147

0.17

20686565

 

rs4420638

LDL cholesterol

1.00E-60

0.2

18193044

 

rs4420638

LDL cholesterol

3.00E-43

0.18

18193043

 

rs4420638

LDL cholesterol

2.00E-40

0.18

20864672

 

rs4420638

LDL cholesterol

4.00E-27

0.16

19060906

 

rs4420638

LDL cholesterol

1.00E-20

0.18

18262040

 

rs4420638

LDL cholesterol

2.00E-07

NR

18802019

 

rs4420638

Lp-PLA2 activity and mass

5.00E-30

0.84

22003152

 

rs4420638

Lp-PLA2 activity and mass

6.00E-24

0.16

20442857

 

rs4420638

Longevity

2.00E-16

0.81

21740922

 

rs4420638

Quantitative traits

3.00E-07

0.21

19197348

 

rs4420638

Triglycerides

3.00E-13

0.22

17463246

Cardiovascular & inflammatory trait linked NCDs cluster

12q24.12, SH2B3

rs3184504

Coronary heart disease

6.00E-06

0.44

21378990

 

rs3184504

Diastolic blood pressure

4.00E-25

0.47

21909115

 

rs3184504

Diastolic blood pressure

3.00E-14

0.48

19430479

 

rs3184504

Eosinophil counts

7.00E-19

0.38

19198610

 

rs3184504

Rheumatoid arthritis

6.00E-06

0.51

20453842

 

rs3184504

Systolic blood pressure

5.00E-09

0.48

19430479

 

rs3184504

Type 1 diabetes

3.00E-27

NR

19430480

 

rs3184504

Type 1 diabetes autoantibodies

2.00E-38

NR

21829393

12q24.12, SH2B3, ATXN2

rs653178

Blood pressure

7.00E-20

0.59

21909110

 

rs653178

Celiac disease

7.00E-21

0.5

20190752

 

rs653178

Celiac disease

8.00E-08

0.48

18311140

 

rs653178

Celiac disease and Rheumatoid arthritis

3.00E-19

NR

21383967

 

rs653178

Chronic kidney disease

4.00E-11

0.5

20383146

 

rs653178

Diastolic blood pressure

3.00E-18

0.53

19430483

Skin pigmentation linked NCDs cluster

11q14.3, TYR

rs1393350

Blue vs. green eyes

3.00E-12

0.23

17952075

 

rs1393350

Eye color

3.00E-09

0.27

20585627

 

rs1393350

Melanoma

2.00E-14

0.27

19578364

 

rs1393350

Melanoma

2.00E-13

0.28

21983787

 

rs1393350

Skin sensitivity to sun

2.00E-06

0.27

17952075

 

rs1393350

Tanning

2.00E-13

NR

19340012

 

rs1393350

Vitiligo

2.00E-18

0.73

20410501

16q24.3, MC1R

rs1805007

Basal cell carcinoma

4.00E-17

0.07

21700618

 

rs1805007

Blond vs. brown hair color

2.00E-13

0.08

17952075

 

rs1805007

Freckles

1.00E-96

0.05

17952075

 

rs1805007

Red vs non-red hair color

2.00E-142

NR

17952075

 

rs1805007

Skin sensitivity to sun

2.00E-55

0.06

17952075

  1. A selection of GWAS identified pleiotropic SNPs implicated in more than one NCD entity are presented here. For a more complete list of pleiotropic loci see Additional file 1. Data has been downloaded (09 March 2012) from the online catalogue of published GWAS available at http://www.genome.gov/gwastudies.
  2. NR, not reported.
  3. Lp-PLA2, lipoprotein-associated Phospholipase A2.
  4. LDLR, Low density lipoprotein receptor.
  5. HDL, High density lipoprotein.
  6. LDLR, Low density lipoprotein.
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