Table 3.
Pleiotropic GWAS loci of NCDs
| 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 | |
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.
NR, not reported.
Lp-PLA2, lipoprotein-associated Phospholipase A2.
LDLR, Low density lipoprotein receptor.
HDL, High density lipoprotein.
LDLR, Low density lipoprotein.