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 webcite.

NR, not reported.

Lp-PLA2, lipoprotein-associated Phospholipase A2.

LDLR, Low density lipoprotein receptor.

HDL, High density lipoprotein.

LDLR, Low density lipoprotein.

Imboden and Probst-Hensch

Imboden and Probst-Hensch BMC Public Health 2013 13:1094   doi:10.1186/1471-2458-13-1094

Open Data