Supplemental Material Supplementary references




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Supplementary Table 2. Robustly replicated candidate associations (p < 10-7): amount of pre-GWAS evidence, linkage-derived initial discovery, and evidence for Mendelian effects.


PMID of GWAS

Phenotype

Locus

Representative SNP

p-value

Pre-GWAS publications

Linkage-derived

Mendelian effects

18179892

Triglyceride levels

APOA5

rs6589566

2.89E-11

19

-

+

18262040

LDL-C levels

APOB

rs562338

1.40E-09

38

-

+

17463246

LDL-C levels

APOE cluster

rs4420638

3.40E-13

41

-

+

17998437

Alzheimer's disease

APOE

rs4420638

2.30E-44

797

-

-

18439548

CRP levels

APOE

rs769449

8.90E-21

3

-

-

17435756

Crohn disease

CARD15/NOD2

rs2076756

7.01E-14

180

+

-

17463246

HDL-C levels

CETP

rs1800775

2.50E-13

23

-

+

18403759

YKL-40 levels

CHI3L1

rs4950928

1.10E-13

2

-

-

18439548

CRP levels

CRP

rs3091244

6.16E-28

4

-

-

17903292

CysC levels

CST3

rs1158167

8.00E-09

1

-

-

18445777

Spine bone mineral density

ESR1

rs2504063

5.68E-08

72

-

+

17903294

Factor VII levels

F7

rs561241

4.50E-16

3

-

+

17767159

HbF levels

HBS1L-MYB intergenic region

rs9399137

2.80E-27

1

+

-

18604267

Soluble ICAM-1 levels

ICAM1

rs1799969

2.10E-28

4

-

-

18464913

sIL-6R levels

IL6R

rs4129267

1.82E-57

2

+

-

17632545

Type 1 diabetes

INS

rs1004446

4.38E-09

28

-

+

18677312

Systemic lupus erythematosus

IRF5

rs12531711

4.03E-12

12

+

-

18179892

Triglyceride levels

LPL

rs17482753

1.17E-09

28

-

+

17999355

Skin pigmentation

MATP/SLC45A2

rs16891982

3.21E-11

4

-

+

18483556

Red vs non-red hair

MC1R

rs258322

5.00E-27

3

-

+

17952075

Blue vs brown eyes

OCA2

rs1667394

1.40E-124

3

-

+

17053108

Wet age-related macular degeneration

PLEKHA1-HTRA1 intergenic region

rs10490924

4.08E-12

1

+

-

17554300

Rheumatoid arthritis

PTPN22

rs6679677

5.55E-25

18

-

-

17554300

Type 1 diabetes

PTPN22

rs6679677

5.43E-26

16

-

-

15761122

Age-related macular degeneration

Region 1q31 (CFH)‡

rs380390

4.10E-08

1

+

-

18650507

Statin-induced myopathy

SLCO1B1

rs4149056

1.00E-08

3

-

+

18204098

Systemic lupus erythematosus

STAT4

rs7574865

9.00E-14

1

+

-

17293876

Type 2 diabetes

TCF7L2

rs7903146

3.20E-17

12

+

-

18445777

Spine bone mineral density

TNFSF11/RANKL

rs9594759

1.17E-08

3

-

+

17999355

Skin pigmentation

TYR

rs1042602

4.48E-10

3

-

+

18488028

Blue vs non-blue eyes

TYRP1

rs1408799

1.50E-09

1

-

+

18535201

Warfarin maintenance dose

VKORC1

rs10871454

6.20E-13

4

-

+

Information shown is according to the HuGE Navigator for pre-GWAS publications, PubMed and references of GWAS articles for linkage-derived initial discovery, and the Online Mendelian Inheritance in Man database for mutations.

The HLA and beta-globin regions are not presented.

‡ The first genome-wide association study and the candidate-gene study (which renders CFH a candidate gene) were published concomitantly in the same journal issue of Science.



PMID: PubMed ID

Supplementary Table 3. Odds ratios and Bayes factors for associations of candidate loci with binary phenotypes


PMID of GWAS

Phenotype

Locus

SNP

OR (95% CI)

OR model

p-value

-logBF

0.136

0.336

0.693

1.386

17998437

Alzheimer's disease

ACE

rs4351

1.42 (1.07-1.98)

dominant

4.70E-02

0.29

0.30

0.08

-0.20

18159244

Obesity

ACE

rs4351

1.47 (1.08-2.04)

dominant1

1.45E-02

0.52

0.69

0.52

0.25

18159244

Obesity

ADIPOQ

rs3774261

1.41 (1.08-1.84)

dominant

1.21E-02

0.63

0.73

0.52

0.25

17998437

Alzheimer's disease

APOE

rs4420638

3.45 (2.89-4.13)

per-allele

2.30E-44

32.65

39.82

40.95

41.00

17293876

Type 2 diabetes

CAPN10

rs7571442

1.67 (1.01-2.76)

recessive

2.70E-02

0.25

0.49

0.43

0.20

17435756

Crohn disease

CARD15/NOD2

rs2076756

1.73 (1.51-1.98)

per-allele

7.01E-14

10.03

11.06

11.00

10.75

17558408

Celiac disease

CD28-CTLA4-ICOS region

rs4675374

1.23 (1.06-1.42)

per-allele

7.00E-03

0.93

0.77

0.50

0.21

17158188

Nicotine dependence

CHRNB3

rs13277254

1.35 (1.08-1.68)

per-allele

6.54E-05

2.15

2.64

2.51

2.26

17634449

Coronary artery disease

COMT

rs4633

1.15 (1.05-1.25)

per-allele1

1.00E-03

1.60

1.35

1.05

0.76

18159244

Obesity

CRHR1

rs17763104

3.13 (1-10)

dominant1

4.40E-02

0.05

0.21

0.35

0.30

17554300

Rheumatoid arthritis

CTLA4

rs11571300

1.13 (1.01-1.27)

per-allele

5.16E-03

1.03

0.80

0.52

0.22

17447842

Crohn disease

DLG5

NA

1.19 (1.09-1.3)

per-allele

1.00E-04

2.48

2.28

1.99

1.70

17293876

Type 2 diabetes

ENPP1

rs7769712

7.75 (1.03-58.3)

dominant

3.10E-02

0.02

0.11

0.30

0.46

18159244

Obesity

ESR1

rs712221

1.54 (1.18-2.01)

dominant

1.40E-03

1.15

1.49

1.35

1.09

18204446

Systemic lupus erythematosus

FCGR2A

rs1801274

1.35 (1.2-1.54)

per-allele1

6.78E-07

4.25

4.41

4.19

3.91

18159244

Obesity

FOXC2

rs3829536

2 (1.25-3.23)

dominant1

2.90E-03

0.55

1.15

1.22

1.03

17558408

Celiac disease

HLA region

rs2187668

7.04 (6.08-8.15)

per-allele

1.00E-19

14.65

16.63

16.74

16.54

17505501

Hepatic adverse events

HLA region

rs2858869

9.54 (2.74-41.51)

per-allele

6.00E-06

0.24

1.13

2.51

3.41

17660530

Multiple sclerosis

HLA region

rs3135388

1.99 (1.84-2.15)

per-allele

8.94E-81

73.98

76.95

77.17

76.99

18364390

Psoriasis

HLA region

rs3134792

4.23 (2.67-6.71)

per allele

1.00E-09

2.7

5.87

6.97

7.09

18369459

Psoriatic arthritis

HLA region

rs10484554

2.53 (1.75-3.64)

per-allele

5.79E-07

2.33

4.14

4.51

4.39

17804836

Rheumatoid arthritis

HLA region

rs2395175

4 (3.57-4.47)

per-allele

8.00E-108

94.42

102.86

104.01

104.06

18723019

Sarcoidosis

HLA region

rs9257453

1.69 (1.22-2.38)

per-allele1

1.90E-03

0.90

1.37

1.30

1.06

18204446

Systemic lupus erythematosus

HLA region

rs3131379

2.36 (2.11-2.64)

per allele

1.70E-522

44.89

48.70

49.09

48.95

17632545

Type 1 diabetes

HLA region

rs2647044

8.3 (6.97-9.89)

per-allele

5.18E-142

109.37

133.09

137.33

138.13

17293876

Type 2 diabetes

HNF4a

rs2425637

1.33 (1.11-1.6)

per-allele

2.90E-03

1.16

1.17

0.93

0.65

17554300

Type 1 diabetes

IL2RA

rs2104286

1.3 (1.02-1.65)

heterozygotes

4.32E-05

2.16

2.79

2.71

2.46

18159244

Obesity

IL6

rs1476483

2.27 (1-5)

dominant1

4.38E-02

0.10

0.30

0.35

0.20

18159244

Obesity

IL6R

rs6696089

1.37 (1.05-1.75)

recessive1

1.81E-02

0.55

0.58

0.36

0.08

17632545

Type 1 diabetes

INS

rs1004446

1.61 (1.37-1.89)

per-allele1

4.38E-09

5.71

6.49

6.39

6.14

18677312

Systemic lupus erythematosus

IRF5

rs12531711

2.01 (1.67-2.42)

per-allele

4.03E-12

7.67

9.29

9.36

9.15

18159244

Obesity

IRS1

rs1922531

1.38 (1.06-1.81)

dominant

1.74E-02

0.54

0.60

0.39

0.11

17463249

Type 2 diabetes

KCNJ11

rs5215

1.15 (1.05-1.25)

per-allele

1.30E-03

1.50

1.24

0.95

0.65

18159244

Obesity

LDLR

rs1799898

6.99 (1.59-30.75)

recessive

2.80E-03

0.08

0.40

0.92

1.23

18159244

Obesity

LEP

rs12706832

1.35 (1.01-1.79)

recessive1

4.00E-02

0.34

0.33

0.11

-0.17

18159244

Obesity

LEPR

rs2025805

1.27 (1.05-1.54)

per-allele1

1.17E-02

0.74

0.66

0.41

0.13

18159244

Obesity

LIPC

rs9920144

1.26 (1.04-1.54)

per-allele

1.95E-02

0.59

0.49

0.23

-0.06

17634449

Coronary artery disease

LPA

rs9346818

1.1 (1.01-1.2)

per-allele1

4.00E-02

0.26

-0.08

-0.38

-0.68

17634449

Coronary artery disease

LPL

rs17411031

1.16 (1.04-1.28)

per-allele1

4.00E-03

1.11

0.87

0.58

0.28

17999355

Skin pigmentation

MATP/SLC45A2

rs16891982

4.86 (2.88-8.21)

per-allele

3.21E-11

2.69

6.55

8.21

8.53

18483556

Red vs non-red hair

MC1R

rs258322

6.62 (4.65-9.42)

per-allele

5.00E-27

11.76

20.87

23.44

23.91

18159244

Obesity

MC3R

rs1326022

1.49 (1.15-1.92)

recessive1

2.70E-03

1.01

1.25

1.08

0.82

18159244

Obesity

NPY

rs6461787

1.26 (1.05-1.53)

per-allele

1.42E-02

0.68

0.59

0.33

0.04

17952075

Blue vs brown eyes

OCA2

rs1667394

29.43 (21.47-40.35)

per-allele

1.40E-124

64.55

106.34

117.58

120.30

17634449

Coronary artery disease

OLR1

rs4495966

1.1 (1.01-1.21)

per-allele

4.00E-02

0.27

-0.06

-0.36

-0.66

16252231

Parkinson disease

PARK2

ssID: 46559884

1.41 (1.08-1.85)

per-allele1

1.27E-02

0.62

0.71

0.51

0.24

18159244

Obesity

PCSK1

rs266695

1.25 (1.03-1.53)

per-allele

2.68E-02

0.50

0.37

0.11

-0.18

17053108

Wet age-related macular degeneration

PLEKHA1-HTRA1 intergenic region

rs10490924

1.66 (1.44-1.92)

per-allele

4.08E-12

8.41

9.37

9.29

9.05

18159244

Obesity

PLIN

rs2119606

1.22 (1.01-1.49)

per-allele1

4.01E-02

0.39

0.23

-0.04

-0.33

17998437

Alzheimer's disease

POMT1

rs7865761

1.53 (1.01-2.33)

dominant

4.00E-02

0.25

0.38

0.24

-0.01

18159244

Obesity

PPARD

rs7758978

1.55 (1.08-2.23)

recessive

1.76E-02

0.43

0.63

0.49

0.23

17463248

Type 2 diabetes

PPARG

rs1801282

1.3 (1.11-1.53)

per-allele

1.10E-03

1.52

1.51

1.26

0.98

17998437

Alzheimer's disease

PSEN1

rs3025787

1.45 (1.02-2.08)

recessive1

4.00E-02

0.29

0.37

0.19

-0.08

17554300

Rheumatoid arthritis

PTPN22

rs6679677

1.9 (1.68-2.15)

per-allele

5.55E-25

19.90

21.80

21.88

21.67

18204446

Systemic lupus erythematosus

PTPN22

rs2476601

1.53 (1.27-1.84)

per-allele

5.20E-06

3.13

3.63

3.49

3.23

17554300

Type 1 diabetes

PTPN22

rs6679677

1.82 (1.59-2.09)

heterozygotes

5.43E-26

20.26

22.71

22.89

22.70

15761122

Age-related macular degeneration

Region 1q31 (CFH)3

rs380390

4.6 (2-11)

dominant

4.10E-08

0.84

3.02

4.88

5.54

17634449

Coronary artery disease

SELE

rs3917392

1.16 (1-1.35)

per-allele1

4.00E-02

0.37

0.14

-0.15

-0.44

17634449

Coronary artery disease

SELP

rs6663533

1.23 (1.01-1.48)

per-allele

2.00E-02

0.58

0.47

0.21

-0.08

18159244

Obesity

SIM1

rs9386144

2.44 (1.25-4.76)

dominant1

6.50E-03

0.27

0.77

0.96

0.83

18650507

Statin-induced myopathy

SLCO1B1

rs4149056

4.5 (2.6-7.7)

per-allele

1.00E-8

1.89

4.72

5.96

6.15

17998437

Alzheimer's disease

SORCS1

rs7907690

1.46 (1.07-1.98)

recessive

4.98E-02

0.28

0.28

0.06

-0.22

18204098

Systemic lupus erythematosus

STAT4

rs7574865

1.51 (1.36-1.66)

per-allele

9.00E-14

10.54

10.97

10.79

10.52

17293876

Type 2 diabetes

TCF7L2

rs7903146

2.09 (1.79-2.46)

per allele

3.20E-17

12.24

14.19

14.30

14.10

18159244

Obesity

TNF

rs1046089

1.21 (1-1.47)

per-allele

4.70E-02

0.34

0.17

-0.10

-0.39

18204446

Systemic lupus erythematosus

TYK2

rs280519

1.14 (1.01-1.28)

per-allele

3.00E-02

0.43

0.15

-0.14

-0.44

17999355

Skin pigmentation

TYR

rs1042602

4.36 (2.64-7.2)

per-allele

4.48E-10

2.52

5.88

7.22

7.43

18488028

Blue vs non-blue eyes

TYRP1

rs1408799

1.4 (1.25-1.57)

per-allele

1.50E-09

6.62

6.92

6.72

6.45

18159244

Obesity

UCP2-UCP3 region

rs1800849

1.45 (1.11-1.89)

recessive1

5.70E-03

0.81

0.99

0.81

0.54

18159244

Obesity

VDR

rs7418

1.28 (1.03-1.59)

per-allele

2.30E-02

0.53

0.46

0.21

-0.08

All SNPs shown belong to candidate loci that had been investigated with at least one previous human population study on the same phenotype.



1 Effect and model shown are of the major allele.

2 p-value = 10-25 in the strict definition of stage 1 discovery

3 The first genome-wide association study and the candidate-gene study (which renders CFH a candidate gene) were published concomitantly in the same journal issue of Science.

PMID: PubMed ID; BF: Bayes factor; NA: Not available


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