Supplemental Material Supplementary references




старонка5/5
Дата канвертавання25.04.2016
Памер1.29 Mb.
1   2   3   4   5

Supplementary Table 4. Associations with p-value < 10-7 that pertain to binary phenotypes in the 100 evaluated GWAS that addressed also candidate loci. One GWAS-discovered association with an unavailable odds ratio is not shown (rs2075555 in COL1A1 gene for breast cancer).


PMID

Phenotype

Locus

Representative SNP

MAF

p-value

OR

Novel GWAS-derived associations

17053108

Wet age-related macular degeneration

HTRA1

rs11200638

NA (Chinese)

8.00E-12

1.6

17068223

Inflammatory bowel disease

IL23R

rs7517847

0.44

4.00E-13

1.61

17293876

Type 2 diabetes

SLC30A8

rs13266634

0.24

6.00E-08

1.18

17401363

Prostate cancer

Intergenic

rs6983267

0.49

9.00E-13

1.26

17401366

Prostate cancer

Intergenic

rs16901979

0.03

1.00E-12

1.79

17435756

Crohn disease

ATG16L1

rs2241880

0.43

1.00E-13

1.45

17435756

Crohn disease

Intergenic

rs224136

0.14

1.00E-10

1.67

17447842

Crohn disease

Intergenic

rs1373692

0.35

2.00E-12

1.46

17463249

Type 2 diabetes

CDKAL1

rs10946398

0.34

4.00E-11

1.12

17463249

Type 2 diabetes

CDKN2A/B

rs10811661

0.20

8.00E-15

1.2

17463249

Type 2 diabetes

FTO

rs8050136

0.46

1.00E-12

1.17

17463249

Type 2 diabetes

HHEX

rs5015480

0.42

6.00E-10

1.13

17463249

Type 2 diabetes

IGF2BP2

rs4402960

0.30

9.00E-16

1.14

17486107

Bipolar disorder

DGKH

rs1012053

0.13

2.00E-08

1.59

17529967

Breast cancer

FGFR2

rs2981582

0.46

2.00E-76

1.26

17529967

Breast cancer

Intergenic

rs13281615

0.46

5.00E-12

1.08

17529967

Breast cancer

LSP1

rs3817198

0.33

3.00E-09

1.07

17529967

Breast cancer

MAP3K1

rs889312

0.31

7.00E-20

1.13

17529967

Breast cancer

TNRC9,LOC643714

rs3803662

0.25

1.00E-36

1.2

17529974

Breast cancer

Intergenic

rs13387042

0.44

1.00E-13

1.2

17554261

Crohn disease

Intergenic

rs10801047

0.10

3.00E-08

1.47

17554261

Crohn disease

IRGM

rs13361189

0.04

2.00E-10

1.38

17554261

Crohn disease

MST1

rs9858542

0.26

5.00E-08

1.17

17554261

Crohn disease

NKX2-3

rs10883365

0.46

4.00E-10

1.18

17554261

Crohn disease

PTPN2

rs2542151

0.12

3.00E-08

1.15

17554300

Bipolar disorder

PALB2,NDUFAB1,DCTN5

rs420259

0.20

6.00E-08

2.08

17554300

Coronary artery disease

CDKN2A,CDKN2B

rs1333049

0.46

1.00E-13

1.47

17554300

Crohn disease

BSN, MST1

rs9858542

0.26

4.00E-08

1.09

17554300

Type 1 diabetes

ERBB3

rs11171739

0.41

1.00E-11

1.34

17554300

Type 1 diabetes

SH2B3,LNK,TRAFD1,PTPN1

rs17696736

0.36

2.00E-14

1.34

17558408

Celiac disease

KIA1109,TENR,IL2,IL21

rs6822844

0.15

1.00E-14

1.59

17603485

Prostate cancer

Intergenic

rs1859962

0.47

3.00E-10

1.2

17603485

Prostate cancer

TCF2

rs4430796

0.49

1.00E-11

1.22

17632509

Gallstone disease

ABCG8

rs11887534

0.08

1.00E-14

2.2

17632545

Type 1 diabetes

KIAA0350

rs2903692

0.31

7.00E-11

1.54

17634449

Coronary artery disease

MTHFD1L

rs6922269

0.26

3.00E-08

1.23

17660530

Multiple sclerosis

IL2RA

rs12722489

0.17

3.00E-08

1.25

17804836

Rheumatoid arthritis

TRAF1-C5

rs3761847

0.48

4.00E-14

1.32

17952075

Blond vs brown hair

KITLG

rs12821256

0.15

4.00E-30

2.32

17952075

Blond vs brown hair

SLC24A4

rs12896399

0.43

1.00E-48

2.56

17952075

Freckles

SEC5L1,IRF4

rs1540771

0.44

4.00E-18

1.4

17999355

Skin pigmentation

SLC24A5

rs1834640

0.01

1.00E-50

12.5

18204098

Systemic lupus erythematosus

C8orf13, BLK

rs13277113

0.24

1.00E-10

1.39

18204098

Systemic lupus erythematosus

ITGAM, ITGAX

rs11574637

0.14

3.00E-11

1.33

18204446

Systemic lupus erythematosus

ITGAM

rs9888739

0.10

2.00E-23

1.62

18204446

Systemic lupus erythematosus

KIAA1542

rs4963128

0.33

3.00E-10

1.28

18204446

Systemic lupus erythematosus

PXK

rs6445975

0.25

7.00E-09

1.25

18264097

Prostate cancer

Intergenic

rs7931342

0.47

2.00E-12

1.19

18264097

Prostate cancer

KLK3

rs2735839

0.14

2.00E-18

1.2

18264097

Prostate cancer

LMTK2

rs6465657

0.49

1.00E-09

1.12

18264097

Prostate cancer

MSMB

rs10993994

0.34

9.00E-29

1.25

18264097

Prostate cancer

SLC22A3

rs9364554

0.27

6.00E-10

1.17

18364390

Psoriasis

SPATA2

rs495337

0.43

1.00E-08

1.25

18483556

Black vs blond hair

EXOC2

rs6918152

0.38

6.00E-08

1.12

18483556

Black vs blond hair

HERC2

rs12913832

0.21

4.00E-103

1.55

18483556

Black vs blond hair

IRF4

rs12203592

0.16

7.00E-127

1.42

18488028

Blond vs brown hair

TPCN2

rs35264875

0.22**

4.00E-30

2.49

18488028

Burning and freckling

ASIP

rs1015362

0.26

6.00E-37

2.56

18660810

Restless legs syndrome

PTPRD

rs4626664

0.13

6.00E-10

1.44

18677312

Systemic lupus erythematosus

TNFAIP3

rs5029939

0.03

3.00E-12

2.28

Candidate loci associations

15761122

Age-related macular degeneration

Region 1q31 (CFH)*

rs380390

0.45

4.10E-08

4.6

17053108

Wet age-related macular degeneration

PLEKHA1-HTRA1 intergenic region

rs10490924

0.20

4.08E-12

1.66

17293876

Type 2 diabetes

TCF7L2

rs7903146

0.28

3.20E-17

2.09

17435756

Crohn disease

CARD15/NOD2

rs2076756

0.32

7.01E-14

1.73

17554300

Type 1 diabetes

PTPN22

rs6679677

0.12

5.43E-26

1.82

17554300

Rheumatoid arthritis

PTPN22

rs6679677

0.12

5.55E-25

1.9

17632545

Type 1 diabetes

INS

rs1004446

0.39

4.38E-09

1.61

17952075

Blue vs brown eyes

OCA2

rs1667394

0.14

1.40E-124

29.43

17998437

Alzheimer's disease

APOE

rs4420638

0.18

2.30E-44

3.45

17999355

Skin pigmentation

TYR

rs1042602

0.43

4.48E-10

4.36

17999355

Skin pigmentation

MATP/SLC45A2

rs16891982

0.02

3.21E-11

4.86

18204098

Systemic lupus erythematosus

STAT4

rs7574865

0.23

9.00E-14

1.51

18483556

Red vs non-red hair

MC1R

rs258322

0.14

5.00E-27

6.62

18488028

Blue vs non-blue eyes

TYRP1

rs1408799

0.30

1.50E-09

1.4

18650507

Statin-induced myopathy

SLCO1B1

rs4149056

0.15

1.00E-08

4.5

18677312

Systemic lupus erythematosus

IRF5

rs12531711

0.12

4.03E-12

2.01

17558408

Celiac disease

HLA region

rs2187668

0.08

1.00E-19

7.04

17632545

Type 1 diabetes

HLA region

rs2647044

0.07

5.18E-142

8.3

17660530

Multiple sclerosis

HLA region

rs3135388

0.19

8.94E-81

1.99

17804836

Rheumatoid arthritis

HLA region

rs2395175

0.24

8.00E-108

4

18204446

Systemic lupus erythematosus

HLA region

rs3131379

0.08

1.00E-25

2.36

18364390

Psoriasis

HLA region

rs3134792

0.10

1.00E-09

4.23

Novel associations were unknown prior to the publication of the GWA study and are derived from the GWA studies that report results on candidate genes. The NHGRI catalog (www.genome.gov/gwastudies) was used for the selection of the novel GWAS-derived SNPs. SNPs with the lowest p-values for each gene across all studies with related phenotypes are shown for both samples.

Minor allele frequencies are according to data of the International HapMap Project (release #27) and pertain to Caucasian populations.

* 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.

** allele frequency derived from the GWAS paper

PMID: PubMed ID; MAF: Minor allele frequency based on HapMap for Caucasian descent populations; NA: Not available



Supplementary Figure 1. Selection and extraction of quantitative data on candidate associations


Supplementary Figure 2. Selection of studies





1   2   3   4   5


База данных защищена авторским правом ©shkola.of.by 2016
звярнуцца да адміністрацыі

    Галоўная старонка