Skip to main content

Table 4 Comparison of point-wise and proxy MA of dBGaP GWAS for known type II diabetes genes

From: Quick, “Imputation-free” meta-analysis with proxy-SNPs

PubMed ID

Genea

rs-Catalogueb

p-Cataloguec

rs-Naived

p-Naivee

rs-Proxyf

p-Proxyg

p-Imputeh

Q(Na/Pro)i

Q(Pro/Imp)j

20581827

BCL11A

rs243021

3.0E-15

rs243021

3.3E-03

rs11697597

3.3E-03

3.2E-03

1

1.03

20818381

C2CD4A,C2CD4B

rs7172432

9.0E-14

rs335302

1.2E-03

rs7172432

1.2E-03

1.98E-04

1

6.04

20581827

CDKAL1

rs10440833

2.0E-22

rs12336110

2.1E-03

rs6950237

2.1E-03

1.0E-03

1

2.10

19401414

CDKN2A, CDKN2B

rs2383208

2.0E-29

rs2383208

2.2E-03

rs2383208

8.4E-04

5.2E-04

2.6

1.60

20581827

CENTD2

rs1552224

1.0E-22

rs1552224

1.1E-01

rs1552224

3.4E-02

4.8E-03

3.33

7.08

17463249

FTO

rs8050136

7.0E-14

rs8050136

8.0E-03

rs8050136

6.7E-04

9.4E-04

11.9

0.71

20581827

HHEX,IDE

rs5015480

1.0E-15

rs5015480

9.6E-03

rs5015480

2.0E-03

4.9E-04

4.8

4.10

20581827

HMGA2

rs1531343

4.0E-09

rs12741948

3.3E-02

rs1122590

1.4E-02

9.1E-05

2.43

149.8

17463249

IGF2BP2

rs4402960

9.0E-16

rs4402960

2.3E-03

rs4402960

7.2E-04

1.2E-04

3.21

6.12

20581827

IRS1

rs7578326

5.0E-20

rs7578326

4.2E-02

rs7578326

1.7E-03

8.8E-04

24.65

1.95

18372903

JAZF1

rs864745

5.0E-14

rs864745

1.6E-03

rs864745

1.9E-04

1.1E-04

8.47

1.78

17463249

KCNJ11

rs5215

5.0E-11

rs5215

8.1E-02

rs4646410

3.1E-03

9.6E-04

26.16

3.24

18711367

KCNQ1

rs2237892

2.0E-42

rs2237892

2.1E-02

rs2237892

2.7E-04

3.5E-04

78.57

0.77

19734900

LOC64673, IRS1

rs2943641

9.0E-12

rs2943641

7.8E-02

rs2943641

1.7E-03

8.8E-04

45.94

1.95

20418489

RBMS1, ITGB6

rs7593730

4.0E-08

rs7593730

1.8E-05

rs7593730

3.4E-06

3.6E-06

5.15

0.94

20581827

SLC30A8

rs3802177

1.0E-08

rs2466295

2.4E-02

rs2466295

1.0E-02

5.3E-05

2.35

193.6

20862305

SPRY2

rs1359790

6.0E-09

rs17249026

4.5E-02

rs17249026

4.5E-02

2.1E-03

1

21.6

19734900

TCF7L2

rs7903146

1.0E-30

rs7903146

3.2E-19

rs7903146

1.5E-22

4.4E-23

2126.7

3.40

18372903

THADA

rs7578597

1.0E-09

rs2236705

1.5E-02

rs7578597

6.7E-03

2.4E-03

2.18

2.79

18372903

TSPAN8,LGR5

rs7961581

1.0E-09

rs4581087

1.1E-02

rs4581087

1.2E-02

2.4E-03

0.70

4.83

19734900

WFS1, PPP2R2C

rs4689388

1.0E-08

rs4689388

5.5E-03

rs4689388

1.6E-03

7.7E-04

3.44

2.08

20581827

ZFAND6

rs11634397

2.0E-09

rs11634397

2.6E-02

rs11634397

2.6E-02

1.0E-02

1

2.46

  1. aEach gene region is listed only once, even if listed several times in the GWAS catalogue.
  2. bMost significant SNP according to GWAS catalog [1].
  3. cp-value according to GWAS catalog.
  4. dMost significant SNP with naïve MA on intersection of marker panels of 6 dbGaP GWAS described before.
  5. ep-value refering to SNP from previous column.
  6. fMost significant SNP with proxy MA on 6 dbGaP GWAS.
  7. gp-value refering to SNP from previous column.
  8. hp-value of the correslonding SNP calculated by imputation/snptest.
  9. iImprovement with proxy algorithm: quotient of columns “p-Pointwise” and “p-Proxy”.
  10. jImprovement with imputation: quotient of columns “p-Proxy” and “p-Impute”.
Back to article page

BMC Bioinformatics

ISSN: 1471-2105

Contact us