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Table 1 Top GWAS hits

From: Exploration of haplotype research consortium imputation for genome-wide association studies in 20,032 Generation Scotland participants

Baseline characteristic

N

dbSNP ID

Minor allele frequency

p value

Gene

Imputation quality

Gene association reported previously?

Region significant in genotyped data?

Cardiometabolic

 Diastolic blood pressure

19,546

rs142892876

0.0010

4.97E-08

CNTN6

0.75

No

No

 

rs528908640

0.0005

1.93E-08

OPA1

0.80

No

No

 

rs568998724

0.0007

2.91E-08

-

0.78

No

No

 

rs187680191

0.0006

2.94E-09

NRG4

0.51

No

No

 Systolic blood pressure

19,547

None

  

None

   

 Pulse pressure

19,546

None

  

None

   

 Heart rate

19,920

rs9970334

0.4474

4.38E-08

ICMT

0.90

Yes

No

 

rs755291044

0.0017

1.80E-08

-

0.90

No

No

 

rs145669495

0.0022

2.01E-08

CSMD1

0.90

No

No

 

rs142916219

0.0037

2.21E-08

ASPH

0.85

No

No

 

rs365990

0.3637

4.04E-10

MYH6

0.99

Yes

GWS

 

rs148397504

0.0008

3.21E-09

-

0.45

No

No

Biochemistry

 Serum creatinine

16,347

rs548873184

0.0010

1.47E-08

LINC00626

0.96

No

No

 

rs573421908

0.0027

1.35E-08

SLC35F3

0.80

Yes

No

 

rs62412107

0.0660

1.87E-08

-

0.79

No

No

 

rs3812036

0.2301

1.13E-10

SLC34A1

0.96

Yes

GWS

 Fasting plasma glucose (with diabetics)

16,174

rs560887

0.2907

6.02E-68

G6PC2

1.00

Yes

GWS

 

rs9873618

0.2871

9.83E-12

SLC2A2

0.99

Yes

GWS

 

rs917793

0.1831

2.51E-24

YKT6

0.98

Yes

GWS

 

rs13266634

0.3153

3.66E-11

SLC30A8

1.00

Yes

GWS

 

rs533883198

0.0027

3.86E-08

-

0.84

No

No

 

rs7981781

0.2337

1.40E-08

PDX1

0.98

Yes

GWS

 

rs370189685

0.0014

7.32E-09

WDR4

0.63

No

No

 Fasting plasma glucose (diabetics removed)

15,226

rs79687284

0.0364

1.87E-08

-

0.78

Yes

GWS

 

rs780095

0.4267

8.20E-09

GCKR

1.00

Yes

GWS

 

rs560887

0.2907

2.09E-75

G6PC2

1.00

Yes

GWS

 

rs8192675

0.2839

8.41E-11

SLC2A2

1.00

Yes

GWS

 

rs917793

0.1831

1.46E-28

YKT6

0.98

Yes

GWS

 

rs11558471

0.3227

4.63E-13

SLC30A8

1.00

Yes

GWS

 

rs143399767

0.0108

1.42E-08

Y_RNA

0.89

No

No

 

rs7981781

0.2337

5.01E-10

PDX1

0.98

Yes

GWS

 

rs370189685

0.0014

2.75E-08

WDR4

0.63

No

Suggestive

 HDL cholesterol

19,223

rs149963466

0.0016

3.18E-08

-

0.76

No

No

 

rs76183280

0.0048

4.14E-08

AC016735.2

0.78

No

No

 

rs4841132

0.0925

1.08E-08

RP11-115 J16.1

1.00

Yes

Suggestive

 

rs15285

0.2675

1.16E-18

LPL

1.00

Yes

GWS

 

rs2740488

0.2745

2.53E-08

ABCA1

1.00

Yes

GWS

 

rs138326449

0.0032

2.92E-20

APOC3

0.85

Yes

No

 

rs114529226

0.0038

6.98E-09

IGHVII-33-1

0.64

No

No

 

rs261290

0.3442

2.78E-25

ALDH1A2

1.00

Yes

GWS

 

rs3764261

0.3261

1.40E-113

CETP

1.00

Yes

GWS

 

rs143264468

0.0010

1.99E-09

LRRC29

0.81

Yes

Suggestive

 

rs72836561

0.0294

1.55E-11

CD300LG

0.87

Yes

No

 

rs149615216

0.0119

3.20E-09

LIPG

0.97

Yes

Suggestive

 

rs116843064

0.0230

5.57E-10

ANGPTL4

0.84

Yes

No

 

rs7412

0.0779

5.95E-14

APOE

0.98

Yes

GWS

 

rs453755

0.2480

3.22E-08

LILRA3

0.92

Yes

No

 

rs435306

0.2547

2.87E-08

PLTP

1.00

Yes

Suggestive

 Cholesterol

19,259

rs11591147

0.0169

1.83E-17

PCSK9

0.98

Yes

GWS

 

rs10889333

0.3601

2.12E-10

DOCK7

1.00

Yes

GWS

 

rs12740374

0.2288

8.19E-22

CELSR2

1.00

Yes

GWS

 

rs672889

0.1356

3.77E-16

-

1.00

Yes

GWS

 

rs75331444

0.0720

1.87E-11

ABCG8

0.99

Yes

GWS

 

rs12916

0.3970

6.35E-11

HMGCR

0.99

Yes

GWS

 

rs74617384

0.0838

3.02E-09

LPA

0.93

Yes

No

 

rs4841133

0.0929

2.51E-09

RP11-115 J16.1

1.00

Yes

Suggestive

 

rs2000999

0.1776

7.01E-09

HPR

0.99

Yes

Suggestive

 

rs10412048

0.1086

5.00E-25

-

0.98

Yes

GWS

 

rs7412

0.0779

5.22E-94

APOE

0.98

Yes

GWS

 Urea

19,293

rs760077

0.4247

6.24E-09

MTX1

0.98

Yes

Suggestive

 

rs16862780

0.1574

3.03E-10

RP11-132 N15.3

1.00

Yes

GWS

 

rs112647987

0.0680

3.07E-08

-

0.99

No

No

 

rs6950388

0.1872

1.57E-08

UNCX

0.95

Yes

GWS

 

rs10224210

0.2799

5.71E-09

PRKAG2

0.92

Yes

Suggestive

Anthropometric

 Body mass index

19900

rs73139123

0.1830

1.34E-09

-

0.96

Yes

GWS

 

rs10498218

0.0012

3.98E-08

COL4A4

0.84

Yes

No

 

rs149913955

0.0059

2.18E-08

RP11-624 L4.1

0.74

No

No

 

rs571835655

0.0011

6.61E-09

-

0.82

No

No

 

rs55872725

0.3951

5.71E-21

FTO

1.00

Yes

GWS

 Height

19,965

rs146949893

0.0031

4.49E-08

RP1-35C21.2

0.72

No

No

 

rs558671668

0.0062

2.53E-08

RP11-317P15.6

0.80

No

No

 

rs6765866

0.0007

2.05E-08

CMTM8

0.59

No

No

 

rs1991431

0.4338

5.25E-13

ZBTB38

1.00

Yes

GWS

 

rs35362908

0.1006

7.04E-09

LCORL

0.73

Yes

No

 

rs552283803

0.0016

3.99E-08

ARHGAP24

0.79

No

No

 

rs755546258

0.0007

2.58E-08

DAP

0.72

No

No

 

rs72742734

0.0537

3.61E-08

NPR3

1.00

Yes

Suggestive

 

rs554379257

0.0006

4.83E-08

CTD-2023 N9.1

0.44

No

No

 

rs7766641

0.2551

3.32E-13

HIST1H2BE

1.00

Yes

GWS

 

rs57026767

0.1550

4.50E-11

C6orf1

1.00

Yes

GWS

 

rs566773279

0.0005

1.17E-08

-

0.69

No

No

 

rs1490384

0.4851

7.09E-10

-

1.00

Yes

GWS

 

rs7753012

0.3072

7.60E-14

GPR126

0.99

Yes

GWS

 

rs184469050

0.0088

1.58E-08

-

0.89

No

No

 

rs144225905

0.0010

2.13E-09

-

0.46

No

No

 

rs7952436

0.0896

1.91E-12

KDM2A

0.88

Yes

No

 

rs634552

0.1365

2.30E-08

SERPINH1

0.98

Yes

GWS

 

rs76895963

0.0285

3.43E-08

CCND2

0.78

Yes [48, 49]

No

 

rs770307181

0.0005

1.09E-08

-

0.50

No

No

 

rs139770682

0.0005

4.55E-08

-

0.72

No

No

 

rs11614062

0.1943

2.09E-08

SOCS2-AS1

0.99

Yes

GWS

 

rs75061684

0.0006

5.33E-10

-

0.49

No

No

 

rs16942323

0.0344

1.09E-11

ACAN

0.93

Yes

No

 

rs8096254

0.2598

4.32E-12

CABLES1

1.00

Yes

GWS

 

rs6060402

0.3585

2.80E-13

-

0.98

Yes

GWS

 Waist-to-hip ratio

19,695

rs72959041

0.0566

2.54E-14

RSPO3

0.90

Yes

Suggestive

 

rs149924309

0.0023

3.70E-08

-

0.81

No

No

 

rs187209742

0.0023

4.91E-08

SERPINA10

0.70

No

No

 

rs751156121

0.0006

1.29E-08

-

0.78

No

No

 Body fat

19,480

rs10921288

0.0235

1.04E-08

-

0.99

No

GWS

 

rs142101835

0.0022

3.25E-08

IRS1

0.69

Yes

No

 

rs560546550

0.0007

3.17E-09

WDR41

0.89

No

No

 

rs571835655

0.0011

2.03E-08

-

0.82

No

No

 

rs55872725

0.3951

5.55E-16

FTO

1.00

Yes

GWS

 

rs141793746

0.0030

3.31E-08

DYM

0.86

No

No

NHS EHR linkage

 Serum urate

2077

rs6449213

0.1652

1.93E-17

SLC2A9

1.00

Yes

GWS

 

rs75869162

0.0054

1.57E-08

FAM134B

0.80

No

No

 

rs141208451

0.0053

3.13E-09

RP11-430H10.4

0.86

No

No

 

rs187171029

0.0060

1.84E-08

ZNF160

0.91

No

No

  1. Summary of the baseline characteristics of the GS:SFHS sub-cohort of 20,032 analysed by GWAS, with genome-wide significant markers from the imputed GWAS listed. We indicate known associations in published research or present in the NHGRI GWAS Catalog within 100 kb of the sentinal SNP reported here. The column called ‘Region significant in genotyped data?’ indicates whether any SNPs within 500 kb of the reported SNP reach genome-wide significance (GWS, p < 5*10–8) or suggestive significance (Suggestive, p < 10–5) in the genotyped data