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Table 1 GWAS significant (p < 5 × 10-8) SNP associations

From: The genetic case for cardiorespiratory fitness as a clinical vital sign and the routine prescription of physical activity in healthcare

SEX

CHR

BP

SNP

LOCUS

A1

A0

A1 FREQ

BETA

SE

P

P (other sex)

CRF-vo2max

 Combined

1

112592672

rs269071

Intergenic1

A

G

0.63

0.031

0.005

3.6 × 10-10

 

 Combined

2

179747068

rs142556838

CCDC141

C

T

0.91

0.049

0.008

2.9 × 10-9

 

 Combined

2

179839888

rs10497529

CCDC141

G

A

0.96

0.085

0.013

1.0 × 10-11

 

 Combined

3

38767315

rs6801957

SCN10A

T

C

0.41

0.030

0.005

1.7 × 10-10

 

 Combined

5

65264090

rs251295

ERBB2IP

A

G

0.59

−0.027

0.005

2.3 × 10-8

 

 Combined

5

121868475

rs111299422

Intergenic2

T

TA

0.69

−0.038

0.005

6.5 × 10-14

 

 Combined

6

122089704

rs58730006

Intergenic3

A

AT

0.90

0.047

0.008

2.7 × 10-9

 

 Combined

10

102552663

rs11190709

PAX2

G

A

0.11

−0.046

0.007

3.8 × 10-10

 

 Combined

16

56803199

rs78291913

NUP93

C

T

0.99

−0.143

0.024

1.4 × 10-9

 

 Combined

17

43668512

rs527325496

Intergenic4

C

CAAA

0.81

−0.036

0.006

4.2 × 10-9

 

 Combined

17

44335579

rs139077859

LOC644172

G

A

0.79

−0.033

0.006

1.7 × 10-8

 

 Combined

20

36849088

rs4811602

KIAA1755

G

A

0.53

−0.028

0.005

3.7 × 10-9

 

 Malea

3

38773805

rs9809798

SCN10A

A

C

0.47

0.040

0.007

2.2 × 10-8

6.3 × 10-3

 Maleb

5

121868475

rs111299422

Intergenic2

T

TA

0.69

−0.050

0.008

2.6 × 10-10

3.3 × 10-5

 Malec

10

102553647

rs1006545

PAX2

G

T

0.11

−0.062

0.011

4.3 × 10-8

2.7 × 10-3

 Maled

14

96864374

rs41317306

AK7

T

G

0.98

−0.137

0.024

2.2 × 10-8

5.1 × 10-1

CRF-slope

 Combined

5

121868475

rs111299422

Intergenic2

T

TA

0.69

0.007

0.001

1.3 × 10-10

 

 Combined

7

100546458

rs4582488

Integenic5

G

T

0.74

0.007

0.001

3.6 × 10-9

 

 Combined

8

8317817

rs2921060

Intergenic6

A

C

0.55

0.006

0.001

1.6 × 10-8

 

 Combined

8

10822431

rs35792458

XKR6

G

C

0.56

−0.006

0.001

1.5 × 10-8

 

 Combined

8

11423072

rs12541800

Intergenic7

A

G

0.52

0.006

0.001

4.7 × 10-8

 

 Combined

10

102554618

10:102554618_AT_A

PAX2

AT

A

0.11

0.012

0.002

1.5 × 10-13

 

 Combined

12

24758480

rs4963772

Intergenic8

G

A

0.85

−0.009

0.001

5.8 × 10-11

 

 Combined

12

33633599

rs7303356

Intergenic9

G

C

0.49

−0.006

0.001

1.5 × 10-10

 

 Femalee

5

121868475

rs111299422

Intergenic2

T

TA

0.69

0.010

0.002

2.5 × 10-8

1.1 × 10-3

 Malef

10

102553647

rs1006545

PAX2

G

T

0.11

0.012

0.002

6.0 × 10-12

2.0 × 10-5

 Maleg

20

4131944

rs1741294

SMOX

C

G

0.96

0.016

0.003

6.0 × 10-9

6.0 × 10-1

PA

 Combined

1

78450517

rs34517439

Intergenic10

C

A

0.88

0.316

0.058

4.6 × 10-8

 

 Combined

5

87942506

rs10067451

LINC00461

G

A

0.89

0.333

0.060

3.0 × 10-8

 

 Combined

5

152238114

5:152238114*

LOC101927134

TTTTTTTTTTTTC

T

0.71

0.230

0.042

4.1 × 10-8

 

 Combined

9

128195657

rs1268539

Intergenic11

C

A

0.58

−0.214

0.038

1.9 × 10-8

 

 Combined

10

21885577

rs34719019

MLLT10

A

T

0.73

0.242

0.042

9.7 × 10-9

 

 Combined

17

43758125

rs62055696

CRHR1

A

G

0.78

−0.309

0.046

1.3 × 10-11

 

 Combined

17

44326864

rs2696625

Intergenic12

A

G

0.77

−0.310

0.045

4.8 × 10-12

 

 Combined

17

44828931

rs199533

NSF

G

A

0.79

−0.250

0.046

4.0 × 10-8

 

 Combined

18

40768309

rs59499656

Intergenic13

A

T

0.66

−0.215

0.039

5.0 × 10-8

 

 Femaleh

16

71464058

rs75986475

Intergenic14

C

G

0.88

−0.436

0.076

7.4 × 10-9

3.3 × 10-1

 Femalei

16

80784797

rs13329850

CDYL2

C

G

0.74

−0.308

0.055

2.8 × 10-8

4.5 × 10-1

 Femalej

17

43758125

rs62055696

CRHR1

A

G

0.78

−0.358

0.059

1.3 × 10-9

2.4 × 10-4

 Femalek

17

44262581

17:44262581_A_C

KANSL1

A

C

0.83

−0.450

0.070

1.5 × 10-10

8.2 × 10-3

 Malel

2

36592600

rs78661713

CRIM1

G

A

0.94

−0.700

0.128

4.8 × 10-8

6.1 × 10-1

  1. Note: These are independent SNP associations determined by p value informed LD clumping (SNPs correlated 0.2 or greater in a 500 kb). 2 CRF-slope-associated SNPs (rs587631263, chr7; rs10623635, chr10) and 16 PA-associated SNPs (rs10828247, chr10; 15 chr17 SNPs listed in supplementary material) not available in LD reference data. LOCUS nearest gene, A1 effect allele, A0 reference allele, A1 FREQ effect allele frequency, BETA effect size (from BOLT-LMM approximation to infinitesimal mixed model), SE standard error of the effect size
  2. *5:152238114_TTTTTTTTTTTTC_T
  3. 1LOC643355 (+51.2kb), CTTNBP2NL (−346.1kb); 2MGC32805 (+53.7kb), LOC101927379 (−96.2kb); 3GJA1 (+318.8kb), HSF2 (−631kb); 4LOC644172 (−9.0kb), LRRC37A4P (+70.62kb); 5MUC3A (−0.593kb), ACHE (+52.87kb); 6SGK223 (+78.47kb), CLDN23 (−241.8kb); 7BLK (+0.964kb), LINC00208 (−10.97kb); 8LINC00477 (+21.38kb), BCAT1 (−204.5kb); 9SYT10 (+40.84kb), ALG10 (−541.6kb); 10FUBP1 (+5.74kb), DNAJB4 (−20.12kb); 11MAPKAP1 (−4.015kb), GAPVD1 (+68.37kb); 12LOC644172 (+3.71kb), LRRC37A (−45.63kb); 13RIT2 (+72.65kb), SYT4 (−79.55kb); 14ZNF23 (−17.44kb), CALB2 (+39.72kb)
  4. aFemale BETA = 0.0163, SE = 0.0060: Q = 6.58, p = 1.0 × 10-2; I2 = 84.8%, 95% CI = 38.0% – 96.3% (nsCRF = not significant at 0.05/7, for 7 CRF SNPs tested)
  5. bFemale BETA = −0.0271, SE = 0.0065: Q = 4.86, p = 2.8 × 10-2; I2 = 79.4%, 95% CI = 11.1–95.2% (nsCRF)
  6. cFemale BETA = −0.0281, SE = 0.0094: Q = 5.34, p = 2.1 × 10-2; I2 = 81.3%, 95% CI = 20.3–95.6% (nsCRF)
  7. dFemale BETA = 0.0136, SE = 0.0206: Q = 22.13, p < 0.001; I2 = 95.5%, 95% CI = 86.8–98.5%
  8. emale BETA = 0.0038, SE = 0.0012: Q = 8.37, p = 3.8 × 10-3; I2 = 88.1%, 95% CI = 54.1–96.9%
  9. fFemale BETA = 0.0111, SE = 0.0026: Q = 0.04, p = 8.3 × 10-1; I2 = 0.0% (nsCRF)
  10. gFemale BETA = 0.0021, SE = 0.0040: Q = 7.96, p = 4.8 × 10-3; I2 = 87.4%, 95% CI = 51.1–96.8%
  11. hMale BETA = −0.0893, SE = 0.0916: Q = 8.51, p = 3.5 × 10-3; I2 = 88.3%, 95% CI = 55.0–96.9%
  12. iMale BETA = 0.0503, SE = 0.0670: Q = 16.98, p < 0.001; I2 = 94.1%, 95% CI = 81.4–98.1%
  13. jMale BETA = -0.2636, SE = 0.0718: Q = 1.03, p = 3.1 × 10-1; I2 = 3.0% (nsPA = not significant at 0.05/5, for 5 PA SNPs tested)
  14. kMale BETA = −0.2258, SE = 0.0855: Q = 4.09, p = 4.3 × 10-2; I2 = 75.6%, 95% CI = 0.0–94.5% (nsPA)
  15. lFemale BETA = 0.0542, SE = 0.1057: Q = 20.63, p < 0.001; I2 = 95.2%, 95% CI = 85.5–98.4%
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