Table 1 Summary of genetic association studies

From: Environmental and genetic predictors of human cardiovascular ageing

Lead variant

GWAS result

Annotation

Evidence

rsID

Chr

Ref

Alt

EAF

Estimate

SE

P

Locus genes

Closest gene

Most likely causal gene

Missense

eQTL

Mech

Evidence qual.

Genome-wide association study results: image-derived cardiovascular age-delta

rs2042995

2

T

C

0.24

0.43

0.08

1.3 × 10−8

TTN

TTN

TTN

Y

Y

Y

High

rs7795735

7

T

A

0.44

0.46

0.06

3.5 × 10−13

ELN

ELN

ELN

N

N

Y

Low

rs1991860

8

C

T

0.41

−0.46

0.08

5.0 × 10−9

PI15

PI15

PI15

N

Y

N

Medium

rs61886308

10

G

A

0.18

0.56

0.08

2.4 × 10−11

PLCE1

LOC107984255, PLCE1

PLCE1

Y

Y

Y

High

rs2986036

10

T

C

0.47

−0.36

0.06

9.5 × 10−9

NEURL1-AS1

NEURL1-AS1

NEURL1-AS1

N

N

N

Low

Genome-Wide Association Study Results: electrocardiogram-derived age-delta

rs4671961

2

G

A

0.32

0.22

0.04

9.1 × 10−9

SPTBN1, EML6

SPTBN1

EML6

N

Y

N

Medium

rs11902709

2

C

T

0.05

0.51

0.08

1.8 × 10−9

TTN, PLEKHA3, FKBP7

TTN

TTN

N

Y

Y

High

rs7373065

3

T

C

0.02

−0.93

0.14

1.2 × 10−11

SCN10A, SCN5A, EXOG

SCN5A

SCN5A

N

N

Y

High

rs35430511

4

T

C

0.25

0.27

0.04

2.5 × 10−11

CAMK2D

CAMK2D

CAMK2D

N

N

Y

High

rs147790633

10

T

C

0.14

−0.37

0.05

1.2 × 10−12

AGAP5, BMS1P4-AGAP5, MYOZ1

AGAP5

MYOZ1

N

Y

Y

High

rs60820984

10

C

T

0.19

−0.28

0.05

1.8 × 10−9

CAMK2G, PLAU, NDST2

CAMK2G

CAMK2G

N

Y

N

Low

rs7132327

12

T

C

0.27

0.25

0.04

5.4 × 10−10

TBX3

TBX3

TBX3

N

N

N

Low

rs35866366

14

A

G

0.24

0.29

0.04

3.4 × 10−12

SNORD56B, SIPA1L1

SNORD56B

SIPA1L1

N

Y

N

Low

Rare variant association study results: image-derived cardiovascular age-delta

 

Chr

  

EAF

Beta

SE

P

   

Gene

   
 

6

 

pLoF (AF <0.001/0.01)

5.9×10−4

5.74

1.25

4.4 × 10−6

   

TREM2

   
 

8

 

pLoF (singletons only)

9.5×10−5

−13.77

3.07

7.1 × 10−6

   

MICU3

   
  1. Summary information on the lead single nucleotide polymorphisms (SNPs) of the genome-wide association study (GWAS)-identified significant loci and the genes identified from the rare variant association study (RVAS). For each significant locus, lead SNP summary information is provided (Chr chromosome, Ref reference allele, Alt alternative allele, EAF effect allele frequency of Alt), with GWAS summary statistics (Estimate, beta coefficient, SE standard error, P P value). Variant to gene annotation is provided, and a summary of the strength of evidence of gene mapping. Abbreviations: Missense (missense variant); eQTL status (co-localisation of GWAS signal with an expression quantitative trait loci for the gene in a plausible tissue type); Mech (the plausible mechanistic link between the gene and the phenotype, i.e. ageing); and Evidence qual. (Quality of evidence of variant to gene mapping, the strength of evidence deemed high, medium or low.). For RVAS, the EAF indicates the frequency of observing pLoF variants in the specified mask, the P values were obtained from one-sided burden tests on the additive effect, the significance level was set after adjusted by the number of genes in the tests (P < 4.7 × 10−6 for AF <0.001/0.01 and P < 1.2 × 10−5 for singletons). Analyses were performed independently for image-derived cardiovascular age-delta (n = 29,506) and electrocardiogram (ECG)-derived age-delta (n = 31,475). Gene and locus names are italicised.
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