Table 1 Lead variants from the HCM GWAS

From: Large-scale genome-wide association analyses identify novel genetic loci and mechanisms in hypertrophic cardiomyopathy

Lead SNP

GRCh37

EA/NEA

EAF

OR (95% CI)

P

Q

Locus name

GWS in HCMSARC+

GWS in HCMSARC−

Genome-wide significant loci from all HCM meta-analysis

rs2234962

10:121429633

C/T

0.21

1.45 (1.38–1.52)

1.39 × 10−49

0.36

BAG3 (missense)

•

•

rs2644262

18:34223566

C/T

0.29

1.38 (1.32–1.45)

1.79 × 10−43

0.43

FHOD3/TPGS2

•

•

rs78310129

11:56793878

T/C

0.01

3.53 (2.92–4.27)

9.79 × 10−39

1.59E-09

MYBPC3

•

 

rs1048302

1:16340879

T/G

0.33

1.28 (1.23–1.34)

8.47 × 10−30

0.59

HSPB7

 

•

rs2070458*

22:24159307

A/T

0.22

1.30 (1.24–1.37)

5.93 × 10−25

0.09

VPREB3/SMARCB1

 

•

rs3176326*

6:36647289

A/G

0.21

1.30 (1.24–1.37)

3.18 × 10−24

0.14

CDKN1A

 

•

rs12212795

6:118654308

C/G

0.05

1.51 (1.39–1.65)

4.76 × 10−22

0.33

SLC35F1/PLN

 

•

rs4577128*

17:64308473

C/T

0.57

1.23 (1.18–1.29)

3.26 × 10−21

0.97

PRKCA

 

•

rs393838

17:43705756

C/G

0.23

1.26 (1.20–1.32)

5.02 × 10−21

0.91

CRHR1/MAPT

 

•

rs8033459*

15:85253258

T/C

0.46

1.20 (1.15–1.25)

7.04 × 10−18

0.66

ALPK3/NMB

•

•

rs11196085*

10:114505037

C/T

0.28

1.22 (1.16–1.28)

1.85 × 10−17

0.75

VTI1A/TCF7L2

 

•

rs7301677

12:115381147

C/T

0.74

1.22 (1.16–1.29)

7.01 × 10−16

0.27

TBX3

 

•

rs2177843*

10:75409877

T/C

0.16

1.26 (1.19–1.34)

2.80 × 10−15

0.91

MYOZ1/SYNPO2L

 

•

rs41306688

13:114078558

C/A

0.03

1.60 (1.42–1.80)

3.04 × 10−15

0.22

ADPRHL1 (missense)

 

•

rs2191445*

5:57011469

T/A

0.80

1.23 (1.17–1.30)

8.22 × 10−14

0.37

ACTBL2

 

•

rs4894803*

3:171800256

G/A

0.41

1.18 (1.13–1.24)

2.19 × 10−13

0.63

FNDC3B

 

•

rs13061705

3:14291129

C/T

0.69

1.19 (1.13–1.25)

5.67 × 10−13

0.68

SLC6A6/LSM3

 

•

rs13021775

2:37059557

C/G

0.50

1.17 (1.12–1.23)

5.98 × 10−13

0.50

STRN

 

•

rs8006225

14:95219657

G/T

0.83

1.22 (1.15–1.30)

2.64 × 10−11

0.15

GSC

 

•

rs10052399*

5:138668504

T/C

0.27

1.18 (1.12–1.24)

3.99 × 10−11

0.03

SPATA24

  

rs66520020*

7:128438284

T/C

0.16

1.21 (1.14–1.28)

5.87 × 10−11

0.96

CCDC136/FLNC

  

rs12460541

19:46312077

G/A

0.66

1.16 (1.11–1.21)

6.01 × 10−11

0.13

DMPK/SYMPK

  

rs7461129

8:125861374

T/C

0.31

1.16 (1.11–1.21)

8.19 × 10−11

0.87

MTSS1

  

rs56005624

2:179774634

G/T

0.14

1.21 (1.14–1.28)

8.31 × 10−11

0.62

CCDC141/SESTD1

 

•

rs7824244

8:21802432

A/G

0.14

1.22 (1.14–1.29)

2.39 × 10−10

0.34

XPO7

•

 

rs12270374

11:14375079

C/T

0.36

1.14 (1.09–1.20)

6.85 × 10−10

0.92

RRAS2/COPB1

  

rs62222424

21:30530131

G/A

0.93

1.32 (1.20–1.44)

1.21 × 10−9

0.69

CCT8

  

rs11687178

2:11584197

C/A

0.65

1.14 (1.09–1.19)

7.70 × 10−9

0.26

E2F6/ROCK2

  

rs9320939

6:123818871

A/G

0.49

1.13 (1.08–1.18)

1.04 × 10−8

0.04

TRDN/HEY2

 

•

rs2540277

2:103426177

C/T

0.94

1.32 (1.19–1.45)

2.31 × 10−8

0.84

TMEM182/MFSD9

  

rs6566955

18:55922789

G/A

0.31

1.14 (1.08–1.19)

2.93 × 10−8

0.16

NEDD4L

  

rs13004994

2:220406239

T/G

0.46

1.13 (1.08–1.18)

3.02 × 10−8

0.12

CHPF

  

rs2645210

10:4098453

A/G

0.19

1.16 (1.10–1.23)

3.94 × 10−8

0.52

KLF6/AKR1E2

  

rs113907726

14:53316867

G/T

0.19

1.16 (1.10–1.22)

4.10 × 10−8

0.27

FERMT2/ERO1A

  

Additional loci discovered in HCMSARC+ or HCMSARC−

rs9311485

3:52987645

T/G

0.25

1.13 (1.08–1.19)

1.86 × 10−7

0.09

ITIH3/SFMBT1

 

•

rs77963625

12:46446897

C/T

0.03

1.38 (1.22–1.57)

2.97 × 10−7

0.24

SCAF11

 

•

rs846111

1:6279370

G/C

0.73

1.14 (1.08–1.20)

6.32 × 10−7

0.52

RNF207 (missense)

 

•

rs58747679

12:26348304

T/C

0.71

1.12 (1.07–1.18)

1.30 × 10−6

0.15

SSPN

 

•

rs112787369

14:68252852

T/A

0.04

1.21 (1.08–1.35)

6.04× 10−4

0.62

ZYVE26 (missense)

•

 
  1. All reported summary statistics refer to the all HCM case–control meta-analysis results, including for loci identified only in the HCMSARC+ and HCMSARC− stratified analyses. The table is sorted in increasing order of the all-comer P values. Novel loci are shown in bold. An asterisk marks loci that reached significance in a previous multitrait analysis of GWAS (MTAG)3 and now reach significance in the present GWAS. Locus naming was performed primarily by OpenTargets13, also considering functional mapping and annotation of GWAS (FUMA)14 mapping, and previous rare variant associations with HCM26. Dots indicate the presence of GWS. EA/NEA, effect and noneffect alleles; EAF, effect allele frequency; GWS, genome-wide significance (P ≤ 5 × 10−8); Q, Cochrane’s heterogeneity test P value.
Back to article page