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Table 2 Genome-wide significant and suggestive loci identified in the meta-analysis

From: Genome-wide association study using family-based cohorts identifies the WLS and CCDC170/ESR1 loci as associated with bone mineral density

      

GENOS (n = 1,042)

TwinsUK (n = 5,654)

Meta-analysis (n = 6,696)

 

Phenotype

Locus

rsID

EA

OA

EAF

Beta

P

Beta

P

Beta

SE

P value

Nearby genes

Spine BMD

1p31.3

rs2566752

C

T

0.38

0.28

2.3E-5

0.14

1.3E-6

0.16

0.03

3.4E-9

WLS

4q28.1

rs4423886

C

T

0.19

−0.17

0.07

−0.22

4.6E-7

−0.21

0.04

2.5E-7

FAT4

6q25.1

rs1038304

G

A

0.51

−0.21

8.3E-4

−0.12

1.8E-5

−0.13

0.03

1.8E-7

CCDC170/ESR1

7p22.1

rs188966536

T

G

0.02

1.21

1.8E-6

0.51

1.6E-4

0.67

0.12

7.8E-8

CCZ1B

8q13.1

rs76115211

A

T

0.07

−0.30

0.04

−0.35

7.9E-7

−0.34

0.07

3.0E-7

LINC00251

10q22.3

rs114936111

A

G

0.22

0.29

3.0E-4

0.14

4.1E-5

0.16

0.03

3.6E-7

KCNMA1

Femoral Neck BMD

2p12

rs12998155

C

T

0.45

−0.15

6.7E-3

−0.13

8.0E-7

−0.13

0.02

5.4E-8

CTNNA2

4p13

rs17885864

T

G

0.03

−0.56

1.6E-3

−0.35

4.2E-6

−0.38

0.07

1.3E-7

PHOX2B

6q21

rs117359272

G

C

0.02

0.55

5.8E-3

0.38

1.6E-5

0.41

0.08

4.6E-7

LINC00222

10p11.23

rs73245065

G

C

0.02

−0.70

1.0E-4

−0.32

1.4E-5

−0.37

0.07

6.9E-8

LYZL2

11q22.1

rs10893396

C

G

0.17

0.17

0.02

0.14

5.9E-6

0.15

0.03

4.1E-7

CNTN5

12q21.33

rs191780267

C

T

0.01

0.69

0.02

0.57

4.7E-6

0.59

0.11

4.1E-7

LOC728084

Total Hip BMD

5q13.1

rs78935958

G

T

0.06

−0.38

2.8E-3

−0.24

6.1E-6

−0.26

0.05

1.9E-7

LOC101928858/PIK3R1

6q21

rs117359272

G

C

0.02

0.56

1.9E-3

0.35

2.9E-5

0.39

0.08

3.6E-7

LINC00222

9q22.31

rs1907805

T

C

0.04

0.21

0.18

0.33

2.5E-7

0.31

0.06

2.9E-7

ROR2

  1. Only the maximally associated variant from each locus is shown. EA effect allele, OA other allele, EAF effect allele frequency, SE standard error