Table 1 Genome-wide significant loci in the discovery HUNT sample.

From: MEPE loss-of-function variant associates with decreased bone mineral density and increased fracture risk

rsID

Chromosome

Position (hg19)

Effect allele/non-effect allele

Annotation (candidate gene)

Effect allele frequency

Imputation quality (R2)

Effect sizea (SE)

Association test P-value

rs115242848

2

119507607

T/C

Intergenic (EN1)

0.011

0.966

0.387 (0.052)

6.9 × 10−14

rs4505759

4

1003022

T/C

Upstream (FGFRL1)

0.304

0.996

0.069 (0.012)

2.8 × 10−9

rs181831514

4

88822746

T/C

Intergenic (MEPE)

0.008

0.988

−0.533 (0.061)

2.1 × 10−18

rs7741021

6

127468274

C/A

Intronic (RSPO3)

0.474

0.998

0.068 (0.011)

2.0 × 10−10

rs4869742

6

151907748

T/C

Intronic (CCDC170)

0.273

0.992

−0.108 (0.012)

2.4 × 10−19

rs6973667

7

38152863

G/A

Intergenic (STARD3NL)

0.337

0.981

0.066 (0.011)

6.2 × 10−9

rs2707518

7

120954908

T/G

Intergenic (WNT16)

0.367

0.989

0.182 (0.011)

1.7 × 10−60

rs489247

11

86881641

G/A

Intronic (TMEM135)

0.258

0.997

−0.083 (0.012)

1.1 × 10−11

rs2147161

13

42982302

C/A

Intergenic (TNSFS11)

0.701

0.957

−0.091 (0.012)

1.2 × 10−14

rs76410205

17

41807508

T/C

Intergenic (SOST/DUSP3)

0.096

0.971

0.111 (0.018)

1.2 × 10−9

  1. This table shows the 10 genome-wide significant (P-value < 5 × 10−8) loci associated to ultradistal forearm bone mineral density (BMD) in the discovery dataset (N = 19,705). As all these are previously known loci, the candidate gene has been taken from the previous publications. The effect of a variant is presented with the SAIGE linear mixed model effect size (Effect size) and standard error (SE) and the significance using the uncorrected two tailed Z-test P-value.
  2. rsID reference SNP cluster ID, SE standard error of the effect estimate.
  3. aMeasured in SD units.
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