Table 1 Replicated GWAS signals associated with gut microbiota species

From: The HUNT study identifies host genetic factors reproducibly associated with human gut microbiota composition

Chr

BP (hg19)

RSID

REF

EA

Locus

  

Discovery

Replication

Meta-analysis

Novel locus

Outcome species

HUNT

(n = 12,652)

Swedish cohorts

(n = 16,017)

(n = 28,669)

Name

Prevalence

EAF

Beta

s.e.

Pvalue

EAF

Beta

s.e.

Pvalue

EAF

Beta

s.e.

Pvalue

Replicated signals

2

136616754

rs182549

C

T

LCT

Bifidobacterium adolescentis

97%

0.76

−0.14

0.02

1.3 × 10−14

0.72

−0.10

0.01

8.5 × 10−17

0.73

−0.11

0.01

3.8 × 10−29

No

6

32626348

rs28407950

C

T

HLA-DQB1

Agathobacter sp000434275

65%

0.27

0.09

0.01

9.8 × 10−11

0.29

0.05

0.01

1.2 × 10−7

0.28

0.06

0.01

6.3 × 10−16

Yes

7

100632790

rs4556017

C

T

MUC12

Coprobacillus cateniformis

33%

0.84

0.11

0.01

1.1 × 10−16

0.83

0.10

0.01

6.0 × 10−17

0.83

0.10

0.01

5.1 × 10−32

Yes

9

136142217

rs644234

T

G

ABO

Mediterraneibacter lactaris

73%

0.38

0.09

0.01

9.1 × 10−14

0.41

0.05

0.01

2.3 × 10−7

0.40

0.07

0.01

2.3 × 10−18

No

9

136146597

rs550057

C

T

ABO

Mediterraneibacter torques

90%

0.30

0.11

0.01

2.4 × 10−18

0.31

0.10

0.01

1.8 × 10−18

0.31

0.08

0.01

8.3 × 10−25

9

136146597

rs550057

C

T

ABO

UMGS1623 sp934647945

73%

0.30

0.11

0.01

1.9 × 10−17

0.31

0.07

0.01

3.7 × 10−10

0.31

0.11

0.01

5.4 × 10−35

9

136149229

rs505922

T

C

ABO

Bifidobacterium bifidum

51%

0.36

−0.09

0.01

7.7 × 10−15

0.40

−0.04

0.01

2.2 × 10−7

0.39

−0.06

0.01

1.5 × 10−18

11

124942269

rs73024305

G

C

SLC37A2

Dysosmobacter sp001916835

91%

0.08

0.19

0.02

1.4 × 10−16

0.06

0.07

0.02

9.5 × 10−4

0.07

0.13

0.02

1.2 × 10−15

Yes

19

49203829

rs35106244

C

T

FUT2

Mediterraneibacter faecis

93%

0.40

−0.08

0.01

5.0 × 10−11

0.40

−0.06

0.01

6.0 × 10−8

0.40

−0.07

0.01

6.0 × 10−17

No*

19

49215095

rs4002471

C

T

FUT2

Streptococcus gordonii

56%

0.48

0.07

0.01

8.3 × 10−11

0.49

0.04

0.01

4.5 × 10−5

0.49

0.05

0.01

2.4 × 10−13

19

49218060

rs35866622

C

T

FUT2

Enterocloster sp900753815

34%

0.43

0.07

0.01

5.9 × 10−12

0.43

0.05

0.01

8.8 × 10−9

0.43

0.06

0.01

9.8 × 10−19

19

49228272

rs2287921

T

C

FUT2

Clostridium sp900540255

31%

0.48

−0.07

0.01

1.7 × 10−13

0.49

−0.06

0.01

1.1 × 10−9

0.49

−0.06

0.01

2.3 × 10−21

Signal not replicated

5

528609

rs6880820

T

C

SLC9A3

Dysosmobacter excrementavium

40%

0.18

0.09

0.01

4.3 × 10−12

0.19

0.02

0.01

7.4 × 10−2

0.19

0.05

0.01

1.1 × 10−8

Not replicated

  1. Locus values were assigned by the Open Target Platform. Bold indicates the most significant SNP–species association in a locus. The prevalences for the outcome species are given for HUNT. Beta values in HUNT and the Swedish cohorts are given as standard deviation change of inverse rank transformed species per effect allele. P value represents the unadjusted P value from a two-sided z-test. Novel locus indicates a locus not previously shown to be reproducibly associated with any microbial species. BP, base pair; Chr, chromosome; EA, effect allele; EAF, effect allele frequency; REF, reference (non-effect) allele; s.e., standard error.
  2. *The FUT2 locus has been reported to pass the traditional genome-wide significance level (P < 5.0 × 10−8), but with no replication and not reaching study-wide significance in previous studies.
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