Table 2 Replicated GWAS signals associated with KEGG functionality modules

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

Chr

BP (hg19)

RSID

Module

Name

REF

EA

Locus

Discovery

Replication

Meta-analyses

HUNT

(n = 12,652)

Swedish cohorts

(n = 16,017)

Discovery + Replication (n = 28,669)

EAF

Beta

s.e.

P value

EAF

Beta

s.e.

P value

EAF

Beta

s.e.

P value

Replicated signals

2

136608646

rs4988235

M00443

SenX3-RegX3 (phosphate starvation response) two-component regulatory system

G

A

LCT

0.76

−0.16

0.02

2.6 × 10−18

0.72

−0.12

0.01

4.8 × 10−21

0.73

−0.13

0.01

5.5 × 10−37

2

136608646

rs4988235

M00233

Glutamate transport system

G

A

LCT

0.76

−0.16

0.02

3.1 × 10−18

0.72

−0.12

0.01

1.4 × 10−21

0.73

−0.13

0.01

2.7 × 10−37

2

136616754

rs182549

M00244

Putative zinc/manganese transport system

C

T

LCT

0.76

−0.15

0.02

4.0 × 10−15

0.72

−0.12

0.01

3.3 × 10−20

0.73

−0.13

0.01

3.3 × 10−33

2

136616754

rs182549

M00168

CAM (crassulacean acid metabolism), dark

C

T

LCT

0.76

−0.13

0.02

2.7 × 10−11

0.72

−0.09

0.01

3.8 × 10−13

0.73

−0.10

0.01

2.0 × 10−22

9

136155000

rs635634

M00228

Putative glutamine transport system

C

T

ABO

0.21

0.10

0.02

1.3 × 10−10

0.22

0.05

0.01

6.8 × 10−5

0.22

0.07

0.01

6.3 × 10−13

19

49218060

rs35866622

M00719

Ihk-Irr (virulence regulation) two-component regulatory system

C

T

FUT2

0.43

0.07

0.01

1.2 × 10−10

0.43

0.03

0.01

2.0 × 10−3

0.43

0.05

0.01

6.1 × 10−11

Signals not replicated

8

11630429

rs804264

M00518

GlnK-GlnL (glutamine utilization) two-component regulatory system

C

A

NEIL2

0.44

−0.08

0.01

6.1 × 10−11

0.44

−0.02

0.01

2.2 × 10−2

0.44

−0.05

0.01

2.1 × 10−9

8

11625235

rs804273

M00747

Bacitracin transport system

G

C

NEIL2

0.52

−0.08

0.01

1.0 × 10−10

0.53

−0.03

0.01

8.2 × 10−3

0.52

−0.05

0.01

5.0 × 10−10

  1. BP, base pair; Chr, chromosome; EA, effect allele; EAF, effect allele frequency; REF, reference (non-effect) allele. Beta values are given as standard deviation of inverse rank-transformed KEGG functionality module per effect allele. P value represent unadjusted P value from a two-sided z-test
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