Table 2 Top metabolite genetic association signals at 47 novel variants with MAF>10-fold greater in METSIM than in gnomAD v3.1 non-Finnish Europeans.

From: Genome-wide association studies of metabolites in Finnish men identify disease-relevant loci

Biochemical name

rsID

MAF(%)

MAFNFE(%)

RMAF

β

P

Gene

X – 17676

rs200711248

0.321

0.009

34.5

1.18

5.40E−11

–

Uracil

rs1254152519

0.613

0.002

395.2

1.33

5.39E−28

DPYD

palmitoyl dihydrosphingomyelin (d18:0/16:0)

rs752521494

0.190

0.000

∞

1.91

2.53E−14

DEGS1

X – 12127

rs189344406

0.302

0.006

48.7

−1.75

3.27E−14

–

Campesterol

rs1247627279

0.362

0.003

116.8

1.11

5.26E−11

ABCG5|ABCG8

Xanthurenate

rs199546957

0.151

0.000

∞

2.07

4.96E−18

KYNU

hydantoin-5-propionate

rs144419430

0.928

0.015

59.9

−0.76

2.16E−13

Unknown

Glycerate

rs192756070

2.917

0.022

134.5

−1.07

8.04E−85

SLC23A3

X – 15666

rs140758280

4.073

0.376

10.8

−0.42

1.40E−19

–

X – 24475

rs202158371

0.814

0.012

65.6

−0.91

9.61E−17

–

methyl glucopyranoside (alpha + beta)

rs186284085

1.370

0.008

176.7

0.69

9.41E−20

GBA3

X – 12844

rs200280202

1.436

0.034

42.1

−0.83

5.21E−26

–

N-acetylglucosaminylasparagine

rs561604250

0.668

0.008

86.3

0.97

1.16E−14

AGA

X – 24544

rs141884785

1.320

0.073

18.1

0.76

1.74E−22

–

Choline

rs200164783

2.634

0.136

19.3

0.70

2.32E−33

Unknown

Serine

rs1297328831

0.162

0.002

104.6

−1.64

6.82E−13

Unknown

N-acetylhistidine

rs146438324

0.946

0.057

16.5

1.51

1.71E−61

NAT16

Sulfate

rs138989506

1.910

0.029

64.9

−1.41

1.55E−99

SLC13A1

X – 26054

rs976212663

0.231

0.019

12.4

−2.08

3.52E−15

–

3-(3-amino-3-carboxypropyl)uridine

rs149926554

2.898

0.175

16.6

0.43

7.97E−14

Unknown

5-oxoproline

rs782359519

0.854

0.019

45.8

0.92

1.43E−24

OPLAH

alpha-ketoglutarate

rs191616586

3.113

0.195

15.9

−0.45

7.65E−17

Unknown

5-oxoproline

rs558946866

0.442

0.034

13.0

0.99

4.54E−15

OPLAH

3beta-hydroxy-5-cholestenoate

rs552968665

0.245

0.003

79.1

1.55

8.62E−16

Unknown

3-amino-2-piperidone

rs121965043

0.346

0.003

111.7

1.91

3.73E−35

OAT

Deoxycarnitine

rs1268699195

0.577

0.002

372.3

0.90

1.25E−12

Unknown

beta-citrylglutamate

rs182295429

4.615

0.064

72.6

0.52

3.73E−28

NAALAD2

Betaine

rs1358634021

0.093

0.005

20.0

2.43

1.56E−16

SLC6A12

Aspartate

rs1209353188

0.578

0.000

∞

0.91

9.92E−14

GNPTAB

Succinylcarnitine (C4-DC)

rs200127857

0.342

0.005

73.6

2.20

2.37E−45

LACTB

Succinylcarnitine (C4-DC)

rs200480788

0.104

0.005

22.4

2.40

3.96E−19

LACTB

5-hydroxylysine

rs201135688

4.513

0.447

10.1

0.39

6.83E−22

HYKK

X – 17676

rs185603444

1.983

0.184

10.8

−0.60

5.56E−16

–

Orotidine

rs201899452

0.143

0.002

92.3

−1.80

2.41E−13

NT5C

N-formylanthranilic acid

rs77585764

5.407

0.378

14.3

1.24

9.55E−218

AFMID

Sphingomyelin (d18:1/18:1, d18:2/18:0)

rs527480139

0.330

0.000

∞

−1.41

2.51E−19

CERS4

Glycosyl-N-stearoyl-sphingosine (d18:1/18:0)

rs1013893365

2.956

0.046

64.2

1.25

2.17E−106

CERS1

X – 11315

rs201742362

1.134

0.033

34.9

1.43

1.62E−61

–

2-O-methylascorbic acid

rs6267

5.778

0.142

40.6

−0.82

9.49E−108

COMT

2-O-methylascorbic acid

rs199637204

0.098

0.005

21.1

−1.87

1.49E−12

COMT

Gamma-tocopherol/beta-tocopherol

rs182488695

1.548

0.008

199.9

0.89

7.37E−33

SEC14L2

N6-succinyladenosine

rs8192461

1.175

0.073

16.1

1.12

9.38E−27

ADSL

N6-succinyladenosine

rs773404017

0.414

0.006

66.8

2.55

2.30E−44

ADSL

5-methyluridine (ribothymidine)

rs548223694

0.448

0.039

11.6

1.36

9.47E−27

TYMP

5-methyluridine (ribothymidine)

rs756647111

0.119

0.000

∞

2.04

2.35E−14

TYMP

2’-deoxyuridine

rs556167510

0.601

0.042

14.4

1.07

2.45E−14

TYMP

Tiglylcarnitine (C5:1-DC)

rs201378370

2.584

0.034

76.7

0.94

5.21E−122

HSD17B10

  1. Biochemical name: biochemical name of the metabolite. rsID: dbSNP variant ID. MAF, MAFNFE, and RMAF: minor allele frequency in METSIM, in gnomAD v3.1 non-Finnish Europeans, and their ratio. When the index variant is monomorphic in gnomAD v3.1 non-Finnish Europeans (n = 34,029), the ratio is labeled as infinite, ∞. β: effect size estimate from the metabolite-specific stepwise conditional association test. P: p-value of metabolite-specific stepwise conditional association test. Gene: the putative causal gene(s) nominated in the knowledge-based approach. Gene symbols are italic. For unnamed metabolites, the putative causal gene results are represented by "–". If no putative causal gene is nominated, it is labeled as “unknown”. If multiple putative causal genes are nominated, they are separated by a vertical bar.
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