Table 3 Sentinel loci from secondary sex-combined, ancestry-specific meta-analysis

From: Large-scale genome-wide analyses of stuttering

rsID

Study

Chr

pos_b37

EA

NEA

EAF

OR [95% CI]

P value

Functional gene(s)

Location

P value heterogeneity

rs13107325

Sex-combined EUR

4

103,188,709

T

C

0.0826

1.09 [1.07–1.12]

1.150 × 10−19

SLC39A8

[SLC39A8]

0.036

rs72808425

Sex-combined EUR

2

58,124,453

T

C

0.7027

0.96 [0.95–0.97]

1.250 × 10−12

VRK2

[]-VRK2

0.273

rs12035477

Sex-combined EUR

1

6,906,171

G

C

0.1567

0.95 [0.94–0.96]

2.160 × 10−12

CAMTA1

[CAMTA1]

0.176

rs11895946

Sex-combined EUR

2

141,004,513

T

C

0.6667

0.96 [0.95–0.97]

2.930 × 10−11

LRP1B

[LRP1B]

0.844

rs12040559

Sex-combined EUR

1

96,337,925

T

G

0.9010

1.06 [1.04–1.08]

5.650 × 10−11

PTBP2

RWDD3–[]–PTBP2

0.870

rs34749698

Sex-combined EUR

11

88,799,731

T

C

0.7464

0.96 [0.95–0.97]

1.940 × 10−10

GRM5

GRM5 []–TYR

0.754

rs4331897

Sex-combined EUR

5

12,019,375

G

A

0.3161

0.96 [0.95–0.97]

3.940 × 10−10

CTNND2

CTNND2–[]

0.159

rs11264408

Sex-combined EUR

1

153,765,007

G

A

0.3712

1.04 [1.03–1.05]

4.420 × 10−10

CREB3L4

[GATAB2D]

0.601

rs11353659*

Sex-combined EUR

15

48,059,138

I

D

0.6374

1.04 [1.02–1.05]

6.770 × 10−10

SEMA6D

[SEMA6D]

0.119

rs6606725

Sex-combined EUR

12

109,905,368

C

A

0.5432

1.03 [1.02–1.04]

2.080 × 10−9

KCTD10

[KCTD10]

0.114

rs10109510

Sex-combined EUR

8

64,882,069

T

C

0.6330

0.97 [0.96–0.98]

2.110 × 10−9

NA

YTHDF3–[]–BHLHE22

0.195

rs559830614

Sex-combined EUR

6

139,031,221

T

C

0.9999

0.25 [0.16–0.39]

2.330 × 10−9

NA

NHSL1-[]–CCDC28A

0.518

rs745532

Sex-combined EUR

9

33,927,325

G

A

0.6261

0.97 [0.96–0.98]

4.820 × 10−9

UBAP2

[UBAP2]

0.577

rs1836999

Sex-combined EUR

5

104,117,403

T

A

0.4733

1.03 [1.02–1.04]

6.060 × 10−9

NA

NUDT12–[]

0.705

rs147393141

Sex-combined EUR

15

100,368,551

T

C

0.0001

3.76 [2.41–5.88]

6.090 × 10−9

LYSMD4

LYSMD4–[]–ADAMTS17

0.009

rs59183769

Sex-combined EUR

17

67,505,113

G

A

0.9999

3.56 [2.31–5.47]

7.530 × 10−9

MAP2K6

[MAP2K6]

0.921

rs9384679

Sex-combined EUR

6

108,864,419

T

C

0.3715

0.97 [0.96–0.98]

9.430 × 10−9

ARMC2

AGFL1–[]-FOXO3

0.279

rs7139049

Sex-combined EUR

12

24,273,754

T

G

0.6771

0.97 [0.96–0.98]

9.460 × 10−9

SOX5

[SOX5]

0.196

rs8100340

Sex-combined EUR

19

36,999,682

T

C

0.2328

1.04 [1.02–1.05]

1.460 × 10−8

ZNF567

ZNF566-[] ZNF260

0.243

rs182518401

Sex-combined EUR

3

19,429,428

T

G

0.0001

3.93 [2.45–6.32]

1.470 × 10−8

KCNH8

[KCNH8]

0.105

rs537077603

Sex-combined EUR

9

84,321,488

I

D

0.4739

1.03 [1.02–1.04]

1.970 × 10−8

NA

TLE1-[]–SPATA31D4

0.195

rs11931307

Sex-combined EUR

4

62,241,650

T

C

0.2584

0.96 [0.95–0.98]

2.750 × 10−8

ADGRL3

[ADGRL3]

0.494

rs235426

Sex-combined EUR

8

133,813,884

G

A

0.3246

1.03 [1.02–1.05]

3.230 × 10−8

TMEM71

[PHF20L1]

0.293

rs11167732

Sex-combined EUR

5

154,970,396

G

A

0.6195

1.03 [1.02–1.04]

3.370 × 10−8

SGCD

KIF4AB–[]–SGCD

0.424

rs758717390

Sex-combined EUR

7

116,332,923

T

G

0.9997

0.45 [0.34–0.60]

3.760 × 10−8

MET

[MET]

0.023

5:115941955

Sex-combined EUR

5

115,941,955

T

C

0.0002

2.69 [1.89–3.84]

4.080 × 10−8

NA

SEMA6A–[]

0.512

rs35026344

Sex-combined EUR

10

95,466,614

I

D

0.4772

1.03 [1.02–1.04]

4.180 × 10−8

NA

FRA10AC1-[]–LGI1

0.623

rs112352911

Sex-combined EUR

7

104,985,287

I

D

0.4793

1.03 [1.02–1.05]

4.450 × 10−8

SRPK2

[SRPK2]

0.085

rs141986240

Sex-combined AMR

8

92,110,308

G

A

0.0016

0.38 [0.28–0.52]

1.360 × 10−9

LRRC69

OTUD6N-[]-LRRC69

0.912

rs146784668

Sex-combined AMR

4

20,903,635

G

A

0.9954

1.64 [1.38–1.95]

1.560 × 10−8

PACRGL

[KCNIP4]

0.944

rs559419877:GA

Sex-combined AMR

4

71,289,806

I

D

0.0035

0.51 [0.40–0.64]

1.590 × 10−8

NA

OPRPN-[]-MUC7

0.849

rs188750450

Sex-combined AMR

15

41,340,355

G

C

0.9992

2.71 [1.91–3.84]

2.010 × 10−8

NA

[INO80]

0.689

rs537943976

Sex-combined AMR

5

165,853,802

T

C

0.0010

2.51 [1.81–3.48]

2.890 × 10−8

NA

[]–TENM2

0.776

rs578220221

Sex-combined AMR

4

17,383,583

G

C

0.9994

4.53 [2.65–7.75]

3.590 × 10−8

CLRN2

[]–[QDPR]

0.741

rs556819764

Sex-combined AMR

16

87,027,400

T

C

0.0003

5.49 [2.99–10.07]

4.050 × 10−8

C16orf95

[]–C16orf95

0.833

rs140279480

Sex-combined EAS

4

123,158,809

T

C

0.0025

5.05 [2.83–9.00]

4.110 × 10−8

ADCY5

[ADCY5]

0.433

  1. The functional gene(s) represents the variant-to-gene predicted by the Open Targets V2G pipeline (see Methods for details). NA reported for variants in which Open Targets did not identify a gene. Base pair positions are listed according to human genome reference build 37. Dashes in the location column indicate distance, where [] is contained within the exons of the specified gene: () <1 kb; (-) <10 kb; (–) <100 kb; (—) <1,000 kb either upstream or downstream of the gene. ‘*’ denotes sentinel variants that were within SNP windows for loci previously associated with sex (see ref. 38). The ‘Study’ column represents sex-combined, ancestry-specific meta-analyses; all ancestries represent genetic ancestry. Chr, chromosome; pos_b37, position in build 37; EA, effect allele; NEA, non-effect allele; OR, odds ratio; I, insertion; D, deletion.
Back to article page