Table 2 Sentinel loci from primary ancestry- and sex-specific GWAS

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

q value

rs35609938

EUR male

2

58,756,729

T

C

0.501

0.95 [0.93–0.96]

5.840 × 10−12

VRK2

FANCL–[]

1.39 × 10−4

rs1040225

EUR male

2

58,139,593

G

A

0.598

1.05 [1.04–1.07]

1.820 × 10−11

VRK2

[VRK2]

1.39 × 10−4

rs34394051

EUR male

1

6,853,091

G

A

0.157

1.07 [1.04–1.09]

1.510 × 10−9

CAMTA1

[CAMTA1]

0.001

rs545889942*

EUR male

2

104,116,510

I

D

0.445

1.05 [1.03–1.06]

5.070 × 10−9

NA

TMEM182–[]

0.003

rs72664949

EUR male

13

109,280,508

G

A

0.245

1.06 [1.04–1.07]

7.420 × 10−9

MYO16

[MYO16]

0.003

rs10850379

EUR male

12

110,002,777

T

C

0.445

1.04 [1.03–1.06]

1.770 × 10−8

MMAB

[MMAB]

0.006

rs62337988

EUR male

5

12,031,700

T

A

0.317

1.05 [1.03–1.07]

2.040 × 10−8

CTNND2

CTNND2–[]

0.007

rs11353659

EUR male

15

48,059,138

I

D

0.637

0.96 [0.94–0.97]

2.560 × 10−8

SEMA6D

[SEMA6D]

0.008

rs58120907

EUR male

13

110,413,514

G

A

0.666

0.96 [0.94–0.97]

4.810 × 10−8

IRS2

[IRS2]

0.013

rs558002155

EUR male

8

121,159,409

G

A

0.999

3.51 [2.09–5.89]

4.990 × 10−8

COL14A1

[COL14A1]

0.013

rs13107325

EUR female

4

103,188,709

T

C

0.0813

1.12 [1.09–1.15]

3.810 × 10−16

SLC39A8

[SLC39A8]

7.12 × 10−8

rs572319557*

EUR female

18

50,846,441

I

D

0.551

1.05 [1.03–1.06]

2.950 × 10−10

DCC

[DCC]

3.46 × 10−4

rs3801279*

EUR female

7

104,904,868

T

C

0.52

0.96 [0.94–0.97]

3.030 × 10−9

SRPK2

[SRPK2]

0.002

15:29934686

EUR female

15

29,934,686

T

C

7.37 × 10−4

0.23 [0.13–0.42]

7.530 × 10−9

NA

FAM189A1–[]–TJP1

0.003

rs535503154

EUR female

5

151,965,756

I

D

0.271

0.95 [0.94–0.97]

2.780 × 10−8

NMUR2

NMUR2–[]–GRIA1

0.009

rs968163

EUR female

20

51,037,935

G

A

0.258

0.95 [0.94–0.97]

3.810 × 10−8

TSHZ2

ZFP64–[]–TSHZ2

0.012

rs529593131

EUR female

17

68,255,397

T

C

2.81 × 10−4

0.04 [0.01–0.23]

3.840 × 10−8

NA

KCNJ2–[]

0.012

rs779897701

EUR female

4

12,449,797

G

C

3.63 × 10−4

0.10 [0.03–0.35]

4.050 × 10−8

NA

[]–RAB28

0.012

rs62252182

EUR female

3

69,881,433

G

A

0.206

1.05 [1.03–1.07]

4.510 × 10−8

MITF

[MITF]

0.013

rs192857772

AFR male

22

37,824,152

G

A

0.998

0.16 [0.09–0.30]

2.240 × 10−8

CYTH4

ELFN2[]–MFNG

0.008

rs7333000

AFR male

13

26,535,079

G

A

0.915

1.40 [1.24–1.59]

4.290 × 10−8

SHISA2

[ATP8A2]

0.012

rs541395135

AFR male

12

80,825,417

I

D

0.945

0.65 [0.56–0.76]

4.360 × 10−8

PTPRQ

[PTPRQ]

0.013

rs35713684

AMR female

10

109,112,494

G

A

0.993

2.23 [1.62–3.06]

4.580 × 10−8

SORCS1

SORCS1–[]

0.013

rs556601931

AMR male

13

41,980,338

T

C

6.76 × 10−4

6.84 [3.65–12.84]

2.240 × 10−8

RGCC

NAA16–[]–RGCC

0.008

  1. The functional gene(s) represents the variant-to-gene predicted by the Open Targets V2G pipeline (see Methods for details). NA (not available) 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. The q value represents the false discovery rate-adjusted P value when correcting for all autosomal and X chromosome variants in the eight ancestry-specific and sex-specific GWAS. ‘*’ denotes sentinel variants that were within SNP windows for loci previously associated with sex (see ref. 38). The ‘Study’ column represents ancestry-specific and sex-specific GWAS; 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.
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