Table 2 Variants identified in association with all migraine (M) or migraine proxy (BRH)

From: Rare variants with large effects provide functional insights into the pathology of migraine subtypes, with and without aura

Phenotypes

Locus

Position hg38

Variants

OA

EA

EAF (%)

Nearest genes

Variant annotation

OR (95% CI)

P

Pbonf

Phet

SNP previously reported at locus (r2 if correlated SNP)

M

1p36.32

3155918

rs10797381

T

A

22.7

PRDM16

Intron

1.094 (1.079, 1.109)

2.1 × 10−37

8.7 × 10−30

0.08

rs10218452 (1.0)a, rs2651899 (0.37)b

M

1p36.1

33302206

rs933718575

A

G

0.01

A3GALT2

Downstream

11.032 (5.11, 23.8)

9.7 × 10−10

0.020

 

–

M

1p34.3

37790755

rs71642605

T

C

25.3

MANEAL

Upstream

1.042 (1.028, 1.056)

1.1 × 10−9

0.023

0.89

–

M

1p34.2

42465863

rs11799356

G

A

34.2

PPCS

Downstream

1.039 (1.026, 1.052)

6.0 × 10−10

0.013

0.67

–

M

1p22.1

91731541

rs12070846

T

C

23.0

TGFBR3

Intron

1.044 (1.030, 1.058)

6.8 × 10−10

0.029

0.16

rs11165300 (0.88)a

M

1p13.2

115135325

rs12134493c

C

A

12.0

TSPAN2

TF-binding site

1.112 (1.092, 1,132)

1.7 × 10−30

7.2 × 10−23

0.03

rs2078371 (1.0)a, rs12134493b

M

1p13.2

115286692

rs6330c

G

A

46.7

NGF

Missense

1.035 (1.023–1.048)

2.1 × 10−8

0.041

0.06

–

M

1q21.1

150538184

rs6693567

T

C

26.0

ADAMSTL4

Regulatory region

1.044 (1.031, 1.058)

1.1 ×  10−10

0.0046

0.64

rs6693567a,b

M

1q22

156480948

rs1925950

A

G

36.0

MEF2D

Synonymous

1.047 (1.034, 1.059)

6.3 × 10−14

1.3 × 10−6

0.08

rs2274319(1.0)a, rs3790455(1.0)b

M

2q33.2

202901033

rs35212307

T

C

12.6

WDR12

Missense

0.949 (0.933, 0.966)

6.7 × 10−9

0.013

0.54

rs149163995 (0.99)b

M

2q37.1

233917239

rs1003540

A

G

19.4

TRPM8

Upstream

0.923 (0.910, 0.937)

3.3 × 10−26

6.9 × 10−19

0.50

rs10166942 (1.0)a

M

3p24.1

30424073

rs4955309

C

A

31.9

TGFBR2

Intergenic

1.042 (1.030, 1.055)

4.0 × 10−11

0.005

0.10

rs7371912 (0.91)a, rs7640543 (0.97)b

M

3p22.2

38894643

rs33985936

C

T

25.0

SCN11A

Missense

1.041 (1.027, 1.054)

3.4 × 10−9

0.0065

0.32

–

M

3q25.2

154572157

rs13078967

A

C

3.5

GPR149

Regulatory region

0.892 (0.862, 0.922)

1.6 × 10−11

0.00066

0.27

rs13078967a,b

M

4p15.1

35563301

rs74992952

G

A

17.9

ARAP2

Intergenic

0.949 (0.935, 0.963)

8.8 × 10−12

0.00037

0.45

rs73805934 (0.92)a

M

6p24.1

12903725

rs9349379

A

G

41.9

PHACTR1

3′ UTR

0.928 (0.917, 0.939)

1.9 × 10−35

3.9 × 10−28

0.43

rs9349379a,b

BRH

6p21.2

39280316

rs72854118

A

G

0.67

KCNK5

TF-binding site

0.697 (0.634, 0.766)

7.6 × 10−14

3.2 × 10−6

0.10

–

M

6q16.1

96610677

rs2273621

A

G

32.3

FHL5

Missense

1.082 (1.069, 1.096)

1.1 × 10−36

2.1 × 10−30

0.14

rs11153082 (0.99)a, rs11759769 (0.55)b

M

6q22.31

121487928

rs7743275

G

A

19.9

GJA1

Regulatory region

1.060 (1.044, 1.077)

9.7 × 10−14

1.2 × 10−5

0.17

rs28455731 (0.73)a,b

M

6q25.1

149721026

rs1359155039

TAAAAAAAA

TAAAAAAAAA

32.8

LATS1

Upstream

0.958 (0.945, 0.971)

8.1 × 10−10

0.017

0.38

rs9383843 (0.87)a

M

7p14.1

40367277

rs186166891

A

T

10.4

SUGCT

Intron

1.084 (1.062, 1.106)

1.1 × 10−14

1.4 × 10−6

0.40

rs10234636 (0.91)a, rs4379368 (0.91)b

BRH

9q21.11

69099647

rs34965002

G

A

43.3

FXN/TJP2

Regulatory region

1.056 (1.039, 1.072)

6.6 × 10−12

0.000277

0.19

rs7034179 (0.87)a

M

9q33.1

116479356

rs12684144d

T

C

22.3

ASTN2

Intron

1.055 (1.041, 1.070)

1.3 × 10−14

5.4 × 10−7

0.01

rs3891689(0.91)a, rs6478241 (0.57)b

M

10q23.33

94279840

rs2274224

G

C

41.5

PLCE1

Missense

0.959 (0.948, 0.970)

2.7 × 10−12

5.1 × 10−6

0.04

rs2274224a, rs11187838 (1.0)b

BRH

10q26.13

122470997

rs12252027

G

T

11.4

HTRA1

Intron

0.926 (0.904, 0.948)

1.2 × 10−10

0.0149

0.73

–

M

11p15.4

10652192

rs4909945

C

T

33.0

MRVI1

Missense

0.945 (0.934, 0.957)

3.1 × 10−19

5.9 × 10−13

0.61

rs4910165(1.0)a,b

M

12p13.32

4416380

rs7957385

G

A

48.6

FGF6

Intergenic

1.045 (1.033, 1.057)

8.2 × 10−14

1.0 ×  10−5

0.03

rs2160875(1.0)a, rs140668749 (1.0)b

M

12q13.3

57133500

rs11172113

T

C

42.3

LRP1

Intron

0.912 (0.901, 0.923)

1.8 × 10−53

7.4 × 10−46

0.42

rs11172113a,b

M

16p11.2

29813694

rs587778771

GC

GCC

0.05

PRRT2

Frameshift

3.038 (2.320, 3.977)

6.6 × 10−16

1.0 × 10−9

0.83

–

M

16q23.1

75289942

rs17685540

C

T

41.0

CFDP1

Downstream

1.037 (1.025, 1.049)

1.4 × 10−9

0.029

0.31

rs8046696 (0.98)a, rs77505915 (0.91)b

M

18q21.31

57494932

rs7233335

C

G

20.4

ONECUT2

Downstream

0.954 (0.941, 0.968)

1.8 × 10−10

0.0038

0.01

rs8087942 (0.45)a

M

20p11.23

19494370

rs3827986

G

A

24.5

SLC24A3

Intron

1.050 (1.036, 1.064)

4.6 × 10−13

1.9 × 10−5

0.52

rs4814864(1.0)a

M

21q22.11

34221526

rs28451064

G

A

13.6

MRPS6

Regulatory region

0.943 (0.927, 0.959)

1.8 × 10−11

0.00075

0.2

rs28451064a

M

22q12.2

30076759

rs5753008

T

C

35.6

HORMAD2

Upstream

1.039 (1.027, 1.051)

4.0 × 10−10

0.0084

0.5

–

  1. Effect allele frequency (EAF) is the average frequency of EA in the cohorts studied. OR and P value for inverse-variance-weighted meta-analysis of association results for all cohorts (Supplementary Table 1; Methods). Pbonf is the P value after a variant class-specific Bonferroni adjustment 21. Phet is the heterogeneity P value from a likelihood ratio test. Bold are variants that associate primarily with MO, not MA or VD, or with larger effects on MO than on MA or VD (Fig. 3).
  2. aSNPs previously reported in ref. 11.
  3. bSNPs previously reported in ref. 69.
  4. cResults presented are after adjusting for the respective effects of these uncorrelated (r2 = 0.02) variants at this locus. Results per cohort for all studied phenotypes are in Supplementary Tables 2–7.
  5. drs12684144-C confers protection against VD and risk against MO.
Back to article page