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. Author manuscript; available in PMC: 2017 Mar 1.
Published in final edited form as: Nat Genet. 2016 Jun 20;48(8):856–866. doi: 10.1038/ng.3598

Table 2.

Summary of the 38 genomic loci associated with the prevalent types of migraine. Ten loci were previously reported (PubMed IDs listed) and 28 are newly found in this study. Each locus is labeled with protein coding genes that overlap the region. Intergenic loci are also labeled with the prefix “near” to highlight the additional uncertainty in identifying relevant genes. Effect sizes and P-values for each SNP were calculated for each study with an additive genetic model using logistic regression adjusted for sex and then combined in a fixed-effects meta-analysis. For loci that contain a secondary LD-independent signal passing genome-wide significance, the secondary index SNP and P-value is given. For the seven loci reaching genome-wide significance in the migraine without aura sub-type analysis, the corresponding index SNP and P-value are also given. Evidence for significant heterogeneity was found at four loci (TRPM8/HJURP, MRVI1, near ZCCHC14, and near CCM2L/HCK) so for those we present the results of a random-effects model.

Locus
Rank		 Locus Chr Index SNP Minor
Allele		 MAF All Migraine Secondary signal Migraine without aura Previous
Publication
PMID
OR [95% CI] P Index SNP P Index SNP P
1 LRP1/STAT6/SDR9C7 12 rs11172113 C 0.42 0.90 [0.89–0.91] 5.6 × 10−49 rs11172055 1.3 × 10−09 rs11172113 4.3 × 10−16 21666692
2 PRDM16 1 rs10218452 G 0.22 1.11 [1.10–1.13] 5.3 × 10−38 rs12135062 3.7 × 10−10 - - 21666692
3 FHL5/UFL1 6 rs67338227 T 0.23 1.09 [1.08–1.11] 2.0 × 10−27 rs4839827 5.7 × 10−10 rs7775721 1.1 × 10−12 23793025
4 near TSPAN2/NGF 1 rs2078371 C 0.12 1.11 [1.09–1.13] 4.1 × 10−24 rs7544256 8.7 × 10−09 rs2078371 7.4 × 10−09 23793025
5 TRPM8/HJURP 2 rs10166942 C 0.20 0.94 [0.89–0.99] 1.0 × 10−23 rs566529 2.5 × 10−09 rs6724624 1.1 × 10−09 21666692
6 PHACTR1 6 rs9349379 G 0.41 0.93 [0.92–0.95] 5.8 × 10−22 - - rs9349379 2.1 × 10−09 22683712
7 MEF2D 1 rs1925950 G 0.35 1.07 [1.06–1.09] 9.1 × 10−22 - - - - 22683712
8 SLC24A3 20 rs4814864 C 0.26 1.07 [1.06–1.09] 2.2 × 10−19 - - - - -
9 near FGF6 12 rs1024905 G 0.47 1.06 [1.04–1.08] 2.1 × 10−17 - - rs1024905 2.5 × 10−09 -
10 C7orf10 7 rs186166891 T 0.11 1.09 [1.07–1.12] 9.7 × 10−16 - - - - 23793025
11 PLCE1 10 rs10786156 G 0.45 0.95 [0.94–0.96] 2.0 × 10−14 rs75473620 5.8 × 10−09 - - -
12 KCNK5 6 rs10456100 T 0.28 1.06 [1.04–1.07] 6.9 × 10−13 - - - - -
13 ASTN2 9 rs6478241 A 0.36 1.05 [1.04–1.07] 1.2 × 10−12 - - rs6478241 1.2 × 10−10 22683712
14 MRVI1 11 rs4910165 C 0.33 0.94 [0.91–0.98] 2.9 × 10−11 - - - - -
15 HPSE2 10 rs12260159 A 0.07 0.92 [0.89–0.94] 3.2 × 10−10 - - - - -
16 CFDP1 16 rs77505915 T 0.45 1.05 [1.03–1.06] 3.3 × 10−10 - - - - -
17 RNF213 17 rs17857135 C 0.17 1.06 [1.04–1.08] 5.2 × 10−10 - - - - -
18 NRP1 10 rs2506142 G 0.17 1.06 [1.04–1.07] 1.5 × 10−09 - - - - -
19 near GPR149 3 rs13078967 C 0.03 0.87 [0.83–0.91] 1.8 × 10−09 - - - - -
20 near JAG1 20 rs111404218 G 0.34 1.05 [1.03–1.07] 2.0 × 10−09 - - - - -
21 near REST/SPINK2 4 rs7684253 C 0.45 0.96 [0.94–0.97] 2.5 × 10−09 - - - - -
22 near ZCCHC14 16 rs4081947 G 0.34 1.03 [1.00–1.06] 2.5 × 10−09 - - - - -
23 HEY2/NCOA7 6 rs1268083 C 0.48 0.96 [0.95–0.97] 5.3 × 10−09 - - - - -
24 near WSCD1/NLRP1 17 rs75213074 T 0.03 0.89 [0.86–0.93] 7.1 × 10−09 - - - - -
25 near GJA1 6 rs28455731 T 0.16 1.06 [1.04–1.08] 7.3 × 10−09 - - - - -
26 near TGFBR2 3 rs6791480 T 0.31 1.04 [1.03–1.06] 7.8 × 10−09 - - - - 22683712
27 near ITPK1 14 rs11624776 C 0.31 0.96 [0.94–0.97] 7.9 × 10−09 - - - - -
28 near ADAMTSL4/ECM1 1 rs6693567 C 0.27 1.05 [1.03–1.06] 1.2 × 10−08 - - - - -
29 near CCM2L/HCK 20 rs144017103 T 0.02 0.85 [0.76–0.96] 1.2 × 10−08 - - - - -
30 YAP1 11 rs10895275 A 0.33 1.04 [1.03–1.06] 1.6 × 10−08 - - - - -
31 near MED14/USP9X X rs12845494 G 0.27 0.96 [0.95–0.97] 1.7 × 10−08 - - - - -
32 near DOCK4/IMMP2L 7 rs10155855 T 0.05 1.08 [1.05–1.12] 2.1 × 10−08 - - - - -
33 1p31.1* 1 rs1572668 G 0.48 1.04 [1.02–1.05] 2.1 × 10−08 - - - - -
34 CARF 2 rs138556413 T 0.03 0.88 [0.84–0.92] 2.3 × 10−08 - - - - -
35 ARMS2/HTRA1 10 rs2223089 C 0.08 0.93 [0.91–0.95] 3.0 × 10−08 - - - - -
36 IGSF9B 11 rs561561 T 0.12 0.94 [0.92–0.96] 3.4 × 10−08 - - - - -
37 MPPED2 11 rs11031122 C 0.24 1.04 [1.03–1.06] 3.5 × 10−08 - - - - -
38 near NOTCH4 6 rs140002913 A 0.06 0.91 [0.88–0.94] 3.8 × 10−08 - - - - -
*

The nearest coding gene (LRRIQ3) to this locus is 592kb away.