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. Author manuscript; available in PMC: 2017 Jun 1.
Published in final edited form as: Lancet Neurol. 2016 Apr 7;15(7):695–707. doi: 10.1016/S1474-4422(16)00102-2

Table 2.

Single nucleotide polymorphism associated with risk of stroke at p<5 × 10−6

Chromosome:
position* 		Function Gene Number
of
variants† 		Minor
allele		 Minor
allele
frequency		 Hazard ratio
(95% CI)		 p value‡ Direction§ Heterogeneity,
I2¶ 		Heterogeneity,
p value|| 		Imputation
quality**
All stroke
rs6433905 2:182138150 Intergenic UBE2E3 2 C 0·08 1·21 (1·12–1·31) 2·54 × 10−6 +++++++++++++++ 0 0·54 0·97
rs12204590 6:1337393 Intergenic FOXF2 6 A 0·21 1·14 (1·08–1·20) 2·17 × 10−6 ++++++++++++−+−++ 0 0·60 1·00
rs790919 6:154298875 Intergenic OPRM1 2 A 0·44 1·12 (1·07–1·17) 2·44 × 10−6 +++++++++++++−−++ 16·2 0·26 0·96
rs11788316 9:13445687 Intergenic MPDZ 4 T 0·28 1·13 (1·07–1·19) 2·49 × 10−6 ++−++++−−++++++−−+ 0 0·84 0·96
rs11627959 14:35160471 Intergenic CFL2 4 A 0·44 0·89 (0·85–0·93) 2·23 × 10−6 −−+−−−−−−+−−+−−−− 0 0·87 0·93
rs4899120 14:64335447 Intronic SYNE2 1 T 0·09 1·19 (1·11–1·29) 4·71 × 10−6 +++−++++++++−−++ 24 0·18 0·98
Ischaemic stroke
rs62262077 3:105014929 Intergenic ALCAM 5 A 0·27 1·17 (1·10–1·24) 6·04 × 10−7 −+++++++++++−+++ 19·2 0·23 0·94
rs10037362 5:31110857 Intergenic CDH6 2 A 0·07 1·27 (1·15–1·40) 4·41 × 10−6 −+−++++++++ 25·7 0·20 0·97
rs4448595 10:21666138 Intergenic C10orf114 8 G 0·16 0·83 (0·77–0·90) 2·50 × 10−6 −−−−−−−−+−−−−−−− 0 0·80 0·98
rs11833579 12:775199 Intergenic NINJ2 2 A 0·24 1·19 (1·12–1·27) 5·74 × 10−8 −+++−++++++−++++ 18·5 0·24 0·92
rs77858481 13:81142325 Intergenic SPRY2 1 G 0·06 1·38 (1·22–1·55) 2·32 × 10−7 ++++++++ 0 0·97 0·83
Cardioembolic ischaemic stroke
rs4284256 1:157675273 Intergenic FCRL3 1 T 0·18 1·41 (1·22–1·64) 3·13 × 10−6 −+++++ 66·5 0·01 0·96
rs12646447 4:111699326 Intergenic PITX2 102 C 0·12 1·53 (1·31–1·80) 1·92 × 10−7 ++++++ 0 0·44 0·99
rs72184 5:123754837 Intergenic ZNF608 1 G 0·43 1·30 (1·17–1·46) 2·29 × 10−6 +++++++++ 9·1 0·6 0·90
rs72794386 5:127479278 Intronic SLC12A2 22 T 0·10 1·67 (1·39–2·00) 4·37 × 10−8 +++++ 0 0·87 0·97
rs1428155 5:151281633 Intronic GLRA1 2 C 0·38 1·28 (1·16–1·43) 3·10 × 10−6 +++++++++ 36·2 0·13 1·00
rs7771564 6:22504092 Intergenic HDGFL1 4 G 0·10 1·53 (1·28–1·82) 2·10 × 10−6 ++++++ 0 0·67 0·99
rs1495081 8:15314955 Intergenic TUSC3 1 C 0·14 1·48 (1·25–1·74) 3·09 × 10−6 ++−+++ 49·9 0·08 0·88
rs2393938 10:44063812 UTR5 ZNF239 1 C 0·12 1·45 (1·24–1·70) 3·47 × 10−6 ++++++ 0 0·51 0·99
rs11021485 11:95968208 Intronic MAML2 1 A 0·12 1·60 (1·32–1·94) 1·24 × 10−6 +++++ 30·5 0·22 0·82
rs710009 14:59184500 Intergenic DACT1 4 G 0·16 1·41 (1·22–1·64) 3·62 × 10−6 +++++++ 0 0·84 0·98
Non-cardioembolic ischaemic stroke
rs77744591 13:81142325 Intergenic SPRY2 1 T 0·08 1·34 (1·18–1·51) 3·44 × 10−6 +++++−+ 0 0·97 0·93

Only associations with the lead single nucleotide polymorphism in each locus are shown, and full set of genetic associations at p<5×10−6 is presented in the appendix (pp 48–54). All results are presented with respect to the minor allele as coded allele. UTR57

*

Chromosome positions with respect to National Center for Biotechnology Information Build 37 data.

†

Number of variants reaching p<5×10−6 in the locus.

‡

p value after genomic control.

§

Direction refers to direction of effect size with respect to the minor allele in each study contributing to the meta-analysis (in alphabetic order), “+” sign refers to positive values of betas and “−” sign referes to negative values of betas with respect to the minor allele.

Heterogeneity (I2) ranges between 0 and 100, with higher values suggesting more heterogeneity.

||

p value for heterogeneity was calculated with the Cochran’s Q test.

**

Mean value of imputation quality across studies.