rs9349379

This is a intron variant variant in the PHACTR1 gene.

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GWAS Catalog Trait Associations (28)

Genome-wide significant associations (p < 5×10⁻⁸) from the NHGRI-EBI GWAS Catalog.

coronary artery disease

Aragam KG et al. “Discovery and systematic characterization of risk variants and genes for coronary artery disease in over a million participants.” Nature Genetics 54(12):1803-1815 (2022)

Allele A

OR 0.89

p 4.0e-114

N 1,165,690

Large GWAS

European, NR

Koskeridis F et al. “Multi-trait association analysis reveals shared genetic loci between Alzheimer's disease and cardiovascular traits.” Nature Communications 15(1):9827 (2024)

Allele A

OR 0.05

p 1.0e-47

N 640,258

Large GWAS

European, East Asian

van der Harst P et al. “Identification of 64 Novel Genetic Loci Provides an Expanded View on the Genetic Architecture of Coronary Artery Disease.” Circulation Research 122(3):433-443 (2018)

Allele A

OR 0.11

p 3.0e-76

N 547,261

Large GWAS

Zhou W et al. “Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies.” Nature Genetics 50(9):1335-1341 (2018)

Allele A

OR —

p 6.0e-19

N 408,458

Large GWAS

European

Verma A et al. “Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.” Science (new York, N.y.) 385(6706):eadj1182 (2024)

Allele A

OR 0.09

p 8.0e-35

N 404,034

Major Consortium StudyLarge GWAS

multi-ancestry

Nikpay M et al. “A comprehensive 1,000 Genomes-based genome-wide association meta-analysis of coronary artery disease.” Nature Genetics 47(10):1121-1130 (2015)

Allele A

OR 1.14

p 2.0e-42

N 187,599

Meta-analysisLarge GWAS

multi-ancestry

Klarin D et al. “Genetic analysis in UK Biobank links insulin resistance and transendothelial migration pathways to coronary artery disease.” Nature Genetics 49(9):1392-1397 (2017)

Allele A

OR 1.15

p 3.0e-11

N 120,286

Major Consortium StudyLarge GWAS

multi-ancestry

Nelson CP et al. “Association analyses based on false discovery rate implicate new loci for coronary artery disease.” Nature Genetics 49(9):1385-1391 (2017)

Allele A

OR 1.11

p 1.0e-35

N 63,731

Large GWAS

European, NR

Lu X et al. “Genome-wide association study in Han Chinese identifies four new susceptibility loci for coronary artery disease.” Nature Genetics 44(8):890-4 (2012)

Allele A

OR 1.15

p 2.0e-9

N 6,534

Large GWAS

East Asian

Saw J et al. “Chromosome 1q21.2 and additional loci influence risk of spontaneous coronary artery dissection and myocardial infarction.” Nature Communications 11(1):4432 (2020)

Allele A

OR 0.40

p 4.0e-8

N 5,529

Large GWAS

East Asian, European

Hager J et al. “Genome-wide association study in a Lebanese cohort confirms PHACTR1 as a major determinant of coronary artery stenosis.” Plos One 7(6):e38663 (2012)

Allele A

OR 1.34

p 8.0e-10

N 1,949

Large GWAS

Greater Middle Eastern (Middle Eastern, North African or Persian)

coronary atherosclerosis

Verma A et al. “Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.” Science (new York, N.y.) 385(6706):eadj1182 (2024)

Allele A

OR 0.09

p 2.0e-96

N 424,341

Major Consortium StudyLarge GWAS

European

heart disease

Verma A et al. “Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.” Science (new York, N.y.) 385(6706):eadj1182 (2024)

Allele A

OR 0.10

p 5.0e-73

N 429,794

Major Consortium StudyLarge GWAS

European

myocardial infarction

Sakaue S et al. “A cross-population atlas of genetic associations for 220 human phenotypes.” Nature Genetics 53(10):1415-1424 (2021)

Allele G

OR 0.15

p 4.0e-63

N 623,029

Large GWAS

multi-ancestry

Hartiala JA et al. “Genome-wide analysis identifies novel susceptibility loci for myocardial infarction.” European Heart Journal 42(9):919-933 (2021)

Allele G

OR 1.13

p 1.0e-27

N 471,717

Large GWAS

European

Verma A et al. “Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.” Science (new York, N.y.) 385(6706):eadj1182 (2024)

Allele G

OR 0.10

p 1.0e-32

N 404,034

Major Consortium StudyLarge GWAS

multi-ancestry

Loya H et al. “A scalable variational inference approach for increased mixed-model association power.” Nature Genetics 57(2):461-468 (2025)

Allele G

OR 0.13

p 2.0e-20

N 394,626

Large GWAS

European

Nikpay M et al. “A comprehensive 1,000 Genomes-based genome-wide association meta-analysis of coronary artery disease.” Nature Genetics 47(10):1121-1130 (2015)

Allele G

OR 1.14

p 9.0e-35

N 166,459

Meta-analysisLarge GWAS

multi-ancestry

migraine disorder

Hautakangas H et al. “Genome-wide analysis of 102,084 migraine cases identifies 123 risk loci and subtype-specific risk alleles.” Nature Genetics 54(2):152-160 (2022)

Allele A

OR 1.08

p 1.0e-47

N 873,341

Large GWAS

European

Choquet H et al. “New and sex-specific migraine susceptibility loci identified from a multiethnic genome-wide meta-analysis.” Communications Biology 4(1):864 (2021)

Allele A

OR 0.92

p 3.0e-18

N 554,569

Meta-analysisLarge GWAS

multi-ancestry

Verma A et al. “Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.” Science (new York, N.y.) 385(6706):eadj1182 (2024)

Allele A

OR 0.06

p 3.0e-12

N 437,667

Major Consortium StudyLarge GWAS

European

Loya H et al. “A scalable variational inference approach for increased mixed-model association power.” Nature Genetics 57(2):461-468 (2025)

Allele A

OR 0.10

p 2.0e-16

N 394,626

Large GWAS

European

Gormley P et al. “Meta-analysis of 375,000 individuals identifies 38 susceptibility loci for migraine.” Nature Genetics 48(8):856-66 (2016)

Allele A

OR 1.08

p 6.0e-22

N 375,752

Meta-analysisLarge GWAS

European

pulse pressure measurement

Keaton JM et al. “Genome-wide analysis in over 1 million individuals of European ancestry yields improved polygenic risk scores for blood pressure traits.” Nature Genetics 56(5):778-791 (2024)

Allele G

OR 0.25

p 2.0e-44

N 1,028,980

Large GWAS

multi-ancestry

Plotnikov D et al. “High Blood Pressure and Intraocular Pressure: A Mendelian Randomization Study.” Investigative Ophthalmology & Visual Science 63(6):29 (2022)

Allele G

OR 0.24

p 4.0e-20

N 526,001

Large GWAS

European

Sakaue S et al. “A cross-population atlas of genetic associations for 220 human phenotypes.” Nature Genetics 53(10):1415-1424 (2021)

Allele G

OR 0.02

p 7.0e-22

N 506,308

Large GWAS

multi-ancestry

Giri A et al. “Trans-ethnic association study of blood pressure determinants in over 750,000 individuals.” Nature Genetics 51(1):51-62 (2019)

Allele G

OR 0.24

p 2.0e-20

N 459,777

Large GWAS

multi-ancestry

Yang ML et al. “Sex-specific genetic architecture of blood pressure.” Nature Medicine 30(3):818-828 (2024)

Allele G

OR 0.02

p 2.0e-22

N 349,328

Large GWAS

multi-ancestry

Hoffmann TJ et al. “Genome-wide association analyses using electronic health records identify new loci influencing blood pressure variation.” Nature Genetics 49(1):54-64 (2017)

Allele G

OR 0.20

p 6.0e-13

N 321,262

Large GWAS

multi-ancestry

Surendran P et al. “Trans-ancestry meta-analyses identify rare and common variants associated with blood pressure and hypertension.” Nature Genetics 48(10):1151-1161 (2016)

Allele G

OR 0.17

p 5.0e-8

N 192,763

Large GWAS

multi-ancestry

spontaneous coronary artery dissection

Adlam D et al. “Genome-wide association meta-analysis of spontaneous coronary artery dissection identifies risk variants and genes related to artery integrity and tissue-mediated coagulation.” Nature Genetics 55(6):964-972 (2023)

Allele A

OR 1.64

p 3.0e-32

N 11,209

Meta-analysisLarge GWAS

European

Turley TN et al. “Identification of Susceptibility Loci for Spontaneous Coronary Artery Dissection.” Jama Cardiology 5(8):929-938 (2020)

Allele A

OR 1.71

p 5.0e-14

N 1,961

Large GWAS

European

coronary artery calcification

Kavousi M et al. “Multi-ancestry genome-wide study identifies effector genes and druggable pathways for coronary artery calcification.” Nature Genetics 55(10):1651-1664 (2023)

Allele A

OR 0.22

p 6.0e-29

N 36,720

Large GWAS

multi-ancestry

Gummesson A et al. “A genome-wide association study of imaging-defined atherosclerosis.” Nature Communications 16(1):2266 (2025)

Allele A

OR 0.06

p 3.0e-21

N 26,000

Large GWAS

European

O'Donnell CJ et al. “Genome-wide association study for coronary artery calcification with follow-up in myocardial infarction.” Circulation 124(25):2855-64 (2011)

Allele A

OR 0.20

p 4.0e-22

N 9,961

Large GWAS

European

Pechlivanis S et al. “Risk loci for coronary artery calcification replicated at 9p21 and 6q24 in the Heinz Nixdorf Recall Study.” Bmc Medical Genetics 14:23 (2013)

Allele A

OR 0.30

p 5.0e-11

N 4,329

Large GWAS

European

cardiovascular disease biomarker measurement

Gummesson A et al. “A genome-wide association study of imaging-defined atherosclerosis.” Nature Communications 16(1):2266 (2025)

Allele G

OR 0.18

p 4.0e-21

N 24,811

Large GWAS

European

Antimigraine preparation use measurement

Sakaue S et al. “A cross-population atlas of genetic associations for 220 human phenotypes.” Nature Genetics 53(10):1415-1424 (2021)

Allele G

OR 0.18

p 2.0e-20

N 298,570

Large GWAS

multi-ancestry

Wu Y et al. “Genome-wide association study of medication-use and associated disease in the UK Biobank.” Nature Communications 10(1):1891 (2019)

Allele G

OR 0.18

p 5.0e-20

N 119,844

Major Consortium StudyLarge GWAS

European

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ClinVar annotation

Benign★☆☆☆

1 submitter

View on ClinVar →

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Research that mentions this SNP (2)

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Using a Genetic Risk Score Approach to Predict Headache Response to Triptans in Migraine Without Aura

AssociationN=172Sarah Cargnin et al.(2019)· The Journal of Clinical Pharmacology

A genetic risk score combining risk alleles at TRPM8 rs6724624 and FGF6 rs1024905 was inversely associated with inconsistent response to triptans in 172 migraine without aura (MwoA) patients (OR 0.62, 95% CI 0.43-0.89, FDR q=0.045). Adding this 2-SNP genetic risk score to a triptan-adjusted model significantly improved discrimination accuracy from AUC 0.57 to 0.64 (P=0.037), suggesting potential utility for predicting poor triptan responders.

Traits studied:Migraine without auraTriptan response

PubMed DOI Metascience Observatory

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Genome‐wide association scan of quantitative traits for attention deficit hyperactivity disorder identifies novel associations and confirms candidate gene associations

AssociationN=3,067Jessica Lasky‐Su et al.(2008)· American Journal of Medical Genetics Part B: Neuropsychiatric Genetics

Familial analysis of 1040 individuals from 155 migraine families identified an increased burden of rare variants in regulatory regions near known migraine risk loci, independent of common variants. Four regulatory regions showed significant associations with migraine: a CpG island near PHACTR1 (OR=1.54, p=5.3×10⁻¹⁵) and three polycomb response elements near KCNK5 (OR=1.24, p=0.014), ASTN2 (OR=1.5, p=0.017), and RNF213 (OR=1.12, p=9.3×10⁻⁵). Findings were replicated in an independent case-control cohort of 2027 migraineurs and 1650 controls.

Traits studied:MigraineMigraine with aura

PubMed DOI Metascience Observatory

About PHACTR1

The protein encoded by this gene is a member of the phosphatase and actin regulator family of proteins. This family member can bind actin and regulate the reorganization of the actin cytoskeleton. It plays a role in tubule formation and in endothelial cell survival. Polymorphisms in this gene are associated with susceptibility to myocardial infarction, coronary artery disease and cervical artery dissection. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Apr 2016]

rs9349379

GWAS Catalog Trait Associations (28)

coronary artery disease

coronary atherosclerosis

heart disease

myocardial infarction

migraine disorder

pulse pressure measurement

spontaneous coronary artery dissection

coronary artery calcification

cardiovascular disease biomarker measurement

Antimigraine preparation use measurement

ClinVar annotation

Research that mentions this SNP (2)

About PHACTR1

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