SNP Detail For rs2108622
1.Mapping Information
Human SNP ID rs2108622
Human chromosome chr19
Human SNP position 15879621
Pig chromosome chr2
Pig SNP position 61345248
2.Annotation Information
PubMed ID21729881
JournalHum Mol Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/21729881
StudyGenome-wide association study identifies common variants associated with circulating vitamin E levels.
Disease/TraitVitamin E levels
Initial sample2,402 European ancestry cases, 1612 European ancestry controls
Replication sample475 European ancestry cases, 517 European ancestry controls, 1,416 cases, 1,359 controls
Region19p13.12
Chromosome idchr19
Chromosome position15879621
Reported geneCYP4F2
Mapped geneCYP4F2
Upstream gene id
Downstream gene id
SNP gene ids8529
Upstream gene distance
Downstream gene distance
SNP risk allelers2108622-T
SNPsrs2108622
Merged0
SNP id current2108622
Contextmissense_variant
Intergenic0
Allele frequency0.21
P value0.0000000001
Pvalue mlog10
P value text
Or beta0.03
%95 Ci[0.01-0.05] unit increase
PlatformIllumina [NR]
CNVN
Mapped traitvitamin E measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004867
Study accessionGCST001142
PubMed ID19300499
JournalPLoS Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/19300499
StudyA genome-wide association study confirms VKORC1, CYP2C9, and CYP4F2 as principal genetic determinants of warfarin dose.
Disease/TraitWarfarin maintenance dose
Initial sample1,053 European ancestry individuals
Replication sample588 European ancestry individuals
Region19p13.12
Chromosome idchr19
Chromosome position15879621
Reported geneCYP4F2
Mapped geneCYP4F2
Upstream gene id
Downstream gene id
SNP gene ids8529
Upstream gene distance
Downstream gene distance
SNP risk allelers2108622-?
SNPsrs2108622
Merged0
SNP id current2108622
Contextmissense_variant
Intergenic0
Allele frequency0.24
P value0.0000000003
Pvalue mlog9.52287874528033
P value text
Or beta0.21
%95 Ci[0.14-0.27] mg/week increase
PlatformIllumina [325997]
CNVN
Mapped traitresponse to anticoagulant
Mapped trait URIhttp://purl.obolibrary.org/obo/GO_0061476
Study accessionGCST000360
PubMed ID19578179
JournalHum Mol Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/19578179
StudyA genome-wide association study of acenocoumarol maintenance dosage.
Disease/TraitAcenocoumarol maintenance dosage
Initial sample1,451 European ancestry individuals
Replication sample287 individuals
Region19p13.12
Chromosome idchr19
Chromosome position15879621
Reported geneCYP4F2
Mapped geneCYP4F2
Upstream gene id
Downstream gene id
SNP gene ids8529
Upstream gene distance
Downstream gene distance
SNP risk allelers2108622-?
SNPsrs2108622
Merged0
SNP id current2108622
Contextmissense_variant
Intergenic0
Allele frequencyNR
P value0.0000000003
Pvalue mlog9.52287874528033
P value text
Or beta
%95 Ci
PlatformIllumina [~ 550000]
CNVN
Mapped traitresponse to anticoagulant
Mapped trait URIhttp://purl.obolibrary.org/obo/GO_0061476
Study accessionGCST000436
PubMed ID20833655
JournalHum Mol Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/20833655
StudyGenome-wide association study identifies genetic determinants of warfarin responsiveness for Japanese.
Disease/TraitWarfarin maintenance dose
Initial sample807 Japanese ancestry low dose individuals, 701 Japanese ancestry high dose individuals
Replication sample444 Japanese ancestry individuals
Region19p13.12
Chromosome idchr19
Chromosome position15879621
Reported geneCYP4F2
Mapped geneCYP4F2
Upstream gene id
Downstream gene id
SNP gene ids8529
Upstream gene distance
Downstream gene distance
SNP risk allelers2108622-T
SNPsrs2108622
Merged0
SNP id current2108622
Contextmissense_variant
Intergenic0
Allele frequencyNR
P value0.00000003
Pvalue mlog7.52287874528033
P value text
Or beta
%95 Ci
PlatformIllumina [485227]
CNVN
Mapped traitresponse to anticoagulant
Mapped trait URIhttp://purl.obolibrary.org/obo/GO_0061476
Study accessionGCST000792
PubMed ID22437554
JournalJ Nutr
Linkwww.ncbi.nlm.nih.gov/pubmed/22437554
StudyGenome-wide association study identifies three common variants associated with serologic response to vitamin E supplementation in men.
Disease/TraitResponse to Vitamin E supplementation
Initial sample2,112 European ancestry individuals
Replication sampleNA
Region19p13.12
Chromosome idchr19
Chromosome position15879621
Reported geneCYP4F2, LOC729645
Mapped geneCYP4F2
Upstream gene id
Downstream gene id
SNP gene ids8529
Upstream gene distance
Downstream gene distance
SNP risk allelers2108622-T
SNPsrs2108622
Merged0
SNP id current2108622
Contextmissense_variant
Intergenic0
Allele frequency0.19
P value0.0000002
Pvalue mlog6.69897000433601
P value text(alpha-TOH)
Or beta0.04
%95 Ci[0.020-0.060] mg/L increase
PlatformIllumina [549989]
CNVN
Mapped traitresponse to vitamin
Mapped trait URIhttp://purl.obolibrary.org/obo/GO_0033273
Study accessionGCST001450
PubMed ID23281178
JournalHum Mutat
Linkwww.ncbi.nlm.nih.gov/pubmed/23281178
StudyA genome-wide assessment of variability in human serum metabolism.
Disease/TraitMetabolite levels
Initial sample214 European ancestry prostate cancer cases, 188 European ancestry controls
Replication sample489 European ancestry prostate cancer cases
Region19p13.12
Chromosome idchr19
Chromosome position15879621
Reported geneCYP4F2
Mapped geneCYP4F2
Upstream gene id
Downstream gene id
SNP gene ids8529
Upstream gene distance
Downstream gene distance
SNP risk allelers2108622-T
SNPsrs2108622
Merged0
SNP id current2108622
Contextmissense_variant
Intergenic0
Allele frequencyNR
P value9E-24
Pvalue mlog23.0457574905606
P value text(Glycerolphosphocholine)
Or beta
%95 Ci
PlatformAffymetrix [333722]
CNVN
Mapped traitmetabolite measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004725
Study accessionGCST001882
PubMed ID25411281
JournalAm J Clin Nutr
Linkwww.ncbi.nlm.nih.gov/pubmed/25411281
StudyMeta-analysis of genome-wide association studies for circulating phylloquinone concentrations.
Disease/TraitCirculating phylloquinone levels
Initial sample2,138 European ancestry individuals
Replication sampleNA
Region19p13.12
Chromosome idchr19
Chromosome position15879621
Reported geneCYP4F2
Mapped geneCYP4F2
Upstream gene id
Downstream gene id
SNP gene ids8529
Upstream gene distance
Downstream gene distance
SNP risk allelers2108622-T
SNPsrs2108622
Merged0
SNP id current2108622
Contextmissense_variant
Intergenic0
Allele frequency0.3
P value0.0000003
Pvalue mlog6.52287874528033
P value text(Model 2)
Or beta0.16
%95 Ci[0.10-0.22] unit increase
PlatformAffymetrix, Illumina [2543887] (imputed)
CNVN
Mapped traitvitamin K measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004618
Study accessionGCST002653