SNP Detail For rs7422339
1.Mapping Information
Human SNP ID rs7422339
Human chromosome chr2
Human SNP position 210675783
Pig chromosome chr15
Pig SNP position 125275425
2.Annotation Information
PubMed ID20031577
JournalCirc Cardiovasc Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/20031577
StudyNovel loci, including those related to Crohn disease, psoriasis, and inflammation, identified in a genome-wide association study of fibrinogen in 17 686 women: the Women__s Genome Health Study.
Disease/TraitFibrinogen
Initial sample17,686 European ancestry female individuals
Replication sampleNA
Region2q34
Chromosome idchr2
Chromosome position210675783
Reported geneCPS1
Mapped geneCPS1
Upstream gene id
Downstream gene id
SNP gene ids1373
Upstream gene distance
Downstream gene distance
SNP risk allelers7422339-A
SNPsrs7422339
Merged1
SNP id current7422339
Contextmissense_variant
Intergenic0
Allele frequency0.31
P value0.000000009
Pvalue mlog8.04575749056067
P value text
Or beta4.84
%95 Ci[NR] mg/dl decrease
PlatformIllumina [337343]
CNVN
Mapped traitfibrinogen measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004623
Study accessionGCST000368
PubMed ID20154341
JournalHum Mol Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/20154341
StudyGenome-wide association study of homocysteine levels in Filipinos provides evidence for CPS1 in women and a stronger MTHFR effect in young adults.
Disease/TraitHomocysteine levels
Initial sample1,786 Filipino ancestry female individuals
Replication sample1,679 Filipino ancestry offspring
Region2q34
Chromosome idchr2
Chromosome position210675783
Reported geneCPS1
Mapped geneCPS1
Upstream gene id
Downstream gene id
SNP gene ids1373
Upstream gene distance
Downstream gene distance
SNP risk allelers7422339-A
SNPsrs7422339
Merged1
SNP id current7422339
Contextmissense_variant
Intergenic0
Allele frequency0.24
P value0.000000005
Pvalue mlog8.30102999566398
P value text
Or beta0.05
%95 Ci[0.03-0.07] log(Hcy) increase
PlatformAffymetrix [2073674] (imputed)
CNVN
Mapped traithomocysteine measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004578
Study accessionGCST000594
PubMed ID20383146
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/20383146
StudyNew loci associated with kidney function and chronic kidney disease.
Disease/TraitChronic kidney disease
Initial sampleUp to 67,093 European ancestry individuals
Replication sampleUp to 22,982 European ancestry individuals
Region2q34
Chromosome idchr2
Chromosome position210675783
Reported geneCPS1
Mapped geneCPS1
Upstream gene id
Downstream gene id
SNP gene ids1373
Upstream gene distance
Downstream gene distance
SNP risk allelers7422339-A
SNPsrs7422339
Merged1
SNP id current7422339
Contextmissense_variant
Intergenic0
Allele frequency0.32
P value0.000000000000001
Pvalue mlog15
P value text(eGFRcrea)
Or beta0.01
%95 Ci[0.005-0.013] ml/min/1.73 m2 decrease
PlatformAffymetrix, Illumina [~ 2500000] (imputed)
CNVN
Mapped traitchronic kidney disease, serum creatinine measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0003884, http://www.ebi.ac.uk/efo/EFO_0004518
Study accessionGCST000649
PubMed ID23824729
JournalAm J Clin Nutr
Linkwww.ncbi.nlm.nih.gov/pubmed/23824729
StudyCommon genetic loci influencing plasma homocysteine concentrations and their effect on risk of coronary artery disease.
Disease/TraitHomocysteine levels
Initial sample44,147 European ancestry individuals
Replication sampleNA
Region2q34
Chromosome idchr2
Chromosome position210675783
Reported geneCPS1
Mapped geneCPS1
Upstream gene id
Downstream gene id
SNP gene ids1373
Upstream gene distance
Downstream gene distance
SNP risk allelers7422339-A
SNPsrs7422339
Merged1
SNP id current7422339
Contextmissense_variant
Intergenic0
Allele frequency0.33
P value5E-27
Pvalue mlog26.3010299956639
P value text
Or beta0.0864
%95 Ci[0.071-0.102] unit increase
PlatformAffymetrix, Illumina [2090256] (imputed)
CNVN
Mapped traithomocysteine measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004578
Study accessionGCST002087
PubMed ID24625756
JournalPLoS Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/24625756
StudyGenetic determinants influencing human serum metabolome among African Americans.
Disease/TraitSerum metabolite levels
Initial sample1,260 African American individuals
Replication sampleNA
Region2q34
Chromosome idchr2
Chromosome position210675783
Reported geneCPS1
Mapped geneCPS1
Upstream gene id
Downstream gene id
SNP gene ids1373
Upstream gene distance
Downstream gene distance
SNP risk allelers7422339-A
SNPsrs7422339
Merged1
SNP id current7422339
Contextmissense_variant
Intergenic0
Allele frequency0.32
P value0.000000000004
Pvalue mlog11.397940008672
P value text(Glycine)
Or beta0.1
%95 Ci[NR] unit increase
PlatformAffymetrix [2341704] (imputed)
CNVN
Mapped traitserum metabolite measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0005653
Study accessionGCST002388