SNP Detail For rs2470893
1.Mapping Information
Human SNP ID rs2470893
Human chromosome chr15
Human SNP position 74727108
Pig chromosome chr7
Pig SNP position 63489931
2.Annotation Information
PubMed ID21876539
JournalMol Psychiatry
Linkwww.ncbi.nlm.nih.gov/pubmed/21876539
StudyGenome-wide association analysis of coffee drinking suggests association with CYP1A1/CYP1A2 and NRCAM.
Disease/TraitCoffee consumption
Initial sample18,176 European ancestry individuals
Replication sample7,929 European ancestry individuals
Region15q24.1
Chromosome idchr15
Chromosome position74727108
Reported geneCYP1A1, CYP1A2
Mapped geneCYP1A1 - CYP1A2
Upstream gene id1543
Downstream gene id1544
SNP gene ids
Upstream gene distance1498
Downstream gene distance21735
SNP risk allelers2470893-T
SNPsrs2470893
Merged0
SNP id current2470893
Contextupstream_gene_variant
Intergenic1
Allele frequencyNR
P value0.00000000002
Pvalue mlog10.698970004336
P value text
Or beta0.0675
%95 Ci[0.05-0.09] unit increase
PlatformAffymetrix, Illumina, Perlegen [~ 2600000] (imputed)
CNVN
Mapped traitcoffee consumption
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004330
Study accessionGCST001215
PubMed ID21490707
JournalPLoS Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/21490707
StudyGenome-wide meta-analysis identifies regions on 7p21 (AHR) and 15q24 (CYP1A2) as determinants of habitual caffeine consumption.
Disease/TraitCaffeine consumption
Initial sample47,431 European ancestry individuals
Replication sampleNA
Region15q24.1
Chromosome idchr15
Chromosome position74727108
Reported geneEDC3, CYP1A1, CYP1A2, LMAN1L, CSK
Mapped geneCYP1A1 - CYP1A2
Upstream gene id1543
Downstream gene id1544
SNP gene ids
Upstream gene distance1498
Downstream gene distance21735
SNP risk allelers2470893-T
SNPsrs2470893
Merged0
SNP id current2470893
Contextupstream_gene_variant
Intergenic1
Allele frequency0.31
P value0.00000000000005
Pvalue mlog13.3010299956639
P value text
Or beta0.12
%95 Ci[0.08-0.16] mg/day increase
PlatformAffymetrix, Illumina [~ 2500000] (imputed)
CNVN
Mapped traitcoffee consumption
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004330
Study accessionGCST001032
PubMed ID25288136
JournalMol Psychiatry
Linkwww.ncbi.nlm.nih.gov/pubmed/25288136
StudyGenome-wide meta-analysis identifies six novel loci associated with habitual coffee consumption.
Disease/TraitCoffee consumption
Initial sample17,479 European ancestry high consumption individuals, 31,049 European ancestry no or low consumption individuals
Replication sample6,497 European ancestry high consumption individuals, 432 African American high consumption individuals, 6,972 European ancestry no or low consumption individuals, 3,413 African American no or low consumption individuals
Region15q24.1
Chromosome idchr15
Chromosome position74727108
Reported geneCYP1A1, CYP1A2
Mapped geneCYP1A1 - CYP1A2
Upstream gene id1543
Downstream gene id1544
SNP gene ids
Upstream gene distance1498
Downstream gene distance21735
SNP risk allelers2470893-T
SNPsrs2470893
Merged0
SNP id current2470893
Contextupstream_gene_variant
Intergenic1
Allele frequency0.31
P value5E-19
Pvalue mlog18.3010299956639
P value text
Or beta0.2
%95 Ci[0.16-0.24] unit increase
PlatformAffymetrix, Illumina [2376205] (imputed)
CNVN
Mapped traitcoffee consumption
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004330
Study accessionGCST002651