SNP Detail For rs1408799
1.Mapping Information
Human SNP ID rs1408799
Human chromosome chr9
Human SNP position 12672097
Pig chromosome chr1
Pig SNP position 233705185
2.Annotation Information
PubMed ID18488028
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/18488028
StudyTwo newly identified genetic determinants of pigmentation in Europeans.
Disease/TraitBlue vs. green eyes
Initial sample5,130 individuals
Replication sample3,330 individuals
Region9p23
Chromosome idchr9
Chromosome position12672097
Reported geneTYRP1
Mapped geneLOC105375976 - TYRP1
Upstream gene id105375976
Downstream gene id7306
SNP gene ids
Upstream gene distance512982
Downstream gene distance21289
SNP risk allelers1408799-C
SNPsrs1408799
Merged0
SNP id current1408799
Contextintergenic_variant
Intergenic1
Allele frequency0.75
P value0.00000000000000006
Pvalue mlog16.2218487496163
P value text
Or beta1.4
%95 Ci[1.25-1.57]
PlatformIllumina [316515]
CNVN
Mapped traiteye color
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0003949
Study accessionGCST000192
PubMed ID23548203
JournalHum Mol Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/23548203
StudyGenome-wide association studies identify several new loci associated with pigmentation traits and skin cancer risk in European Americans.
Disease/TraitEye color
Initial sample3871 European ancestry individuals
Replication sample2,496 European ancestry individuals
Region9p23
Chromosome idchr9
Chromosome position12672097
Reported geneTYRP1
Mapped geneLOC105375976 - TYRP1
Upstream gene id105375976
Downstream gene id7306
SNP gene ids
Upstream gene distance512982
Downstream gene distance21289
SNP risk allelers1408799-C
SNPsrs1408799
Merged0
SNP id current1408799
Contextintergenic_variant
Intergenic1
Allele frequencyNR
P value0.0000005
Pvalue mlog6.30102999566398
P value text(Blue eye color)
Or beta0.27
%95 Ci[0.17-0.37] unit decrease
PlatformAffymetrix, Illumina [2469762] (imputed)
CNVN
Mapped traiteye color
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0003949
Study accessionGCST001929