SNP Detail For rs4814176
1.Mapping Information
Human SNP ID rs4814176
Human chromosome chr20
Human SNP position 12978750
Pig chromosome chr17
Pig SNP position 24311103
2.Annotation Information
PubMed ID24816252
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/24816252
StudyAn atlas of genetic influences on human blood metabolites.
Disease/TraitBlood metabolite levels
Initial sample7,824 European ancestry individuals
Replication sampleNA
Region20p12.1
Chromosome idchr20
Chromosome position12978750
Reported geneSPTLC3
Mapped geneLOC101929486 - SPTLC3
Upstream gene id101929486
Downstream gene id55304
SNP gene ids
Upstream gene distance26231
Downstream gene distance30229
SNP risk allelers4814176-T
SNPsrs4814176
Merged0
SNP id current4814176
Contextintergenic_variant
Intergenic1
Allele frequency0.39
P value0.00000000000000003
Pvalue mlog16.5228787452803
P value text(X-08402)
Or beta0.022
%95 Ci[0.016-0.028] unit increase
PlatformAffymetrix, Illumina [2100000] (imputed)
CNVN
Mapped traitblood metabolite measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0005664
Study accessionGCST002443
PubMed ID24816252
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/24816252
StudyAn atlas of genetic influences on human blood metabolites.
Disease/TraitBlood metabolite ratios
Initial sampleUp to 5,591 European ancestry individuals
Replication sampleUp to 1,767 European ancestry individuals
Region20p12.1
Chromosome idchr20
Chromosome position12978750
Reported geneSPTLC3
Mapped geneLOC101929486 - SPTLC3
Upstream gene id101929486
Downstream gene id55304
SNP gene ids
Upstream gene distance26231
Downstream gene distance30229
SNP risk allelers4814176-T
SNPsrs4814176
Merged0
SNP id current4814176
Contextintergenic_variant
Intergenic1
Allele frequency0.4
P value7E-33
Pvalue mlog32.1549019599857
P value text(X-10510/palmitoyl sphingomyelin)
Or beta0.021
%95 Ci[0.017-0.025] unit increase
PlatformAffymetrix, Illumina [2100000] (imputed)
CNVN
Mapped traitblood metabolite measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0005664
Study accessionGCST002442
PubMed ID26068415
JournalNat Commun
Linkwww.ncbi.nlm.nih.gov/pubmed/26068415
StudyGenome-wide association study identifies novel genetic variants contributing to variation in blood metabolite levels.
Disease/TraitSphingolipid levels
Initial sampleup to 7,478 European ancestry individuals
Replication sample1,182 European ancestry individuals
Region20p12.1
Chromosome idchr20
Chromosome position12978750
Reported geneSPTLC3
Mapped geneLOC101929486 - SPTLC3
Upstream gene id101929486
Downstream gene id55304
SNP gene ids
Upstream gene distance26231
Downstream gene distance30229
SNP risk allelers4814176-T
SNPsrs4814176
Merged0
SNP id current4814176
Contextintergenic_variant
Intergenic1
Allele frequency0.3758
P value0.0000000000004
Pvalue mlog12.397940008672
P value text(Hydroxysphingomyeline C16:1)
Or beta0.0369
%95 Ci[0.027-0.047] unit increase
PlatformAffymetrix, Illumina [up to 296619] (imputed)
CNVN
Mapped traitsphingolipid measurement, blood metabolite measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004622, http://www.ebi.ac.uk/efo/EFO_0005664
Study accessionGCST002964
PubMed ID26068415
JournalNat Commun
Linkwww.ncbi.nlm.nih.gov/pubmed/26068415
StudyGenome-wide association study identifies novel genetic variants contributing to variation in blood metabolite levels.
Disease/TraitSphingolipid levels
Initial sampleup to 7,478 European ancestry individuals
Replication sample1,182 European ancestry individuals
Region20p12.1
Chromosome idchr20
Chromosome position12978750
Reported geneSPTLC3
Mapped geneLOC101929486 - SPTLC3
Upstream gene id101929486
Downstream gene id55304
SNP gene ids
Upstream gene distance26231
Downstream gene distance30229
SNP risk allelers4814176-T
SNPsrs4814176
Merged0
SNP id current4814176
Contextintergenic_variant
Intergenic1
Allele frequency0.3752
P value2E-32
Pvalue mlog31.698970004336
P value text(Hydroxysphingomyeline C24:1)
Or beta0.062
%95 Ci[0.052-0.072] unit increase
PlatformAffymetrix, Illumina [up to 296619] (imputed)
CNVN
Mapped traitsphingolipid measurement, blood metabolite measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004622, http://www.ebi.ac.uk/efo/EFO_0005664
Study accessionGCST002964