SNP Detail For rs10468017
1.Mapping Information
Human SNP ID rs10468017
Human chromosome chr15
Human SNP position 58386313
Pig chromosome chr1
Pig SNP position 125715800
2.Annotation Information
PubMed ID21943158
JournalBMC Med Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/21943158
StudyGenetic variants in LPL, OASL and TOMM40/APOE-C1-C2-C4 genes are associated with multiple cardiovascular-related traits.
Disease/TraitCardiovascular disease risk factors
Initial sample11,683 European ancestry individuals
Replication sampleNA
Region15q21.3
Chromosome idchr15
Chromosome position58386313
Reported geneLIPC
Mapped geneLOC102724766
Upstream gene id
Downstream gene id
SNP gene ids102724766
Upstream gene distance
Downstream gene distance
SNP risk allelers10468017-T
SNPsrs10468017
Merged0
SNP id current10468017
Contextintron_variant
Intergenic0
Allele frequency0.33
P value0.000000000003
Pvalue mlog11.5228787452803
P value text(HDL)
Or beta0.104
%95 Ci[0.075-0.133] mmol/l increase
PlatformIllumina [NR] (imputed)
CNVN
Mapped traithigh density lipoprotein cholesterol measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004612
Study accessionGCST001247
PubMed ID19060906
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/19060906
StudyCommon variants at 30 loci contribute to polygenic dyslipidemia.
Disease/TraitHDL cholesterol
Initial sample19,840 European ancestry individuals
Replication sampleUp to 20,623 European ancestry individuals
Region15q21.3
Chromosome idchr15
Chromosome position58386313
Reported geneLIPC
Mapped geneLOC102724766
Upstream gene id
Downstream gene id
SNP gene ids102724766
Upstream gene distance
Downstream gene distance
SNP risk allelers10468017-T
SNPsrs10468017
Merged0
SNP id current10468017
Contextintron_variant
Intergenic0
Allele frequency0.3
P value8E-23
Pvalue mlog22.096910013008
P value text
Or beta0.1
%95 Ci[0.06-0.14] s.d. increase
PlatformAffymetrix, Illumina [~ 2600000] (imputed)
CNVN
Mapped traithigh density lipoprotein cholesterol measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004612
Study accessionGCST000290
PubMed ID21386085
JournalDiabetes
Linkwww.ncbi.nlm.nih.gov/pubmed/21386085
StudyA bivariate genome-wide approach to metabolic syndrome: STAMPEED consortium.
Disease/TraitMetabolic syndrome (bivariate traits)
Initial sample22,161 European ancestry individuals
Replication sampleNA
Region15q21.3
Chromosome idchr15
Chromosome position58386313
Reported geneLIPC
Mapped geneLOC102724766
Upstream gene id
Downstream gene id
SNP gene ids102724766
Upstream gene distance
Downstream gene distance
SNP risk allelers10468017-C
SNPsrs10468017
Merged0
SNP id current10468017
Contextintron_variant
Intergenic0
Allele frequencyNR
P value0.00000006
Pvalue mlog7.22184874961635
P value text(HDLC-WC)
Or beta0.16
%95 Ci[0.10-0.22] unit increase
PlatformAffymetrix, Illumina [~ 2500000] (imputed)
CNVN
Mapped traitmetabolic syndrome
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000195
Study accessionGCST001007
PubMed ID21665990
JournalHum Mol Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/21665990
StudyCommon variants near FRK/COL10A1 and VEGFA are associated with advanced age-related macular degeneration.
Disease/TraitAge-related macular degeneration
Initial sample2,594 European ancestry cases, 4,134 European ancestry controls
Replication sample5,640 European ancestry cases, 52,174 European ancestry controls
Region15q21.3
Chromosome idchr15
Chromosome position58386313
Reported geneLIPC
Mapped geneLOC102724766
Upstream gene id
Downstream gene id
SNP gene ids102724766
Upstream gene distance
Downstream gene distance
SNP risk allelers10468017-?
SNPsrs10468017
Merged0
SNP id current10468017
Contextintron_variant
Intergenic0
Allele frequency0.71
P value0.000000000003
Pvalue mlog11.5228787452803
P value text
Or beta1.19
%95 Ci[NR]
PlatformAffymetrix [6036699] (imputed)
CNVN
Mapped traitage-related macular degeneration
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0001365
Study accessionGCST001100
PubMed ID22359512
JournalPLoS Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/22359512
StudyGenome-wide association study identifies novel loci associated with circulating phospho- and sphingolipid concentrations.
Disease/TraitPhospholipid levels (plasma)
Initial sample4,034 European ancestry individuals
Replication sampleNA
Region15q21.3
Chromosome idchr15
Chromosome position58386313
Reported geneLIPC
Mapped geneLOC102724766
Upstream gene id
Downstream gene id
SNP gene ids102724766
Upstream gene distance
Downstream gene distance
SNP risk allelers10468017-?
SNPsrs10468017
Merged0
SNP id current10468017
Contextintron_variant
Intergenic0
Allele frequencyNR
P value7E-43
Pvalue mlog42.1549019599857
P value text(levels)
Or beta0
%95 Ci[0.80-4.70] % increase
PlatformIllumina [NR] (imputed)
CNVN
Mapped traitphospholipid measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004639
Study accessionGCST001414
PubMed ID20385826
JournalProc Natl Acad Sci U S A
Linkwww.ncbi.nlm.nih.gov/pubmed/20385826
StudyGenome-wide association study of advanced age-related macular degeneration identifies a role of the hepatic lipase gene (LIPC).
Disease/TraitAge-related macular degeneration
Initial sample979 cases, 1,709 controls
Replication sample868 European ancestry cases, 410 European ancestry controls, 4,921 cases, 3,824 controls
Region15q21.3
Chromosome idchr15
Chromosome position58386313
Reported geneLIPC
Mapped geneLOC102724766
Upstream gene id
Downstream gene id
SNP gene ids102724766
Upstream gene distance
Downstream gene distance
SNP risk allelers10468017-?
SNPsrs10468017
Merged0
SNP id current10468017
Contextintron_variant
Intergenic0
Allele frequency0.7
P value0.00000001
Pvalue mlog8
P value text
Or beta1.22
%95 Ci[1.14-1.30]
PlatformAffymetrix [632932]
CNVN
Mapped traitage-related macular degeneration
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0001365
Study accessionGCST000653
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
Region15q21.3
Chromosome idchr15
Chromosome position58386313
Reported geneLIPC
Mapped geneLOC102724766
Upstream gene id
Downstream gene id
SNP gene ids102724766
Upstream gene distance
Downstream gene distance
SNP risk allelers10468017-T
SNPsrs10468017
Merged0
SNP id current10468017
Contextintron_variant
Intergenic0
Allele frequency0.29
P value0.000000000003
Pvalue mlog11.5228787452803
P value text(1-palmitoylglycerophosphoethanolamine)
Or beta0.019
%95 Ci[0.013-0.025] unit increase
PlatformAffymetrix, Illumina [2100000] (imputed)
CNVN
Mapped traitblood metabolite measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0005664
Study accessionGCST002443