SNP Detail For rs1367117
1.Mapping Information
Human SNP ID rs1367117
Human chromosome chr2
Human SNP position 21041028
Pig chromosome chr3
Pig SNP position 125231047
2.Annotation Information
PubMed ID20686565
JournalNature
Linkwww.ncbi.nlm.nih.gov/pubmed/20686565
StudyBiological, clinical and population relevance of 95 loci for blood lipids.
Disease/TraitLDL cholesterol
Initial sample95,454 European ancestry individuals
Replication sampleNA
Region2p24.1
Chromosome idchr2
Chromosome position21041028
Reported geneAPOB
Mapped geneAPOB
Upstream gene id
Downstream gene id
SNP gene ids338
Upstream gene distance
Downstream gene distance
SNP risk allelers1367117-A
SNPsrs1367117
Merged0
SNP id current1367117
Contextmissense_variant
Intergenic0
Allele frequency0.3
P value4E-114
Pvalue mlog113.397940008672
P value text
Or beta4.05
%95 Ci[3.68-4.42] mg/dL increase
PlatformAffymetrix, Illumina, Perlegen [~ 2600000] (imputed)
CNVN
Mapped traitlow density lipoprotein cholesterol measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004611
Study accessionGCST000759
PubMed ID20686565
JournalNature
Linkwww.ncbi.nlm.nih.gov/pubmed/20686565
StudyBiological, clinical and population relevance of 95 loci for blood lipids.
Disease/TraitCholesterol, total
Initial sample100,184 European ancestry individuals
Replication sampleNA
Region2p24.1
Chromosome idchr2
Chromosome position21041028
Reported geneAPOB
Mapped geneAPOB
Upstream gene id
Downstream gene id
SNP gene ids338
Upstream gene distance
Downstream gene distance
SNP risk allelers1367117-A
SNPsrs1367117
Merged0
SNP id current1367117
Contextmissense_variant
Intergenic0
Allele frequency0.3
P value4E-96
Pvalue mlog95.397940008672
P value text
Or beta4.16
%95 Ci[3.73-4.59] mg/dL increase
PlatformAffymetrix, Illumina, Perlegen [~ 2600000] (imputed)
CNVN
Mapped traittotal cholesterol measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004574
Study accessionGCST000760
PubMed ID19936222
JournalPLoS Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/19936222
StudyForty-three loci associated with plasma lipoprotein size, concentration, and cholesterol content in genome-wide analysis.
Disease/TraitLipid metabolism phenotypes
Initial sampleUp to 17,296 European ancestry female individuals
Replication sampleUp to 2,700 individuals, Up to 2,000 European ancestry cardiovascular heart disease cases and controls
Region2p24.1
Chromosome idchr2
Chromosome position21041028
Reported geneAPOB
Mapped geneAPOB
Upstream gene id
Downstream gene id
SNP gene ids338
Upstream gene distance
Downstream gene distance
SNP risk allelers1367117-?
SNPsrs1367117
Merged0
SNP id current1367117
Contextmissense_variant
Intergenic0
Allele frequencyNR
P value0.00000000000000002
Pvalue mlog16.698970004336
P value text(LDL-C.assay, fasting)
Or beta3.916
%95 Ci[NR] unit increase
PlatformIllumina [335603]
CNVN
Mapped traitlipid measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004529
Study accessionGCST000533
PubMed ID19936222
JournalPLoS Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/19936222
StudyForty-three loci associated with plasma lipoprotein size, concentration, and cholesterol content in genome-wide analysis.
Disease/TraitLipid metabolism phenotypes
Initial sampleUp to 17,296 European ancestry female individuals
Replication sampleUp to 2,700 individuals, Up to 2,000 European ancestry cardiovascular heart disease cases and controls
Region2p24.1
Chromosome idchr2
Chromosome position21041028
Reported geneAPOB
Mapped geneAPOB
Upstream gene id
Downstream gene id
SNP gene ids338
Upstream gene distance
Downstream gene distance
SNP risk allelers1367117-?
SNPsrs1367117
Merged0
SNP id current1367117
Contextmissense_variant
Intergenic0
Allele frequencyNR
P value6E-25
Pvalue mlog24.2218487496163
P value text(LDL-C.assay, whole)
Or beta4.027
%95 Ci[NR] unit increase
PlatformIllumina [335603]
CNVN
Mapped traitlipid measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004529
Study accessionGCST000533
PubMed ID24097068
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/24097068
StudyDiscovery and refinement of loci associated with lipid levels.
Disease/TraitLDL cholesterol
Initial sample94,595 European ancestry individuals
Replication sample93,982 European ancestry individuals
Region2p24.1
Chromosome idchr2
Chromosome position21041028
Reported geneAPOB
Mapped geneAPOB
Upstream gene id
Downstream gene id
SNP gene ids338
Upstream gene distance
Downstream gene distance
SNP risk allelers1367117-A
SNPsrs1367117
Merged0
SNP id current1367117
Contextmissense_variant
Intergenic0
Allele frequency0.32
P value1E-182
Pvalue mlog182
P value text
Or beta0.119
%95 Ci[NR] unit increase
PlatformNR [NR] (imputed)
CNVN
Mapped traitlow density lipoprotein cholesterol measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004611
Study accessionGCST002222
PubMed ID24097068
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/24097068
StudyDiscovery and refinement of loci associated with lipid levels.
Disease/TraitCholesterol, total
Initial sample94,595 European ancestry individuals
Replication sample93,982 European ancestry individuals
Region2p24.1
Chromosome idchr2
Chromosome position21041028
Reported geneAPOB
Mapped geneAPOB
Upstream gene id
Downstream gene id
SNP gene ids338
Upstream gene distance
Downstream gene distance
SNP risk allelers1367117-A
SNPsrs1367117
Merged0
SNP id current1367117
Contextmissense_variant
Intergenic0
Allele frequency0.32
P value3E-139
Pvalue mlog138.52287874528
P value text
Or beta0.1
%95 Ci[NR] unit increase
PlatformNR [NR] (imputed)
CNVN
Mapped traittotal cholesterol measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004574
Study accessionGCST002221