SNP Detail For rs2479409
1.Mapping Information
Human SNP ID rs2479409
Human chromosome chr1
Human SNP position 55038977
Pig chromosome chr6
Pig SNP position 145473861
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
Region1p32.3
Chromosome idchr1
Chromosome position55038977
Reported genePCSK9
Mapped geneBSND - PCSK9
Upstream gene id7809
Downstream gene id255738
SNP gene ids
Upstream gene distance30185
Downstream gene distance499
SNP risk allelers2479409-G
SNPsrs2479409
Merged0
SNP id current2479409
Contextupstream_gene_variant
Intergenic1
Allele frequency0.3
P value2E-28
Pvalue mlog27.698970004336
P value text
Or beta2.01
%95 Ci[1.58-2.44] 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
Region1p32.3
Chromosome idchr1
Chromosome position55038977
Reported genePCSK9
Mapped geneBSND - PCSK9
Upstream gene id7809
Downstream gene id255738
SNP gene ids
Upstream gene distance30185
Downstream gene distance499
SNP risk allelers2479409-G
SNPsrs2479409
Merged0
SNP id current2479409
Contextupstream_gene_variant
Intergenic1
Allele frequency0.3
P value4E-24
Pvalue mlog23.397940008672
P value text
Or beta1.96
%95 Ci[1.49-2.43] 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 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
Region1p32.3
Chromosome idchr1
Chromosome position55038977
Reported genePCSK9
Mapped geneBSND - PCSK9
Upstream gene id7809
Downstream gene id255738
SNP gene ids
Upstream gene distance30185
Downstream gene distance499
SNP risk allelers2479409-G
SNPsrs2479409
Merged0
SNP id current2479409
Contextupstream_gene_variant
Intergenic1
Allele frequency0.32
P value3E-50
Pvalue mlog49.5228787452803
P value text
Or beta0.064
%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
Region1p32.3
Chromosome idchr1
Chromosome position55038977
Reported genePCSK9
Mapped geneBSND - PCSK9
Upstream gene id7809
Downstream gene id255738
SNP gene ids
Upstream gene distance30185
Downstream gene distance499
SNP risk allelers2479409-G
SNPsrs2479409
Merged0
SNP id current2479409
Contextupstream_gene_variant
Intergenic1
Allele frequency0.32
P value2E-39
Pvalue mlog38.698970004336
P value text
Or beta0.054
%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