SNP Detail For rs1883025
1.Mapping Information
Human SNP ID rs1883025
Human chromosome chr9
Human SNP position 104902020
Pig chromosome chr1
Pig SNP position 275817661
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/TraitHDL cholesterol
Initial sample99,900 European ancestry individuals
Replication sampleNA
Region9q31.1
Chromosome idchr9
Chromosome position104902020
Reported geneABCA1
Mapped geneABCA1
Upstream gene id
Downstream gene id
SNP gene ids19
Upstream gene distance
Downstream gene distance
SNP risk allelers1883025-T
SNPsrs1883025
Merged0
SNP id current1883025
Contextintron_variant
Intergenic0
Allele frequency0.25
P value2E-33
Pvalue mlog32.698970004336
P value text
Or beta0.94
%95 Ci[0.76-1.12] mg/dL decrease
PlatformAffymetrix, Illumina, Perlegen [~ 2600000] (imputed)
CNVN
Mapped traithigh density lipoprotein cholesterol measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004612
Study accessionGCST000755
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
Region9q31.1
Chromosome idchr9
Chromosome position104902020
Reported geneABCA1
Mapped geneABCA1
Upstream gene id
Downstream gene id
SNP gene ids19
Upstream gene distance
Downstream gene distance
SNP risk allelers1883025-T
SNPsrs1883025
Merged0
SNP id current1883025
Contextintron_variant
Intergenic0
Allele frequency0.26
P value0.000000001
Pvalue mlog9
P value text
Or beta0.08
%95 Ci[0.04-0.12] s.d. decrease
PlatformAffymetrix, Illumina [~ 2600000] (imputed)
CNVN
Mapped traithigh density lipoprotein cholesterol measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004612
Study accessionGCST000290
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
Region9q31.1
Chromosome idchr9
Chromosome position104902020
Reported geneABCA1
Mapped geneABCA1
Upstream gene id
Downstream gene id
SNP gene ids19
Upstream gene distance
Downstream gene distance
SNP risk allelers1883025-T
SNPsrs1883025
Merged0
SNP id current1883025
Contextintron_variant
Intergenic0
Allele frequency0.25
P value3E-27
Pvalue mlog26.5228787452803
P value text
Or beta2.24
%95 Ci[1.77-2.71] mg/dL decrease
PlatformAffymetrix, Illumina, Perlegen [~ 2600000] (imputed)
CNVN
Mapped traittotal cholesterol measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004574
Study accessionGCST000760
PubMed ID22399527
JournalCirc Cardiovasc Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/22399527
StudyGenome-wide screen for metabolic syndrome susceptibility Loci reveals strong lipid gene contribution but no evidence for common genetic basis for clustering of metabolic syndrome traits.
Disease/TraitMetabolic syndrome
Initial sample2,637 European ancestry cases, 7,927 European ancestry controls
Replication sampleNA
Region9q31.1
Chromosome idchr9
Chromosome position104902020
Reported geneABCA1
Mapped geneABCA1
Upstream gene id
Downstream gene id
SNP gene ids19
Upstream gene distance
Downstream gene distance
SNP risk allelers1883025-T
SNPsrs1883025
Merged0
SNP id current1883025
Contextintron_variant
Intergenic0
Allele frequency0.19
P value0.0000000006
Pvalue mlog9.22184874961635
P value text(HDL)
Or beta0.1
%95 Ci[NR] mmol/l decrease
PlatformIllumina [1257079] (imputed)
CNVN
Mapped traitmetabolic syndrome
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000195
Study accessionGCST001436
PubMed ID24097068
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/24097068
StudyDiscovery and refinement of loci associated with lipid levels.
Disease/TraitHDL cholesterol
Initial sample94,595 European ancestry individuals
Replication sample93,982 European ancestry individuals
Region9q31.1
Chromosome idchr9
Chromosome position104902020
Reported geneABCA1
Mapped geneABCA1
Upstream gene id
Downstream gene id
SNP gene ids19
Upstream gene distance
Downstream gene distance
SNP risk allelers1883025-T
SNPsrs1883025
Merged0
SNP id current1883025
Contextintron_variant
Intergenic0
Allele frequency0.25
P value2E-65
Pvalue mlog64.698970004336
P value text
Or beta0.07
%95 Ci[NR] unit decrease
PlatformNR [NR] (imputed)
CNVN
Mapped traithigh density lipoprotein cholesterol measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004612
Study accessionGCST002223
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
Region9q31.1
Chromosome idchr9
Chromosome position104902020
Reported geneABCA1
Mapped geneABCA1
Upstream gene id
Downstream gene id
SNP gene ids19
Upstream gene distance
Downstream gene distance
SNP risk allelers1883025-T
SNPsrs1883025
Merged0
SNP id current1883025
Contextintron_variant
Intergenic0
Allele frequency0.25
P value6E-53
Pvalue mlog52.2218487496163
P value text
Or beta0.067
%95 Ci[NR] unit decrease
PlatformNR [NR] (imputed)
CNVN
Mapped traittotal cholesterol measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004574
Study accessionGCST002221