SNP Detail For rs6065906
1.Mapping Information
Human SNP ID rs6065906
Human chromosome chr20
Human SNP position 45925376
Pig chromosome chr17
Pig SNP position 53753739
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
Region20q13.12
Chromosome idchr20
Chromosome position45925376
Reported genePLTP
Mapped genePLTP - PCIF1
Upstream gene id5360
Downstream gene id63935
SNP gene ids
Upstream gene distance13012
Downstream gene distance9298
SNP risk allelers6065906-C
SNPsrs6065906
Merged0
SNP id current6065906
Contextregulatory_region_variant
Intergenic1
Allele frequency0.18
P value2E-22
Pvalue mlog21.698970004336
P value text
Or beta0.93
%95 Ci[0.73-1.13] 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 ID20686565
JournalNature
Linkwww.ncbi.nlm.nih.gov/pubmed/20686565
StudyBiological, clinical and population relevance of 95 loci for blood lipids.
Disease/TraitTriglycerides
Initial sample96,598 European ancestry individuals
Replication sampleNA
Region20q13.12
Chromosome idchr20
Chromosome position45925376
Reported genePLTP
Mapped genePLTP - PCIF1
Upstream gene id5360
Downstream gene id63935
SNP gene ids
Upstream gene distance13012
Downstream gene distance9298
SNP risk allelers6065906-C
SNPsrs6065906
Merged0
SNP id current6065906
Contextregulatory_region_variant
Intergenic1
Allele frequency0.24
P value0.000000000000000005
Pvalue mlog17.3010299956639
P value text
Or beta3.32
%95 Ci[2.5-4.14] mg/dL increase
PlatformAffymetrix, Illumina, Perlegen [~ 2600000] (imputed)
CNVN
Mapped traittriglyceride measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004530
Study accessionGCST000758
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
Region20q13.12
Chromosome idchr20
Chromosome position45925376
Reported genePLTP
Mapped genePLTP - PCIF1
Upstream gene id5360
Downstream gene id63935
SNP gene ids
Upstream gene distance13012
Downstream gene distance9298
SNP risk allelers6065906-?
SNPsrs6065906
Merged0
SNP id current6065906
Contextregulatory_region_variant
Intergenic1
Allele frequencyNR
P value3E-49
Pvalue mlog48.5228787452803
P value text(HDL.large, whole)
Or beta0.693
%95 Ci[NR] unit decrease
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
Region20q13.12
Chromosome idchr20
Chromosome position45925376
Reported genePLTP
Mapped genePLTP - PCIF1
Upstream gene id5360
Downstream gene id63935
SNP gene ids
Upstream gene distance13012
Downstream gene distance9298
SNP risk allelers6065906-?
SNPsrs6065906
Merged0
SNP id current6065906
Contextregulatory_region_variant
Intergenic1
Allele frequencyNR
P value8E-37
Pvalue mlog36.096910013008
P value text(HDL.mean.size, fasting)
Or beta0.087
%95 Ci[NR] unit decrease
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
Region20q13.12
Chromosome idchr20
Chromosome position45925376
Reported genePLTP
Mapped genePLTP - PCIF1
Upstream gene id5360
Downstream gene id63935
SNP gene ids
Upstream gene distance13012
Downstream gene distance9298
SNP risk allelers6065906-?
SNPsrs6065906
Merged0
SNP id current6065906
Contextregulatory_region_variant
Intergenic1
Allele frequencyNR
P value1E-45
Pvalue mlog45
P value text(HDL.mean.size, whole)
Or beta0.083
%95 Ci[NR] unit decrease
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/TraitHDL cholesterol
Initial sample94,595 European ancestry individuals
Replication sample93,982 European ancestry individuals
Region20q13.12
Chromosome idchr20
Chromosome position45925376
Reported genePLTP
Mapped genePLTP - PCIF1
Upstream gene id5360
Downstream gene id63935
SNP gene ids
Upstream gene distance13012
Downstream gene distance9298
SNP risk allelers6065906-C
SNPsrs6065906
Merged0
SNP id current6065906
Contextregulatory_region_variant
Intergenic1
Allele frequency0.19
P value5E-40
Pvalue mlog39.3010299956639
P value text
Or beta0.059
%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/TraitTriglycerides
Initial sample94,595 European ancestry individuals
Replication sample93,982 European ancestry individuals
Region20q13.12
Chromosome idchr20
Chromosome position45925376
Reported genePLTP
Mapped genePLTP - PCIF1
Upstream gene id5360
Downstream gene id63935
SNP gene ids
Upstream gene distance13012
Downstream gene distance9298
SNP risk allelers6065906-C
SNPsrs6065906
Merged0
SNP id current6065906
Contextregulatory_region_variant
Intergenic1
Allele frequency0.19
P value2E-34
Pvalue mlog33.698970004336
P value text
Or beta0.053
%95 Ci[NR] mg/dL increase
PlatformNR [NR] (imputed)
CNVN
Mapped traittriglyceride measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004530
Study accessionGCST002216