SNP Detail For rs1553318
1.Mapping Information
Human SNP ID rs1553318
Human chromosome chr5
Human SNP position 157052312
Pig chromosome chr16
Pig SNP position 71956334
2.Annotation Information
PubMed ID25961943
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/25961943
StudyThe impact of low-frequency and rare variants on lipid levels.
Disease/TraitCholesterol, total
Initial sampleup to 62,166 European ancestry individuals
Replication sampleNA
Region5q33.3
Chromosome idchr5
Chromosome position157052312
Reported geneTIMD4, HAVCR1
Mapped geneHAVCR1
Upstream gene id
Downstream gene id
SNP gene ids26762
Upstream gene distance
Downstream gene distance
SNP risk allelers1553318-C
SNPsrs1553318
Merged
SNP id current1553318
Contextintron_variant
Intergenic0
Allele frequency0.65
P value2E-21
Pvalue mlog20.698970004336
P value text
Or beta0.058
%95 Ci[0.046-0.07] s.d. increase
PlatformAffymetrix, Illumina, Perlegen [up to 9657952] (imputed)
CNVN
Mapped traittotal cholesterol measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004574
Study accessionGCST002896
PubMed ID25961943
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/25961943
StudyThe impact of low-frequency and rare variants on lipid levels.
Disease/TraitTriglycerides
Initial sampleup to 62,166 European ancestry individuals
Replication sampleNA
Region5q33.3
Chromosome idchr5
Chromosome position157052312
Reported geneTIMD4, HAVCR1
Mapped geneHAVCR1
Upstream gene id
Downstream gene id
SNP gene ids26762
Upstream gene distance
Downstream gene distance
SNP risk allelers1553318-C
SNPsrs1553318
Merged
SNP id current1553318
Contextintron_variant
Intergenic0
Allele frequency0.65
P value0.00000000002
Pvalue mlog10.698970004336
P value text
Or beta0.042
%95 Ci[0.03-0.054] s.d. increase
PlatformAffymetrix, Illumina, Perlegen [up to 9657952] (imputed)
CNVN
Mapped traittriglyceride measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004530
Study accessionGCST002897
PubMed ID25961943
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/25961943
StudyThe impact of low-frequency and rare variants on lipid levels.
Disease/TraitLDL cholesterol
Initial sampleup 62,166 European ancestry individuals
Replication sampleNA
Region5q33.3
Chromosome idchr5
Chromosome position157052312
Reported geneTIMD4, HAVCR1
Mapped geneHAVCR1
Upstream gene id
Downstream gene id
SNP gene ids26762
Upstream gene distance
Downstream gene distance
SNP risk allelers1553318-C
SNPsrs1553318
Merged
SNP id current1553318
Contextintron_variant
Intergenic0
Allele frequency0.65
P value0.000000000000002
Pvalue mlog14.698970004336
P value text
Or beta0.05
%95 Ci[0.038-0.062] s.d. increase
PlatformAffymetrix, Illumina, Perlegen [up to 9657952] (imputed)
CNVN
Mapped traitlow density lipoprotein cholesterol measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004611
Study accessionGCST002898