SNP Detail For rs12229654
1.Mapping Information
Human SNP ID rs12229654
Human chromosome chr12
Human SNP position 110976657
Pig chromosome chr14
Pig SNP position 34233803
2.Annotation Information
PubMed ID21909109
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/21909109
StudyLarge-scale genome-wide association studies in East Asians identify new genetic loci influencing metabolic traits.
Disease/TraitHDL cholesterol
Initial sample12,545 Korean ancestry individuals
Replication sampleUp to 30,395 East Asian ancestry individuals
Region12q24.11
Chromosome idchr12
Chromosome position110976657
Reported geneMYL2
Mapped geneLOC105369980 - LOC105369981
Upstream gene id105369980
Downstream gene id105369981
SNP gene ids
Upstream gene distance18896
Downstream gene distance35586
SNP risk allelers12229654-G
SNPsrs12229654
Merged0
SNP id current12229654
Contextintergenic_variant
Intergenic1
Allele frequency0.14
P value3E-23
Pvalue mlog22.5228787452803
P value text
Or beta0.028
%95 Ci[0.023-0.033] mg/dL decrease
PlatformAffymetrix [~ 2200000] (imputed)
CNVN
Mapped traithigh density lipoprotein cholesterol measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004612
Study accessionGCST001237
PubMed ID21909109
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/21909109
StudyLarge-scale genome-wide association studies in East Asians identify new genetic loci influencing metabolic traits.
Disease/TraitGamma glutamyl transpeptidase
Initial sample12,545 Korean ancestry individuals
Replication sampleUp to 30,395 East Asian ancestry individuals
Region12q24.11
Chromosome idchr12
Chromosome position110976657
Reported geneMYL2
Mapped geneLOC105369980 - LOC105369981
Upstream gene id105369980
Downstream gene id105369981
SNP gene ids
Upstream gene distance18896
Downstream gene distance35586
SNP risk allelers12229654-G
SNPsrs12229654
Merged0
SNP id current12229654
Contextintergenic_variant
Intergenic1
Allele frequency0.14
P value9E-58
Pvalue mlog57.0457574905606
P value text
Or beta0.0119
%95 Ci[0.011-0.013] IU/L increase
PlatformAffymetrix [~ 2200000] (imputed)
CNVN
Mapped traitserum gamma-glutamyl transferase measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004532
Study accessionGCST001234
PubMed ID21270382
JournalAm J Clin Nutr
Linkwww.ncbi.nlm.nih.gov/pubmed/21270382
StudyGenome-wide association studies identify genetic loci related to alcohol consumption in Korean men.
Disease/TraitAlcohol consumption
Initial sample1,721 Korean ancestry male individuals
Replication sample1,113 Korean ancestry male individuals
Region12q24.11
Chromosome idchr12
Chromosome position110976657
Reported geneMYL2
Mapped geneLOC105369980 - LOC105369981
Upstream gene id105369980
Downstream gene id105369981
SNP gene ids
Upstream gene distance18896
Downstream gene distance35586
SNP risk allelers12229654-G
SNPsrs12229654
Merged0
SNP id current12229654
Contextintergenic_variant
Intergenic1
Allele frequency0.14
P value4E-35
Pvalue mlog34.397940008672
P value text
Or beta0.79
%95 Ci[0.67-0.91] unit decrease
PlatformAffymetrix [315914]
CNVN
Mapped traitalcohol drinking
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004329
Study accessionGCST000954
PubMed ID23575436
JournalJ Hum Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/23575436
StudyNew susceptibility loci in MYL2, C12orf51 and OAS1 associated with 1-h plasma glucose as predisposing risk factors for type 2 diabetes in the Korean population.
Disease/TraitGlycemic traits
Initial sample7,696 Korean ancestry individuals
Replication sample6,536 Korean ancestry individuals
Region12q24.11
Chromosome idchr12
Chromosome position110976657
Reported geneMYL2
Mapped geneLOC105369980 - LOC105369981
Upstream gene id105369980
Downstream gene id105369981
SNP gene ids
Upstream gene distance18896
Downstream gene distance35586
SNP risk allelers12229654-G
SNPsrs12229654
Merged0
SNP id current12229654
Contextintergenic_variant
Intergenic1
Allele frequency
P value0.0000000000009
Pvalue mlog12.0457574905606
P value text(1-hPG)
Or beta0.277
%95 Ci[0.20-0.35] mmol-1 decrease
PlatformAffymetrix [357789]
CNVN
Mapped traittype II diabetes mellitus
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0001360
Study accessionGCST001965
PubMed ID24861553
JournalHum Mol Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/24861553
StudyMeta-analysis of genome-wide association studies in East Asian-ancestry populations identifies four new loci for body mass index.
Disease/TraitBody mass index
Initial sample82,438 East Asian ancestry individuals, 4,301 South East Asian ancestry individuals
Replication sampleUp to 47,352 East Asian ancestry individuals
Region12q24.11
Chromosome idchr12
Chromosome position110976657
Reported geneMYL2
Mapped geneLOC105369980 - LOC105369981
Upstream gene id105369980
Downstream gene id105369981
SNP gene ids
Upstream gene distance18896
Downstream gene distance35586
SNP risk allelers12229654-T
SNPsrs12229654
Merged0
SNP id current12229654
Contextintergenic_variant
Intergenic1
Allele frequency0.8
P value0.000000005
Pvalue mlog8.30102999566398
P value text
Or beta0.0341
%95 Ci[0.023-0.045] unit increase
PlatformAffymetrix, Illumina [~ 2500000] (imputed)
CNVN
Mapped traitbody mass index
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004340
Study accessionGCST002461
PubMed ID25705158
JournalGenomics Inform
Linkwww.ncbi.nlm.nih.gov/pubmed/25705158
StudyPathway Analysis of Metabolic Syndrome Using a Genome-Wide Association Study of Korea Associated Resource (KARE) Cohorts.
Disease/TraitMetabolic syndrome
Initial sample3,253 Korean ancestry cases, 5,589 Korean ancestry controls
Replication sampleNA
Region12q24.11
Chromosome idchr12
Chromosome position110976657
Reported geneMYL2
Mapped geneLOC105369980 - LOC105369981
Upstream gene id105369980
Downstream gene id105369981
SNP gene ids
Upstream gene distance18896
Downstream gene distance35586
SNP risk allelers12229654-?
SNPsrs12229654
Merged0
SNP id current12229654
Contextintergenic_variant
Intergenic1
Allele frequencyNR
P value0.000003
Pvalue mlog5.52287874528033
P value text
Or beta
%95 Ci
PlatformAffymetrix [312121]
CNVN
Mapped traitmetabolic syndrome
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000195
Study accessionGCST002732