SNP Detail For rs2028299
1.Mapping Information
Human SNP ID rs2028299
Human chromosome chr15
Human SNP position 89831025
Pig chromosome chr7
Pig SNP position 60281382
2.Annotation Information
PubMed ID21874001
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/21874001
StudyGenome-wide association study in individuals of South Asian ancestry identifies six new type 2 diabetes susceptibility loci.
Disease/TraitType 2 diabetes
Initial sample5,561 South Asian ancestry cases, 14,458 South Asian ancestry controls
Replication sample13,170 South Asian ancestry cases, 25,398 South Asian ancestry controls
Region15q26.1
Chromosome idchr15
Chromosome position89831025
Reported geneAP3S2
Mapped geneC15orf38-AP3S2, AP3S2
Upstream gene id
Downstream gene id
SNP gene ids100526783, 10239
Upstream gene distance
Downstream gene distance
SNP risk allelers2028299-C
SNPsrs2028299
Merged0
SNP id current2028299
Context3_prime_UTR_variant
Intergenic0
Allele frequency0.31
P value0.00000000002
Pvalue mlog10.698970004336
P value text
Or beta1.1
%95 Ci[1.07-1.13]
PlatformIllumina [568976]
CNVN
Mapped traittype II diabetes mellitus
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0001360
Study accessionGCST001213
PubMed ID23945395
JournalHum Mol Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/23945395
StudyGenome-wide association study identifies three novel loci for type 2 diabetes.
Disease/TraitType 2 diabetes
Initial sample5,976 Japanese ancestry cases, 20,829 Japanese ancestry controls
Replication sample24,416 East Asian ancestry cases, 13,985 East Asian ancestry controls
Region15q26.1
Chromosome idchr15
Chromosome position89831025
Reported geneAP3S2
Mapped geneC15orf38-AP3S2, AP3S2
Upstream gene id
Downstream gene id
SNP gene ids100526783, 10239
Upstream gene distance
Downstream gene distance
SNP risk allelers2028299-C
SNPsrs2028299
Merged0
SNP id current2028299
Context3_prime_UTR_variant
Intergenic0
Allele frequency0.23
P value0.000003
Pvalue mlog5.52287874528033
P value text
Or beta1.13
%95 Ci[1.07-1.19]
PlatformIllumina [6209637] (imputed)
CNVN
Mapped traittype II diabetes mellitus
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0001360
Study accessionGCST002128
PubMed ID24509480
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/24509480
StudyGenome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility.
Disease/TraitType 2 diabetes
Initial sample12,171 European ancestry cases, 56,862 European ancestry controls, 6,952 East Asian ancestry cases, 11,865 East Asian ancestry controls, 5,561 South Asian ancestry cases, 14,458 South Asian ancestry controls, 1,804 Mexican ancestry cases, 779 Mexican ance
Replication sample21,491 European ancestry cases, 55,647 European ancestry controls
Region15q26.1
Chromosome idchr15
Chromosome position89831025
Reported geneAP3S2
Mapped geneC15orf38-AP3S2, AP3S2
Upstream gene id
Downstream gene id
SNP gene ids100526783, 10239
Upstream gene distance
Downstream gene distance
SNP risk allelers2028299-C
SNPsrs2028299
Merged0
SNP id current2028299
Context3_prime_UTR_variant
Intergenic0
Allele frequency0.29
P value0.0000005
Pvalue mlog6.30102999566398
P value text
Or beta1.04
%95 Ci[1.00-1.09]
PlatformAffymetrix, Illumina [2500000] (imputed)
CNVN
Mapped traittype II diabetes mellitus
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0001360
Study accessionGCST002352