SNP Detail For rs560887
1.Mapping Information
Human SNP ID rs560887
Human chromosome chr2
Human SNP position 168906638
Pig chromosome chr15
Pig SNP position 84491385
2.Annotation Information
PubMed ID18451265
JournalScience
Linkwww.ncbi.nlm.nih.gov/pubmed/18451265
StudyA polymorphism within the G6PC2 gene is associated with fasting plasma glucose levels.
Disease/TraitFasting plasma glucose
Initial sample654 European ancestry individuals
Replication sample9,353 European ancestry individuals
Region2q31.1
Chromosome idchr2
Chromosome position168906638
Reported geneG6PC2
Mapped geneG6PC2
Upstream gene id
Downstream gene id
SNP gene ids57818
Upstream gene distance
Downstream gene distance
SNP risk allelers560887-A
SNPsrs560887
Merged0
SNP id current560887
Contextintron_variant
Intergenic0
Allele frequency0.3
P value4E-23
Pvalue mlog22.397940008672
P value text
Or beta0.06
%95 Ci[0.05-0.08] mmol/l decrease
PlatformIllumina [392935]
CNVN
Mapped traitfasting blood glucose measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004465
Study accessionGCST000205
PubMed ID19060910
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/19060910
StudyGenome-wide association analysis of metabolic traits in a birth cohort from a founder population.
Disease/TraitMetabolic traits
Initial sample4,763 Northern Finnish founder individuals
Replication sampleNA
Region2q31.1
Chromosome idchr2
Chromosome position168906638
Reported geneG6PC2, ABCB11
Mapped geneG6PC2
Upstream gene id
Downstream gene id
SNP gene ids57818
Upstream gene distance
Downstream gene distance
SNP risk allelers560887-A
SNPsrs560887
Merged0
SNP id current560887
Contextintron_variant
Intergenic0
Allele frequency0.31
P value0.0000000006
Pvalue mlog9.22184874961635
P value text(GLU)
Or beta0.06
%95 Ci[0.04-0.07] mmol/l decrease
PlatformIllumina [329091]
CNVN
Mapped traitglucose measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004468
Study accessionGCST000292
PubMed ID19060907
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/19060907
StudyVariants in MTNR1B influence fasting glucose levels.
Disease/TraitFasting plasma glucose
Initial sample35,812 European ancestry individuals
Replication sampleNA
Region2q31.1
Chromosome idchr2
Chromosome position168906638
Reported geneG6PC2
Mapped geneG6PC2
Upstream gene id
Downstream gene id
SNP gene ids57818
Upstream gene distance
Downstream gene distance
SNP risk allelers560887-C
SNPsrs560887
Merged0
SNP id current560887
Contextintron_variant
Intergenic0
Allele frequency0.7
P value1E-57
Pvalue mlog57
P value text
Or beta0.06
%95 Ci[0.05-0.07] mmol/l increase
PlatformAffymetrix, Illumina, Perlegen [up to 2557249] (imputed)
CNVN
Mapped traitfasting blood glucose measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004465
Study accessionGCST000276
PubMed ID22286219
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/22286219
StudyGenome-wide association study identifies multiple loci influencing human serum metabolite levels.
Disease/TraitMetabolite levels
Initial sample8,330 European ancestry individuals
Replication sampleNA
Region2q31.1
Chromosome idchr2
Chromosome position168906638
Reported geneG6PC2
Mapped geneG6PC2
Upstream gene id
Downstream gene id
SNP gene ids57818
Upstream gene distance
Downstream gene distance
SNP risk allelers560887-?
SNPsrs560887
Merged0
SNP id current560887
Contextintron_variant
Intergenic0
Allele frequencyNR
P value0.00000000000000002
Pvalue mlog16.698970004336
P value text(Glc)
Or beta0.15
%95 Ci[0.11-0.19] unit increase
PlatformIllumina [~ 7700000] (imputed)
CNVN
Mapped traitmetabolite measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004725
Study accessionGCST001391
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
Region2q31.1
Chromosome idchr2
Chromosome position168906638
Reported geneG6PC2
Mapped geneG6PC2
Upstream gene id
Downstream gene id
SNP gene ids57818
Upstream gene distance
Downstream gene distance
SNP risk allelers560887-G
SNPsrs560887
Merged0
SNP id current560887
Contextintron_variant
Intergenic0
Allele frequency0.69
P value5E-26
Pvalue mlog25.3010299956639
P value text(GLU)
Or beta0.15
%95 Ci[NR] mmol/l increase
PlatformIllumina [1257079] (imputed)
CNVN
Mapped traitmetabolic syndrome
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000195
Study accessionGCST001436
PubMed ID22508271
JournalGenet Epidemiol
Linkwww.ncbi.nlm.nih.gov/pubmed/22508271
StudyFasting glucose GWAS candidate region analysis across ethnic groups in the Multiethnic Study of Atherosclerosis (MESA).
Disease/TraitFasting plasma glucose
Initial sample2,349 European ancestry individuals, 664 Chinese ancestry individuals, 1,366 African American individuals, 1,171 Hispanic individuals
Replication sampleNA
Region2q31.1
Chromosome idchr2
Chromosome position168906638
Reported geneG6PC2
Mapped geneG6PC2
Upstream gene id
Downstream gene id
SNP gene ids57818
Upstream gene distance
Downstream gene distance
SNP risk allelers560887-T
SNPsrs560887
Merged0
SNP id current560887
Contextintron_variant
Intergenic0
Allele frequency0.2
P value0.000002
Pvalue mlog5.69897000433601
P value text(fasting glucose)
Or beta1.29
%95 Ci[0.84-1.74] mg/dL decrease
PlatformAffymetrix [NR] (imputed)
CNVN
Mapped traitfasting blood glucose measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004465
Study accessionGCST001486
PubMed ID20081858
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/20081858
StudyNew genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk.
Disease/TraitFasting glucose-related traits
Initial sampleup to 46,186 European ancestry individuals
Replication sampleup to 76,558 European ancestry individuals
Region2q31.1
Chromosome idchr2
Chromosome position168906638
Reported geneG6PC2
Mapped geneG6PC2
Upstream gene id
Downstream gene id
SNP gene ids57818
Upstream gene distance
Downstream gene distance
SNP risk allelers560887-C
SNPsrs560887
Merged0
SNP id current560887
Contextintron_variant
Intergenic0
Allele frequency0.7
P value9E-218
Pvalue mlog217.04575749056
P value text(FPG)
Or beta
%95 Ci
PlatformAffymetrix, Illumina [~ 2500000] (imputed)
CNVN
Mapped traitfasting blood glucose measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004465
Study accessionGCST000568
PubMed ID20081858
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/20081858
StudyNew genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk.
Disease/TraitFasting glucose-related traits
Initial sampleup to 46,186 European ancestry individuals
Replication sampleup to 76,558 European ancestry individuals
Region2q31.1
Chromosome idchr2
Chromosome position168906638
Reported geneG6PC2
Mapped geneG6PC2
Upstream gene id
Downstream gene id
SNP gene ids57818
Upstream gene distance
Downstream gene distance
SNP risk allelers560887-C
SNPsrs560887
Merged0
SNP id current560887
Contextintron_variant
Intergenic0
Allele frequency0.7
P value2E-66
Pvalue mlog65.698970004336
P value text(HOMA-B)
Or beta
%95 Ci
PlatformAffymetrix, Illumina [~ 2500000] (imputed)
CNVN
Mapped traitHOMA-B
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004469
Study accessionGCST000568
PubMed ID22581228
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/22581228
StudyA genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance.
Disease/TraitFasting glucose-related traits (interaction with BMI)
Initial sampleUp to 58,074 European ancestry individuals
Replication sampleUp tp 38,422 European ancestry individuals
Region2q31.1
Chromosome idchr2
Chromosome position168906638
Reported geneG6PC2
Mapped geneG6PC2
Upstream gene id
Downstream gene id
SNP gene ids57818
Upstream gene distance
Downstream gene distance
SNP risk allelers560887-?
SNPsrs560887
Merged0
SNP id current560887
Contextintron_variant
Intergenic0
Allele frequencyNR
P value2E-113
Pvalue mlog112.698970004336
P value text
Or beta
%95 Ci
PlatformAffymetrix, Illumina [~ 2400000] (imputed)
CNVN
Mapped traitbody mass index, fasting blood glucose measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004340, http://www.ebi.ac.uk/efo/EFO_0004465
Study accessionGCST001527
PubMed ID22916037
JournalPLoS Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/22916037
StudyNovel Loci for metabolic networks and multi-tissue expression studies reveal genes for atherosclerosis.
Disease/TraitMetabolite levels
Initial sample6,608 European ancestry individuals
Replication sampleNA
Region2q31.1
Chromosome idchr2
Chromosome position168906638
Reported geneG6PC2
Mapped geneG6PC2
Upstream gene id
Downstream gene id
SNP gene ids57818
Upstream gene distance
Downstream gene distance
SNP risk allelers560887-?
SNPsrs560887
Merged0
SNP id current560887
Contextintron_variant
Intergenic0
Allele frequency0.31
P value0.000000000000004
Pvalue mlog14.397940008672
P value text
Or beta
%95 Ci
PlatformIllumina [~ 2000000] (imputed)
CNVN
Mapped traitcoronary artery calcification
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004723
Study accessionGCST001639
PubMed ID23903356
JournalDiabetes
Linkwww.ncbi.nlm.nih.gov/pubmed/23903356
StudyIdentification of HKDC1 and BACE2 as genes influencing glycemic traits during pregnancy through genome-wide association studies.
Disease/TraitGlycemic traits (pregnancy)
Initial sample1,367 European ancestry individuals, 817 Hispanic individuals, 1,075 Afro-Caribbean individuals, 1,178 Thai ancestry individuals
Replication sample2,798 European ancestry individuals, 228 French Canadian founder population individuals
Region2q31.1
Chromosome idchr2
Chromosome position168906638
Reported geneG6PC2
Mapped geneG6PC2
Upstream gene id
Downstream gene id
SNP gene ids57818
Upstream gene distance
Downstream gene distance
SNP risk allelers560887-T
SNPsrs560887
Merged0
SNP id current560887
Contextintron_variant
Intergenic0
Allele frequency0.291
P value0.0000000000000002
Pvalue mlog15.698970004336
P value text(FPG)
Or beta0.0061
%95 Ci[NR] unit decrease
PlatformIllumina [up to 945994] (imputed)
CNVN
Mapped traitfasting blood glucose measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004465
Study accessionGCST002110
PubMed ID24405752
JournalMetabolism
Linkwww.ncbi.nlm.nih.gov/pubmed/24405752
StudyGenome-wide association study identifies common loci influencing circulating glycated hemoglobin (HbA1c) levels in non-diabetic subjects: the Long Life Family Study (LLFS).
Disease/TraitGlycated hemoglobin levels
Initial sample4,088 European ancestry non-diabetic elderly individuals
Replication sampleup to 47,822 European ancestry non-diabetic elderly individuals
Region2q31.1
Chromosome idchr2
Chromosome position168906638
Reported geneG6PC2
Mapped geneG6PC2
Upstream gene id
Downstream gene id
SNP gene ids57818
Upstream gene distance
Downstream gene distance
SNP risk allelers560887-T
SNPsrs560887
Merged0
SNP id current560887
Contextintron_variant
Intergenic0
Allele frequency0.33
P value0.00000000000000001
Pvalue mlog17
P value text
Or beta0.032
%95 Ci[0.024-0.040] unit decrease
PlatformIllumina [9250000] (imputed)
CNVN
Mapped traitA1C measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004541
Study accessionGCST002303