SNP Detail For rs1042725
1.Mapping Information
Human SNP ID rs1042725
Human chromosome chr12
Human SNP position 65964567
Pig chromosome chr5
Pig SNP position 33517696
2.Annotation Information
PubMed ID17767157
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/17767157
StudyA common variant of HMGA2 is associated with adult and childhood height in the general population.
Disease/TraitHeight
Initial sample4,921 European ancestry individuals
Replication sample19,064 European ancestry adult individuals, 6,827 European ancestry children
Region12q14.3
Chromosome idchr12
Chromosome position65964567
Reported geneHMGA2
Mapped geneHMGA2
Upstream gene id
Downstream gene id
SNP gene ids8091
Upstream gene distance
Downstream gene distance
SNP risk allelers1042725-C
SNPsrs1042725
Merged0
SNP id current1042725
Context3_prime_UTR_variant
Intergenic0
Allele frequency0.51
P value0.0000000000000006
Pvalue mlog15.2218487496163
P value text
Or beta0.4
%95 Ci[NR] cm increase
PlatformAffymetrix [364301]
CNVN
Mapped traitbody height
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004339
Study accessionGCST000068
PubMed ID22504419
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/22504419
StudyCommon variants at 12q15 and 12q24 are associated with infant head circumference.
Disease/TraitHead circumference (infant)
Initial sample10,768 European ancestry infants
Replication sample8,321 European ancestry infants
Region12q14.3
Chromosome idchr12
Chromosome position65964567
Reported geneHMGA2
Mapped geneHMGA2
Upstream gene id
Downstream gene id
SNP gene ids8091
Upstream gene distance
Downstream gene distance
SNP risk allelers1042725-T
SNPsrs1042725
Merged0
SNP id current1042725
Context3_prime_UTR_variant
Intergenic0
Allele frequency0.49
P value0.0000000003
Pvalue mlog9.52287874528033
P value text
Or beta0.065
%95 Ci[0.045-0.085] SD decrease
PlatformAffymetrix, Illumina [~ 2400000] (imputed)
CNVN
Mapped traitinfant head circumference
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004577
Study accessionGCST001484
PubMed ID23202124
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/23202124
StudyNew loci associated with birth weight identify genetic links between intrauterine growth and adult height and metabolism.
Disease/TraitBirth weight
Initial sampleUp to 26,836 European ancestry individuals
Replication sampleUp to 42,519 European ancestry individuals
Region12q14.3
Chromosome idchr12
Chromosome position65964567
Reported geneHMGA2
Mapped geneHMGA2
Upstream gene id
Downstream gene id
SNP gene ids8091
Upstream gene distance
Downstream gene distance
SNP risk allelers1042725-T
SNPsrs1042725
Merged0
SNP id current1042725
Context3_prime_UTR_variant
Intergenic0
Allele frequency0.5
P value1E-19
Pvalue mlog19
P value text
Or beta0.047
%95 Ci[0.037-0.057] gram decrease
PlatformAffymetrix, Illumina [~ 2700000] (imputed)
CNVN
Mapped traitbirth weight
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004344
Study accessionGCST001758
PubMed ID18391950
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/18391950
StudyIdentification of ten loci associated with height highlights new biological pathways in human growth.
Disease/TraitHeight
Initial sample15,821 European ancestry individuals
Replication sampleUp to 17,801 European ancestry individuals
Region12q14.3
Chromosome idchr12
Chromosome position65964567
Reported geneHMGA2
Mapped geneHMGA2
Upstream gene id
Downstream gene id
SNP gene ids8091
Upstream gene distance
Downstream gene distance
SNP risk allelers1042725-T
SNPsrs1042725
Merged0
SNP id current1042725
Context3_prime_UTR_variant
Intergenic0
Allele frequency0.49
P value3E-20
Pvalue mlog19.5228787452803
P value text
Or beta0.48
%95 Ci[0.58-1.09] cm decrease
PlatformAffymetrix, Illumina [2260683] (imputed)
CNVN
Mapped traitbody height
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004339
Study accessionGCST000176
PubMed ID18391952
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/18391952
StudyGenome-wide association analysis identifies 20 loci that influence adult height.
Disease/TraitHeight
Initial sample13,665 European ancestry individuals
Replication sample16,482 European ancestry individuals
Region12q14.3
Chromosome idchr12
Chromosome position65964567
Reported geneHMGA2
Mapped geneHMGA2
Upstream gene id
Downstream gene id
SNP gene ids8091
Upstream gene distance
Downstream gene distance
SNP risk allelers1042725-C
SNPsrs1042725
Merged0
SNP id current1042725
Context3_prime_UTR_variant
Intergenic0
Allele frequency0.49
P value0.000000000000000003
Pvalue mlog17.5228787452803
P value text
Or beta0.05
%95 Ci[0.03-0.08] s.d. increase (males)
PlatformAffymetrix [402951]
CNVN
Mapped traitbody height
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004339
Study accessionGCST000174
PubMed ID25429064
JournalHum Mol Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/25429064
StudyMeta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
Disease/TraitHeight
Initial sample36,227 East Asian ancestry individuals
Replication sample57,699 East Asian ancestry individuals
Region12q14.3
Chromosome idchr12
Chromosome position65964567
Reported geneHMGA2
Mapped geneHMGA2
Upstream gene id
Downstream gene id
SNP gene ids8091
Upstream gene distance
Downstream gene distance
SNP risk allelers1042725-T
SNPsrs1042725
Merged0
SNP id current1042725
Context3_prime_UTR_variant
Intergenic0
Allele frequency0.73
P value0.0000002
Pvalue mlog6.69897000433601
P value text
Or beta0.024
%95 Ci[0.01-0.038] unit decrease
PlatformAffymetrix, Illumina [2704730] (imputed)
CNVN
Mapped traitbody height
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004339
Study accessionGCST002702