SNP Detail For rs7642134
1.Mapping Information
Human SNP ID rs7642134
Human chromosome chr3
Human SNP position 86867732
Pig chromosome chr13
Pig SNP position 179826880
2.Annotation Information
PubMed ID21102462
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/21102462
StudyThirty new loci for age at menarche identified by a meta-analysis of genome-wide association studies.
Disease/TraitMenarche (age at onset)
Initial sample86,142 European ancestry female individuals, 557 Old Order Amish female individuals, 1,103 Erasmus Rucphen female individuals
Replication sampleUp to 12,813 European ancestry female individuals, 910 Val Borbera female individuals, 348 Orcadian female individuals, 338 Friuli Venezia Giulia female individuals, 322 Carlantino female individuals
Region3p12.1
Chromosome idchr3
Chromosome position86867732
Reported geneVGLL3
Mapped geneLOC101927518 - LOC105377196
Upstream gene id101927518
Downstream gene id105377196
SNP gene ids
Upstream gene distance130472
Downstream gene distance36352
SNP risk allelers7642134-A
SNPsrs7642134
Merged0
SNP id current7642134
Contextintergenic_variant
Intergenic1
Allele frequency0.38
P value0.0000000004
Pvalue mlog9.39794000867203
P value text
Or beta2.4
%95 Ci[1.62-3.18] week decrease
PlatformAffymetrix, Illumina [~ 2500000] (imputed)
CNVN
Mapped traitage at menarche
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004703
Study accessionGCST000880
PubMed ID25231870
JournalNature
Linkwww.ncbi.nlm.nih.gov/pubmed/25231870
StudyParent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
Disease/TraitMenarche (age at onset)
Initial sampleUp to 182,413 European ancestry females
Replication sampleNA
Region3p12.1
Chromosome idchr3
Chromosome position86867732
Reported genePOU1F1, PIT1
Mapped geneLOC101927518 - LOC105377196
Upstream gene id101927518
Downstream gene id105377196
SNP gene ids
Upstream gene distance130472
Downstream gene distance36352
SNP risk allelers7642134-G
SNPsrs7642134
Merged0
SNP id current7642134
Contextintergenic_variant
Intergenic1
Allele frequency0.61
P value0.0000000000000003
Pvalue mlog15.5228787452803
P value text
Or beta0.04
%95 Ci[0.03-0.05] unit increase
PlatformAffymetrix, Illumina [2441815] (imputed)
CNVN
Mapped traitage at menarche
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004703
Study accessionGCST002541