SNP Detail For rs900400
1.Mapping Information
Human SNP ID rs900400
Human chromosome chr3
Human SNP position 157080986
Pig chromosome chr13
Pig SNP position 105078605
2.Annotation Information
PubMed ID20372150
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/20372150
StudyVariants in ADCY5 and near CCNL1 are associated with fetal growth and birth weight.
Disease/TraitBirth weight
Initial sample10,623 European ancestry individuals
Replication sample27,591 European ancestry individuals, 1,415 Filipino ancestry individuals, 746 North African ancestry individuals, 333 Turkish ancestry individuals
Region3q25.31
Chromosome idchr3
Chromosome position157080986
Reported geneLEKR1, CCNL1
Mapped geneLEKR1 - LINC00880
Upstream gene id389170
Downstream gene id339894
SNP gene ids
Upstream gene distance33327
Downstream gene distance681
SNP risk allelers900400-C
SNPsrs900400
Merged0
SNP id current900400
Contextupstream_gene_variant
Intergenic1
Allele frequency
P value2E-35
Pvalue mlog34.698970004336
P value text
Or beta0.09
%95 Ci[0.073-0.10] s.d. decrease
PlatformAffymetrix, Illumina [~ 2400000] (imputed)
CNVN
Mapped traitbirth weight
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004344
Study accessionGCST000648
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
Region3q25.31
Chromosome idchr3
Chromosome position157080986
Reported geneCCNL1
Mapped geneLEKR1 - LINC00880
Upstream gene id389170
Downstream gene id339894
SNP gene ids
Upstream gene distance33327
Downstream gene distance681
SNP risk allelers900400-C
SNPsrs900400
Merged0
SNP id current900400
Contextupstream_gene_variant
Intergenic1
Allele frequency0.39
P value4E-38
Pvalue mlog37.397940008672
P value text
Or beta0.072
%95 Ci[0.060-0.084] gram decrease
PlatformAffymetrix, Illumina [~ 2700000] (imputed)
CNVN
Mapped traitbirth weight
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004344
Study accessionGCST001758
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
Region3q25.31
Chromosome idchr3
Chromosome position157080986
Reported geneLEKR1, CCNL1
Mapped geneLEKR1 - LINC00880
Upstream gene id389170
Downstream gene id339894
SNP gene ids
Upstream gene distance33327
Downstream gene distance681
SNP risk allelers900400-T
SNPsrs900400
Merged0
SNP id current900400
Contextupstream_gene_variant
Intergenic1
Allele frequency0.61
P value0.00000000002
Pvalue mlog10.698970004336
P value text
Or beta0.03
%95 Ci[0.02-0.04] unit increase
PlatformAffymetrix, Illumina [2441815] (imputed)
CNVN
Mapped traitage at menarche
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004703
Study accessionGCST002541