SNP Detail For rs987525
1.Mapping Information
Human SNP ID rs987525
Human chromosome chr8
Human SNP position 128933908
Pig chromosome chr4
Pig SNP position 11788625
2.Annotation Information
PubMed ID19270707
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/19270707
StudyKey susceptibility locus for nonsyndromic cleft lip with or without cleft palate on chromosome 8q24.
Disease/TraitOrofacial clefts
Initial sample224 European ancestry cases, 383 European ancestry controls
Replication sample246 cases, 954 controls
Region8q24.21
Chromosome idchr8
Chromosome position128933908
Reported geneGSDMC, PVT1
Mapped geneLOC105375756 - LINC00977
Upstream gene id105375756
Downstream gene id728724
SNP gene ids
Upstream gene distance117241
Downstream gene distance282559
SNP risk allelers987525-A
SNPsrs987525
Merged0
SNP id current987525
Contextintron_variant
Intergenic1
Allele frequency0.2
P value3E-24
Pvalue mlog23.5228787452803
P value text
Or beta2.57
%95 Ci[2.02-3.26]
PlatformIllumina [521176]
CNVN
Mapped traitcleft lip
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0003959
Study accessionGCST000353
PubMed ID19656524
JournalJ Pediatr
Linkwww.ncbi.nlm.nih.gov/pubmed/19656524
StudyA genome-wide association study identifies a locus for nonsyndromic cleft lip with or without cleft palate on 8q24.
Disease/TraitOrofacial clefts
Initial sample111 European ancestry cases, 5,951 European ancestry controls
Replication sampleNA
Region8q24.21
Chromosome idchr8
Chromosome position128933908
Reported geneintergenic
Mapped geneLOC105375756 - LINC00977
Upstream gene id105375756
Downstream gene id728724
SNP gene ids
Upstream gene distance117241
Downstream gene distance282559
SNP risk allelers987525-?
SNPsrs987525
Merged0
SNP id current987525
Contextintron_variant
Intergenic1
Allele frequency0.22
P value0.00000009
Pvalue mlog7.04575749056067
P value text
Or beta2.09
%95 Ci[1.59-2.76]
PlatformIllumina [495858]
CNVN
Mapped traitcleft lip
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0003959
Study accessionGCST000458
PubMed ID20436469
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/20436469
StudyA genome-wide association study of cleft lip with and without cleft palate identifies risk variants near MAFB and ABCA4.
Disease/TraitCleft lip
Initial sample825 European ancestry trios, 1,038 Asian ancestry trios
Replication sample2,194 Asian ancestry family members, 322 South Asian ancestry family members, 3,830 European ancestry family members, 1,769 South and Central American ancestry family members
Region8q24.21
Chromosome idchr8
Chromosome position128933908
Reported geneintergenic
Mapped geneLOC105375756 - LINC00977
Upstream gene id105375756
Downstream gene id728724
SNP gene ids
Upstream gene distance117241
Downstream gene distance282559
SNP risk allelers987525-A
SNPsrs987525
Merged0
SNP id current987525
Contextintron_variant
Intergenic1
Allele frequency0.17
P value0.0000000000000004
Pvalue mlog15.397940008672
P value text
Or beta1.78
%95 Ci[1.55-2.05]
PlatformIllumina [589945]
CNVN
Mapped traitcleft lip
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0003959
Study accessionGCST000673
PubMed ID22863734
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/22863734
StudyGenome-wide meta-analyses of nonsyndromic cleft lip with or without cleft palate identify six new risk loci.
Disease/TraitOrofacial clefts
Initial sampleUp to 666 European ancestry trios, 399 European ancestry cases, 1,318 European ancestry controls
Replication sampleup to 795 East Asian ancestry trios
Region8q24.21
Chromosome idchr8
Chromosome position128933908
Reported geneNR
Mapped geneLOC105375756 - LINC00977
Upstream gene id105375756
Downstream gene id728724
SNP gene ids
Upstream gene distance117241
Downstream gene distance282559
SNP risk allelers987525-A
SNPsrs987525
Merged0
SNP id current987525
Contextintron_variant
Intergenic1
Allele frequencyNR
P value5E-35
Pvalue mlog34.3010299956639
P value text(Meta-All, NSCL/P)
Or beta1.919
%95 Ci[1.66-2.218]
PlatformNR [497084]
CNVN
Mapped traitprogranulin measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004625
Study accessionGCST001628
PubMed ID22863734
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/22863734
StudyGenome-wide meta-analyses of nonsyndromic cleft lip with or without cleft palate identify six new risk loci.
Disease/TraitOrofacial clefts
Initial sampleUp to 666 European ancestry trios, 399 European ancestry cases, 1,318 European ancestry controls
Replication sampleup to 795 East Asian ancestry trios
Region8q24.21
Chromosome idchr8
Chromosome position128933908
Reported geneNR
Mapped geneLOC105375756 - LINC00977
Upstream gene id105375756
Downstream gene id728724
SNP gene ids
Upstream gene distance117241
Downstream gene distance282559
SNP risk allelers987525-A
SNPsrs987525
Merged0
SNP id current987525
Contextintron_variant
Intergenic1
Allele frequencyNR
P value1E-26
Pvalue mlog26
P value text(Meta-All, NSCLP)
Or beta
%95 Ci
PlatformNR [497084]
CNVN
Mapped traitprogranulin measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004625
Study accessionGCST001628
PubMed ID22863734
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/22863734
StudyGenome-wide meta-analyses of nonsyndromic cleft lip with or without cleft palate identify six new risk loci.
Disease/TraitOrofacial clefts
Initial sampleUp to 666 European ancestry trios, 399 European ancestry cases, 1,318 European ancestry controls
Replication sampleup to 795 East Asian ancestry trios
Region8q24.21
Chromosome idchr8
Chromosome position128933908
Reported geneNR
Mapped geneLOC105375756 - LINC00977
Upstream gene id105375756
Downstream gene id728724
SNP gene ids
Upstream gene distance117241
Downstream gene distance282559
SNP risk allelers987525-A
SNPsrs987525
Merged0
SNP id current987525
Contextintron_variant
Intergenic1
Allele frequencyNR
P value0.00000000002
Pvalue mlog10.698970004336
P value text(Meta-All, NSCLO)
Or beta
%95 Ci
PlatformNR [497084]
CNVN
Mapped traitprogranulin measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004625
Study accessionGCST001628