Human SNP ID | rs987525 |
---|---|
Human chromosome | chr8 |
Human SNP position | 128933908 |
Pig chromosome | chr4 |
Pig SNP position | 11788625 |
PubMed ID | 19270707 |
---|---|
Journal | Nat Genet |
Link | www.ncbi.nlm.nih.gov/pubmed/19270707 |
Study | Key susceptibility locus for nonsyndromic cleft lip with or without cleft palate on chromosome 8q24. |
Disease/Trait | Orofacial clefts |
Initial sample | 224 European ancestry cases, 383 European ancestry controls |
Replication sample | 246 cases, 954 controls |
Region | 8q24.21 |
Chromosome id | chr8 |
Chromosome position | 128933908 |
Reported gene | GSDMC, PVT1 |
Mapped gene | LOC105375756 - LINC00977 |
Upstream gene id | 105375756 |
Downstream gene id | 728724 |
SNP gene ids | |
Upstream gene distance | 117241 |
Downstream gene distance | 282559 |
SNP risk allele | rs987525-A |
SNPs | rs987525 |
Merged | 0 |
SNP id current | 987525 |
Context | intron_variant |
Intergenic | 1 |
Allele frequency | 0.2 |
P value | 3E-24 |
Pvalue mlog | 23.5228787452803 |
P value text | |
Or beta | 2.57 |
%95 Ci | [2.02-3.26] |
Platform | Illumina [521176] |
CNV | N |
Mapped trait | cleft lip |
Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0003959 |
Study accession | GCST000353 |
PubMed ID | 19656524 |
Journal | J Pediatr |
Link | www.ncbi.nlm.nih.gov/pubmed/19656524 |
Study | A genome-wide association study identifies a locus for nonsyndromic cleft lip with or without cleft palate on 8q24. |
Disease/Trait | Orofacial clefts |
Initial sample | 111 European ancestry cases, 5,951 European ancestry controls |
Replication sample | NA |
Region | 8q24.21 |
Chromosome id | chr8 |
Chromosome position | 128933908 |
Reported gene | intergenic |
Mapped gene | LOC105375756 - LINC00977 |
Upstream gene id | 105375756 |
Downstream gene id | 728724 |
SNP gene ids | |
Upstream gene distance | 117241 |
Downstream gene distance | 282559 |
SNP risk allele | rs987525-? |
SNPs | rs987525 |
Merged | 0 |
SNP id current | 987525 |
Context | intron_variant |
Intergenic | 1 |
Allele frequency | 0.22 |
P value | 0.00000009 |
Pvalue mlog | 7.04575749056067 |
P value text | |
Or beta | 2.09 |
%95 Ci | [1.59-2.76] |
Platform | Illumina [495858] |
CNV | N |
Mapped trait | cleft lip |
Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0003959 |
Study accession | GCST000458 |
PubMed ID | 20436469 |
Journal | Nat Genet |
Link | www.ncbi.nlm.nih.gov/pubmed/20436469 |
Study | A genome-wide association study of cleft lip with and without cleft palate identifies risk variants near MAFB and ABCA4. |
Disease/Trait | Cleft lip |
Initial sample | 825 European ancestry trios, 1,038 Asian ancestry trios |
Replication sample | 2,194 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 |
Region | 8q24.21 |
Chromosome id | chr8 |
Chromosome position | 128933908 |
Reported gene | intergenic |
Mapped gene | LOC105375756 - LINC00977 |
Upstream gene id | 105375756 |
Downstream gene id | 728724 |
SNP gene ids | |
Upstream gene distance | 117241 |
Downstream gene distance | 282559 |
SNP risk allele | rs987525-A |
SNPs | rs987525 |
Merged | 0 |
SNP id current | 987525 |
Context | intron_variant |
Intergenic | 1 |
Allele frequency | 0.17 |
P value | 0.0000000000000004 |
Pvalue mlog | 15.397940008672 |
P value text | |
Or beta | 1.78 |
%95 Ci | [1.55-2.05] |
Platform | Illumina [589945] |
CNV | N |
Mapped trait | cleft lip |
Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0003959 |
Study accession | GCST000673 |
PubMed ID | 22863734 |
Journal | Nat Genet |
Link | www.ncbi.nlm.nih.gov/pubmed/22863734 |
Study | Genome-wide meta-analyses of nonsyndromic cleft lip with or without cleft palate identify six new risk loci. |
Disease/Trait | Orofacial clefts |
Initial sample | Up to 666 European ancestry trios, 399 European ancestry cases, 1,318 European ancestry controls |
Replication sample | up to 795 East Asian ancestry trios |
Region | 8q24.21 |
Chromosome id | chr8 |
Chromosome position | 128933908 |
Reported gene | NR |
Mapped gene | LOC105375756 - LINC00977 |
Upstream gene id | 105375756 |
Downstream gene id | 728724 |
SNP gene ids | |
Upstream gene distance | 117241 |
Downstream gene distance | 282559 |
SNP risk allele | rs987525-A |
SNPs | rs987525 |
Merged | 0 |
SNP id current | 987525 |
Context | intron_variant |
Intergenic | 1 |
Allele frequency | NR |
P value | 5E-35 |
Pvalue mlog | 34.3010299956639 |
P value text | (Meta-All, NSCL/P) |
Or beta | 1.919 |
%95 Ci | [1.66-2.218] |
Platform | NR [497084] |
CNV | N |
Mapped trait | progranulin measurement |
Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004625 |
Study accession | GCST001628 |
PubMed ID | 22863734 |
Journal | Nat Genet |
Link | www.ncbi.nlm.nih.gov/pubmed/22863734 |
Study | Genome-wide meta-analyses of nonsyndromic cleft lip with or without cleft palate identify six new risk loci. |
Disease/Trait | Orofacial clefts |
Initial sample | Up to 666 European ancestry trios, 399 European ancestry cases, 1,318 European ancestry controls |
Replication sample | up to 795 East Asian ancestry trios |
Region | 8q24.21 |
Chromosome id | chr8 |
Chromosome position | 128933908 |
Reported gene | NR |
Mapped gene | LOC105375756 - LINC00977 |
Upstream gene id | 105375756 |
Downstream gene id | 728724 |
SNP gene ids | |
Upstream gene distance | 117241 |
Downstream gene distance | 282559 |
SNP risk allele | rs987525-A |
SNPs | rs987525 |
Merged | 0 |
SNP id current | 987525 |
Context | intron_variant |
Intergenic | 1 |
Allele frequency | NR |
P value | 1E-26 |
Pvalue mlog | 26 |
P value text | (Meta-All, NSCLP) |
Or beta | |
%95 Ci | |
Platform | NR [497084] |
CNV | N |
Mapped trait | progranulin measurement |
Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004625 |
Study accession | GCST001628 |
PubMed ID | 22863734 |
Journal | Nat Genet |
Link | www.ncbi.nlm.nih.gov/pubmed/22863734 |
Study | Genome-wide meta-analyses of nonsyndromic cleft lip with or without cleft palate identify six new risk loci. |
Disease/Trait | Orofacial clefts |
Initial sample | Up to 666 European ancestry trios, 399 European ancestry cases, 1,318 European ancestry controls |
Replication sample | up to 795 East Asian ancestry trios |
Region | 8q24.21 |
Chromosome id | chr8 |
Chromosome position | 128933908 |
Reported gene | NR |
Mapped gene | LOC105375756 - LINC00977 |
Upstream gene id | 105375756 |
Downstream gene id | 728724 |
SNP gene ids | |
Upstream gene distance | 117241 |
Downstream gene distance | 282559 |
SNP risk allele | rs987525-A |
SNPs | rs987525 |
Merged | 0 |
SNP id current | 987525 |
Context | intron_variant |
Intergenic | 1 |
Allele frequency | NR |
P value | 0.00000000002 |
Pvalue mlog | 10.698970004336 |
P value text | (Meta-All, NSCLO) |
Or beta | |
%95 Ci | |
Platform | NR [497084] |
CNV | N |
Mapped trait | progranulin measurement |
Mapped trait URI | http://www.ebi.ac.uk/efo/EFO_0004625 |
Study accession | GCST001628 |