SNP Detail For rs2412971
1.Mapping Information
Human SNP ID rs2412971
Human chromosome chr22
Human SNP position 30098382
Pig chromosome chr14
Pig SNP position 50123647
2.Annotation Information
PubMed ID21399633
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/21399633
StudyGenome-wide association study identifies susceptibility loci for IgA nephropathy.
Disease/TraitNephropathy
Initial sample1,194 Han Chinese ancestry cases, 902 Han Chinese ancestry controls
Replication sample712 Han Chinese ancestry cases, 748 Han Chinese ancestry controls, 1,238 European ancestry cases, 1,172 European ancestry controls
Region22q12.2
Chromosome idchr22
Chromosome position30098382
Reported geneLIF, HORMAD2, MTMR3, OSM
Mapped geneHORMAD2
Upstream gene id
Downstream gene id
SNP gene ids150280
Upstream gene distance
Downstream gene distance
SNP risk allelers2412971-?
SNPsrs2412971
Merged0
SNP id current2412971
Contextintron_variant
Intergenic0
Allele frequency0.49 (EA)
P value0.000000002
Pvalue mlog8.69897000433601
P value text
Or beta1.25
%95 Ci[NR]
PlatformIllumina [498322]
CNVN
Mapped traitkidney disease
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0003086
Study accessionGCST001009
PubMed ID25305756
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/25305756
StudyDiscovery of new risk loci for IgA nephropathy implicates genes involved in immunity against intestinal pathogens.
Disease/TraitIgA nephropathy
Initial sample1,194 Han Chinese ancestry cases, 902 Han Chinese ancestry controls, 1,553 European ancestry cases, 3,050 European ancestry controls
Replication sample2,491 East Asian ancestry cases, 1,780 East Asian ancestry controls, 2,420 European ancestry cases, 7,222 European ancestry controls
Region22q12.2
Chromosome idchr22
Chromosome position30098382
Reported geneHORMAD2
Mapped geneHORMAD2
Upstream gene id
Downstream gene id
SNP gene ids150280
Upstream gene distance
Downstream gene distance
SNP risk allelers2412971-G
SNPsrs2412971
Merged0
SNP id current2412971
Contextintron_variant
Intergenic0
Allele frequency0.54
P value0.000000000005
Pvalue mlog11.3010299956639
P value text
Or beta1.2
%95 Ci[NR]
PlatformIllumina [> 1000000] (imputed)
CNVN
Mapped traitIGA glomerulonephritis
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004194
Study accessionGCST002655
PubMed ID25305756
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/25305756
StudyDiscovery of new risk loci for IgA nephropathy implicates genes involved in immunity against intestinal pathogens.
Disease/TraitIgA nephropathy
Initial sample1,194 Han Chinese ancestry cases, 902 Han Chinese ancestry controls, 1,553 European ancestry cases, 3,050 European ancestry controls
Replication sample2,491 East Asian ancestry cases, 1,780 East Asian ancestry controls, 2,420 European ancestry cases, 7,222 European ancestry controls
Region22q12.2
Chromosome idchr22
Chromosome position30098382
Reported geneHORMAD2
Mapped geneHORMAD2
Upstream gene id
Downstream gene id
SNP gene ids150280
Upstream gene distance
Downstream gene distance
SNP risk allelers2412971-G
SNPsrs2412971
Merged0
SNP id current2412971
Contextintron_variant
Intergenic0
Allele frequency0.67
P value0.00000000006
Pvalue mlog10.2218487496163
P value text(East Asian)
Or beta1.35
%95 Ci[NR]
PlatformIllumina [> 1000000] (imputed)
CNVN
Mapped traitIGA glomerulonephritis
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004194
Study accessionGCST002655