SNP Detail For rs429358
1.Mapping Information
Human SNP ID rs429358
Human chromosome chr19
Human SNP position 44908684
Pig chromosome chr6
Pig SNP position 47271504
2.Annotation Information
PubMed ID21123754
JournalNeurology
Linkwww.ncbi.nlm.nih.gov/pubmed/21123754
StudyGenome-wide association study of CSF biomarkers Abeta1-42, t-tau, and p-tau181p in the ADNI cohort.
Disease/TraitAlzheimer__s disease biomarkers
Initial sample96 European ancestry Alzheimer disease cases, 176 European ancestry individuals with mild cognitive impairment, 102 European ancestry controls
Replication sampleNA
Region19q13.32
Chromosome idchr19
Chromosome position44908684
Reported geneAPOE
Mapped geneAPOE
Upstream gene id
Downstream gene id
SNP gene ids348
Upstream gene distance
Downstream gene distance
SNP risk allelers429358-?
SNPsrs429358
Merged0
SNP id current429358
Contextmissense_variant
Intergenic0
Allele frequencyNR
P value0.000001
Pvalue mlog6
P value text(AB1-42, p-tau181p, p-tau181p/AB1-42, t-tau/AB1-42)
Or beta
%95 Ci
PlatformIllumina [322557]
CNVN
Mapped traitp-tau measurement, beta-amyloid 1-42 measurement, Alzheimers disease, t-tau measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004763, http://www.ebi.ac.uk/efo/EFO_0004670, http://www.ebi.ac.uk/efo/EFO_0000249, http://www.ebi.ac.uk/efo/EFO_0004760
Study accessionGCST000900
PubMed ID20100581
JournalNeuroimage
Linkwww.ncbi.nlm.nih.gov/pubmed/20100581
StudyWhole genome association study of brain-wide imaging phenotypes for identifying quantitative trait loci in MCI and AD: A study of the ADNI cohort.
Disease/TraitBrain imaging
Initial sample175 European ancestry Alzheimer cases, 354 European ancestry amnestic mild cognitive impairment cases, 204 European ancestry controls
Replication sampleNA
Region19q13.32
Chromosome idchr19
Chromosome position44908684
Reported geneAPOE
Mapped geneAPOE
Upstream gene id
Downstream gene id
SNP gene ids348
Upstream gene distance
Downstream gene distance
SNP risk allelers429358-?
SNPsrs429358
Merged0
SNP id current429358
Contextmissense_variant
Intergenic0
Allele frequencyNR
P value
Pvalue mlog
P value text<1 x 10-6 (multiple phenotypes)
Or beta
%95 Ci
PlatformIllumina [530992]
CNVN
Mapped traitneuroimaging measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004346
Study accessionGCST000573
PubMed ID23419831
JournalMol Psychiatry
Linkwww.ncbi.nlm.nih.gov/pubmed/23419831
StudyAPOE and BCHE as modulators of cerebral amyloid deposition: a florbetapir PET genome-wide association study.
Disease/TraitAlzheimer__s disease biomarkers
Initial sample555 European ancestry individuals
Replication sampleNA
Region19q13.32
Chromosome idchr19
Chromosome position44908684
Reported geneAPOE
Mapped geneAPOE
Upstream gene id
Downstream gene id
SNP gene ids348
Upstream gene distance
Downstream gene distance
SNP risk allelers429358-C
SNPsrs429358
Merged0
SNP id current429358
Contextmissense_variant
Intergenic0
Allele frequency0.28
P value0.00000000000005
Pvalue mlog13.3010299956639
P value text(Cortical Ab)
Or beta
%95 Ci
PlatformIllumina [6108668] (imputed)
CNVN
Mapped traitamyloid-beta measurement, Alzheimers disease
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0005194, http://www.ebi.ac.uk/efo/EFO_0000249
Study accessionGCST001868
PubMed ID25027320
JournalHum Mol Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/25027320
StudySUCLG2 identified as both a determinator of CSF A脽1-42-levels and an attenuator of cognitive decline in Alzheimer__s disease.
Disease/TraitCerebrospinal AB1-42 levels in Alzheimer__s disease dementia
Initial sample363 European ancestry individuals
Replication sample515 individuals
Region19q13.32
Chromosome idchr19
Chromosome position44908684
Reported geneAPOE
Mapped geneAPOE
Upstream gene id
Downstream gene id
SNP gene ids348
Upstream gene distance
Downstream gene distance
SNP risk allelers429358-?
SNPsrs429358
Merged0
SNP id current429358
Contextmissense_variant
Intergenic0
Allele frequency0.442
P value0.00000000000000004
Pvalue mlog16.397940008672
P value text
Or beta0.4
%95 Ci[0.30-0.50] unit decrease
PlatformIllumina [6812394] (imputed)
CNVN
Mapped traitbeta-amyloid 1-42 measurement, Alzheimers disease
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004670, http://www.ebi.ac.uk/efo/EFO_0000249
Study accessionGCST002531
PubMed ID26252872
JournalPLoS One
Linkwww.ncbi.nlm.nih.gov/pubmed/26252872
StudyVariations in the FRA10AC1 Fragile Site and 15q21 Are Associated with Cerebrospinal Fluid Aå°¾1-42 Level.
Disease/TraitCerebral amyloid deposition (PET imaging)
Initial sampleup to 883 European and other ancestry individuals
Replication sampleNA
Region19q13.32
Chromosome idchr19
Chromosome position44908684
Reported genePVRL2, APOE, APOC1, APOC1P1, TOMM40
Mapped geneAPOE
Upstream gene id
Downstream gene id
SNP gene ids348
Upstream gene distance
Downstream gene distance
SNP risk allelers429358-T
SNPsrs429358
Merged0
SNP id current429358
Contextmissense_variant
Intergenic0
Allele frequency0.02
P value8E-32
Pvalue mlog31.096910013008
P value text
Or beta0.13
%95 Ci[NR] unit decrease
PlatformIllumina [~ 9000000] (imputed)
CNVN
Mapped traitcerebral amyloid deposition measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0007707
Study accessionGCST003073
PubMed ID25961943
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/25961943
StudyThe impact of low-frequency and rare variants on lipid levels.
Disease/TraitHDL cholesterol
Initial sampleup to 62,166 European ancestry individuals
Replication sampleNA
Region19q13.32
Chromosome idchr19
Chromosome position44908684
Reported geneAPOE
Mapped geneAPOE
Upstream gene id
Downstream gene id
SNP gene ids348
Upstream gene distance
Downstream gene distance
SNP risk allelers429358-T
SNPsrs429358
Merged0
SNP id current429358
Contextmissense_variant
Intergenic0
Allele frequency0.84
P value0.00000000000001
Pvalue mlog14
P value text
Or beta0.066
%95 Ci[0.048-0.084] s.d. increase
PlatformAffymetrix, Illumina, Perlegen [up to 9657952] (imputed)
CNVN
Mapped traithigh density lipoprotein cholesterol measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004612
Study accessionGCST002899
PubMed ID26252872
JournalPLoS One
Linkwww.ncbi.nlm.nih.gov/pubmed/26252872
StudyVariations in the FRA10AC1 Fragile Site and 15q21 Are Associated with Cerebrospinal Fluid Aå°¾1-42 Level.
Disease/TraitCerebral amyloid deposition positivity (PET imaging)
Initial sampleup to 350 European and other ancestry positive individuals, up to 296 European and other ancestry negative individuals
Replication sampleNA
Region19q13.32
Chromosome idchr19
Chromosome position44908684
Reported geneAPOE, APOC1, APOC1P1, PVRL2, TOMM40
Mapped geneAPOE
Upstream gene id
Downstream gene id
SNP gene ids348
Upstream gene distance
Downstream gene distance
SNP risk allelers429358-C
SNPsrs429358
Merged0
SNP id current429358
Contextmissense_variant
Intergenic0
Allele frequency0.85
P value5E-20
Pvalue mlog19.3010299956639
P value text
Or beta4.72
%95 Ci[4.39-5.05]
PlatformIllumina [~ 9000000] (imputed)
CNVN
Mapped traitcerebral amyloid deposition measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0007707
Study accessionGCST003077
PubMed ID25188341
JournalPLoS Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/25188341
StudyGenome-Wide Association Meta-analysis of Neuropathologic Features of Alzheimer__s Disease and Related Dementias.
Disease/TraitLewy body disease
Initial sampleup to 3,526 individuals
Replication sampleNA
Region19q13.32
Chromosome idchr19
Chromosome position44908684
Reported geneAPOE, LOC100129500
Mapped geneAPOE
Upstream gene id
Downstream gene id
SNP gene ids348
Upstream gene distance
Downstream gene distance
SNP risk allelers429358-C
SNPsrs429358
Merged0
SNP id current429358
Contextmissense_variant
Intergenic0
Allele frequency0.732
P value0.000000000001
Pvalue mlog12
P value text(Ordinal I)
Or beta0.4997
%95 Ci[0.36-0.64] unit decrease
PlatformAffymetrix, Illumina [NR] (imputed)
CNVN
Mapped traitLewy body dementia, Lewy body dementia measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0006792, http://www.ebi.ac.uk/efo/EFO_0006799
Study accessionGCST002591
PubMed ID25188341
JournalPLoS Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/25188341
StudyGenome-Wide Association Meta-analysis of Neuropathologic Features of Alzheimer__s Disease and Related Dementias.
Disease/TraitLewy body disease
Initial sampleup to 3,526 individuals
Replication sampleNA
Region19q13.32
Chromosome idchr19
Chromosome position44908684
Reported geneAPOE, LOC100129500
Mapped geneAPOE
Upstream gene id
Downstream gene id
SNP gene ids348
Upstream gene distance
Downstream gene distance
SNP risk allelers429358-C
SNPsrs429358
Merged0
SNP id current429358
Contextmissense_variant
Intergenic0
Allele frequency0.7347
P value0.000000000005
Pvalue mlog11.3010299956639
P value text(Ordinal II)
Or beta0.508
%95 Ci[0.36-0.65] unit decrease
PlatformAffymetrix, Illumina [NR] (imputed)
CNVN
Mapped traitLewy body dementia, Lewy body dementia measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0006792, http://www.ebi.ac.uk/efo/EFO_0006799
Study accessionGCST002591
PubMed ID25188341
JournalPLoS Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/25188341
StudyGenome-Wide Association Meta-analysis of Neuropathologic Features of Alzheimer__s Disease and Related Dementias.
Disease/TraitLewy body disease
Initial sampleup to 3,526 individuals
Replication sampleNA
Region19q13.32
Chromosome idchr19
Chromosome position44908684
Reported geneAPOE, LOC100129500
Mapped geneAPOE
Upstream gene id
Downstream gene id
SNP gene ids348
Upstream gene distance
Downstream gene distance
SNP risk allelers429358-C
SNPsrs429358
Merged0
SNP id current429358
Contextmissense_variant
Intergenic0
Allele frequency0.7344
P value0.00000000003
Pvalue mlog10.5228787452803
P value text(Case/control)
Or beta0.4905
%95 Ci[0.35-0.63] unit decrease
PlatformAffymetrix, Illumina [NR] (imputed)
CNVN
Mapped traitLewy body dementia, Lewy body dementia measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0006792, http://www.ebi.ac.uk/efo/EFO_0006799
Study accessionGCST002591
PubMed ID26691988
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/26691988
StudyA large genome-wide association study of age-related macular degeneration highlights contributions of rare and common variants.
Disease/TraitAdvanced age-related macular degeneration
Initial sample16,144 European ancestry cases, 17,832 European ancestry controls
Replication sample473 Asian ancestry cases, 1,099 Asian ancestry controls, 52 African ancestry cases, 361 African ancestry cases, 254 other non-European ancestry cases, 694 other non-European ancestry controls
Region19q13.32
Chromosome idchr19
Chromosome position44908684
Reported geneAPOE
Mapped geneAPOE
Upstream gene id
Downstream gene id
SNP gene ids348
Upstream gene distance
Downstream gene distance
SNP risk allelers429358-?
SNPsrs429358
Merged0
SNP id current429358
Contextmissense_variant
Intergenic0
Allele frequencyNR
P value2E-42
Pvalue mlog41.698970004336
P value text(EA)
Or beta1.4285715
%95 Ci
PlatformIllumina [12023830] (imputed)
CNVN
Mapped traitage-related macular degeneration, wet macular degeneration
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0001365, http://www.ebi.ac.uk/efo/EFO_0004683
Study accessionGCST003219