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1:207757515:A:G (rs12034598)

ATCATAGCCTGGCATCATCAAGAAAA/GATTAAATCACTGATATACAAATAAT

single-nucleotide variant

ADSP Variant WGS

WGS Filter Status: PASS: pass in both GATK and ATLAS

More information

NOTE: Corresponding records for this variant may not exist in the ExAC or GTex resources.

Genomic Context

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This variant falls within the genes: CR1, RP11-78B10.2.

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Population Frequencies

Alternative/minor allele frequencies reported by various studies or from standard resources (1000 Genomes, dbSNP, ExAC) for specific populations.

When the population is identified as Global, it typically refers to a meta-value calculated across all populations in the study or resource; mouse over for more information.

Frequencies are reported as documented in the orignial data source or calculated as a ratio of observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present.

Data sources are listed in the documentation.

The 1000Genomes Phase 1 frequencies were obtained from dbSNP.

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Population Ethnicity Resource Allele Frequency
GAF Global 1000 Genomes Phase 1 G 0.266
AFR African 1000 Genomes Phase 3 G 0.120
AMR Ad Mixed American 1000 Genomes Phase 3 G 0.262
EAS East Asian 1000 Genomes Phase 3 G 0.327
EUR European 1000 Genomes Phase 3 G 0.182
GAF Global 1000 Genomes Phase 3 G 0.266
SAS South Asian 1000 Genomes Phase 3 G 0.490
KGAF Global Kaviar G 0.213

Variant-based Trait Associations (GWAS)

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The following variants have been found to be associated with Alzheimer's disease in a GWAS study:

NIAGADS: Alzheimer's Disease

NIAGADS AD GWAS summary statistics datasets in which this variant has a genome-wide significance supported by a p-value ≤ 5 x 10-8.

For exome array studies, a cutoff of p-value < 1 x 10-3 was used.

Click on accession numbers to view a detailed report about the dataset or to request access to the data.

NHGRI GWAS Catalog: Alzheimer's Disease

Alzheimer's Disease-related annotations for the dbSNP refSNP associated with this variant in the NHGRI GWAS Catalog.

The following variants have been associated with AD-relevant neuropathologies in a GWAS study:

NIAGADS: Related neuropathologies and AD biomarkers

NIAGADS AD GWAS summary statistics datasets in which this variant has a genome-wide significance supported by a p-value ≤ 5 x 10-8.

For exome array studies, a cutoff of p-value < 1 x 10-3 was used.

Click on accession numbers to view a detailed report about the dataset or to request access to the data.

NHGRI: Other Traits (incl. related neuropathologies and AD biomarkers)

Trait associations for the dbSNP refSNP associated with this variant in the NHGRI GWAS Catalog.

Predicted Variant Effect

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Combined Annotation Dependent Depletion (CADD) PHRED-normalized scores.

The higher the score, the more deleterious the substitution is predicted to be.

PHRED-normalized scores indicate ranked deleteriousness across ~8.6 billion SNVs on the human genome (GRCh37/hg19).

A normalized-score ≥10 indicates that the variant is predicted to be among the 10% most deleterious substitutions on the human genome.

A score ≥20 indicates that the variant is among the top 1% most deleterious.

The ranked deleteriousness of this variant (CADD PHRED-score) is: 13.11

This variant is colocated with 9 transcripts in 2 genes, with the following predicted effects:

All Predictd Effects (incl. intergenic)

Most Severe Predicted Effects

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Group By: Analysis Consequence Impact Gene

Analysis Gene Ranked Over Consequence Impact
SnpEff CR1 all transcripts intron variant MODIFIER
SnpEff RP11-78B10.2 all transcripts intron variant MODIFIER

Functional Genomics

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Transcription Factor Occupancy (CATO)
contextual analysis of transcription factor occupancy (CATO) scores precomputed for dbSNP 142 in humans (hg19)

Transcription Factor Binding Site Overlap (ENCODE ChIP-SEQ)

DNase Hotspots Overlap (ENCODE DNase-SEQ)

Expressed Enhancer Overlap (FANTOM5)