NCBI
dbSNP
dbVar ClinVar GaP PubMed Nucleotide Protein
Search small variations in dbSNP or large structural variations in dbVar
transparent GIF
Attention: This page will be retired!
This legacy RefSNP page contains old data from dbSNP build 151 (March 2018) and is no longer maintained. Please update your links and bookmarks to use the re-designed RefSNP Report page.
Spacer gif
Have a question about dbSNP? Try searching the SNP FAQ Archive!

Spacer gif
Reference SNP (refSNP) Cluster Report: rs77888940                 ** With Pathogenic allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:131/151
Map to Genome Build:108/Weight 1
Validation Status:byCluster
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/C/G/T (FWD)
Allele Origin:C:germline
G:inherited
Ancestral Allele:C
Variation Viewer:link to VariationViewer
Clinical Significance:With Pathogenic allele [ClinVar]
MAF/MinorAlleleCount:G=0.0002/29 (TOPMED)
HGVS Names
  • CM000668.2:g.1610017C>A
  • CM000668.2:g.1610017C>G
  • CM000668.2:g.1610017C>T
  • NC_000006.11:g.1610252C>G
  • NC_000006.12:g.1610017C>A
  • NC_000006.12:g.1610017C>G
  • NC_000006.12:g.1610017C>T
  • NG_009368.1:g.4572C>A
  • NG_009368.1:g.4572C>G
  • NG_009368.1:g.4572C>T
  • NM_001453.2:c.-429C>A
  • NM_001453.2:c.-429C>G
  • NM_001453.2:c.-429C>T
Links
SNP Details are organized in the following sections:
GeneView Map Submission Fasta Resource Diversity Validation

  Integrated Maps (Hint: click on 'Chr Pos' to see variant in the new NCBI variation viewer) back to top

  GeneView back to top

GeneView via direct blast against RefSeq sequences (used when no gene model is available): N/A


  Submitter records for this RefSNP Cluster back to top
The submission ss158146055 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs77888940 during BLAST analysis for the current build.


NCBI
Assay ID
Handle|Submitter IDValidation
Status
ss to rs
Orientation
/Strand
Alleles5' Near Seq 30 bp3' Near Seq 30 bpEntry
Date
Update
Date
Build
Added
Molecule
Type
Freq
Warning
Ancestral
Allele
Success
Rate
ss158146055EGP_SNPS|FOXC1-001570fwd/C/Gcggggcccgggcaggcggccggcgcgcggcccccccccccccgccctggttatttggccg06/26/0906/26/09131Genomicunknown
ss1584194660CRISTINAMEDINA|PCG96; PCG169fwd/C/Gcggggcccgggcaggcggccggcgcgcggcccccccccccccgccctggttatttggccg03/02/1503/02/15142Genomicunknown
ss2834974343GNOMAD|rs77888940fwd/C/G/Tcccgggcaggcggccggcgcgcggcccccccccccccgccctggttattt05/18/1705/18/17151Genomicunknown
ss3488286368TOPMED|TOPMed_freeze_5?chr6:1,610,017-01fwd/A/Ccccgggcaggcggccggcgcgcggcccccccccccccgccctggttattt10/05/1710/05/17151Genomicunknown
ss3488286369TOPMED|TOPMed_freeze_5?chr6:1,610,017-02fwd/C/Gcccgggcaggcggccggcgcgcggcccccccccccccgccctggttattt10/05/1710/05/17151Genomicunknown
ss3488286370TOPMED|TOPMed_freeze_5?chr6:1,610,017-03fwd/C/Tcccgggcaggcggccggcgcgcggcccccccccccccgccctggttattt10/05/1710/05/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs77888940|allelePos=256|totalLen=511|taxid=9606|snpclass=1|alleles='A/C/G/T'|mol=Genomic|build=151
 TCCGGCCTCC GGGAGCGGGC CGGCAGGGCT CGGCCTCCGG CTCATTCGGA GGCGGTTCTC
 ACCTCCCATT GGCTGCCGCC GCTGGCGGGG CGGGGCTCCG CTGCCCGGAA AAAAGTGTAA
 CTGCGTAAAA AAGTCCTCGC CTGGGTGACG GATGCTCAAA AGTTCAGAAG TTTTCCCAAT
 GCTTCCTTAA GCGGCTGGCG CGCGAGAGAC CGAGAAAAGG TGACGCGGGG CCCGGGCAGG
 CGGCCGGCGC GCGGC
 N
 CCCCCCCCCC CCGCCCTGGT TATTTGGCCG CCTTCGCCGG CAGCTCAGGG CAGAGTCTCC
 TGGAAGGCGC AGGCAGTGTG GCGAGAAGGG CGCCTGCTTG TTCTTTCTTT TTGTCTGCTT
 TCCCCCGTTT GCGCCTGGAA GCTGCGCCGC GAGTTCCTGC AAGGCGGTCT GCCGCGGCCG
 GGCCCGGCCT TCTCCCCTCG CAGCGACCCC GCCTCGCGGC CGCGCGGGCC CCGAGGTAGC
 CCGAGGCGCC GGAGG

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
GQ282997
dbSNP Blast Analysis

  Population Diversity (Alleles in RefSNP orientation) back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceC/C
HWPC
ss158146055EGP_CEPH-PANELEuropean 42IG1.00000000 1.00000000
EGP_AD-PANELAfrican American 18IG1.00000000 1.00000000
EGP_ASIAN-PANELAsian 30IG1.00000000 1.00000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterUNKNOWNUNKNOWNYES

GENERAL: Contact Us | Homepage | Announcements |dbSNP Summary | Genome | FTP SERVER | Build History | Handle Request
DOCUMENTATION: FAQ | Searchable FAQ Archive | Overview | How to Submit | RefSNP Summary Info | Database Schema
SEARCH: Entrez SNP | Blast SNP | Batch Query | By Submitter |New Batches | Method | Population | Publication | Batch | Locus Info | Between Marker
NCBI: PubMed | Entrez | BLAST | OMIM | Taxonomy | Structure

Disclaimer     Privacy statement