Skip to main content
NCBI
 dbSNP
PubMed Nucleotide Protein Genome Structure PopSet Taxonomy OMIM Books SNP
Search for SNP on NCBI Reference Assembly
transparent GIF
Spacer gif
BUILD 130
Have a question about dbSNP? Try searching the SNP FAQ Archive!

Spacer gif
Reference SNP(refSNP) Cluster Report: rs730488          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:86/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/T
Ancestral Allele:C
Clinical Association:unknown
HGVS Names
NM_021945.4:c.71-25949G>A
NT_034880.3:g.3290184T>C
Links , Linkout

SNP Details are organized in the following sections:
Submission Fasta Resource GeneView Map Diversity Validation

  Submitter records for this RefSNP Cluster back to top
The submission ss75529 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs730488 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
ss75529TSC-CSHL|TSC0017645byFreqfwd/BC/Tatacacgaaggcagatgatcacggtcgcctcatcccctcttgggggctaagtacattcac09/06/0010/25/0686Genomic95 %
ss11836547WI_SSAHASNP|chr6.NT_034880.2_3290184fwd/BC/Tatacacgaaggcagatgatcacggtcgcctcatcccctcttgggggctaagtacattcac07/04/0310/10/03116Genomicunknown
ss12860321SC_SNP|NT_034880.2_3290184fwd/BC/Tatacacgaaggcagatgatcacggtcgcctcatcccctcttgggggctaagtacattcac10/21/0310/31/03119Genomicunknown
ss15689181SC_SNP|NT_034880.3_3290184fwd/BC/Tatacacgaaggcagatgatcacggtcgcctcatcccctcttgggggctaagtacattcac11/17/0311/22/03120Genomicunknown
ss17880330CSHL-HAPMAP|CSHL-HuCC-200402.chr6.NT_034880.3_3290184fwd/BC/Tatacacgaaggcagatgatcacggtcgcctcatcccctcttgggggctaagtacattcac02/19/0403/04/04120Genomicunknown
ss44758340ABI|hCV2711245fwd/BC/Tatacacgaaggcagatgatcacggtcgcctcatcccctcttgggggctaagtacattcac07/19/0507/19/05126Genomicunknown
ss1138099821000GENOMES|NA19240_2008_12_16_1293164_chr6_3295184fwd/BC/Tatacacgaaggcagatgatcacggtcgcctcatcccctcttgggggctaagtacattcac12/18/0812/18/08130Genomicunknown
ss116274819ILLUMINA-UK|NA18507_000005132_NCBI36.1_chr6_3295184fwd/BC/Tatacacgaaggcagatgatcacggtcgcctcatcccctcttgggggctaagtacattcac01/17/0901/17/09130Genomic99 %

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs730488|allelePos=365|totalLen=735|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 CTGGCATGAG CTGTTTTCAT CAGATTAAAA TGCATGGCCC TTCTTCCCAC ACACTATTGT
 ATTTCTGTTT GGTGAAGAAT ATTGAATGCT CAACCACCCA AGTGCTTTAA ATATCACTGA
 ATCTCAGGAG GTGGAAGAGC AGAGTGGAGA AGATGAATTA TTTGAACTAC TCAGAAATAA
 GCCTAACATG AAAGCAGGAA ATTCATATGG AGTGGGCAGT GCCTCAAGCA ACCTGATATC
 TTCAGGAAAG ATAAGGTGGT GGCTTATTGC TCCCATCGCT CTCTGATCAC AGACCTGGGA
 CAGAGCACCT CTTCCAGGGC TCTTGATTCC TGTGATACAC GAAGGCAGAT GATCACGGTC
 GCCT
 Y
 CATCCCCTCT TGGGGGCTAA GTACATTCAC AGTCCCTTGG TTCTTGGTCT TTGTGTCCTT
 TGAAGCACAT AAAAGTCTGG TGGATGAGTA GGACCATGGT TGATAGAAAA TTATTTCCCA
 GTACTGGACA GCATAGTGAC TCAGCATGCA TGCACACACA CACCCCAAAT TTTCATGAAA
 CGATACTTAA CCCTTATTGT GTGTGATGCA CTTAattcta tttttttctt taaaaatgct
 gggcaggacc cacccgatgg attctataac ccttaaccca agcctaatgt gtcataaacc
 acagttttaa aGCTGCTCTA AAGTAGGGTT GGAATACTAT GACCCTCGGG CCAAATCTGC
 TGAAGCTGCT

  GeneView back to top

GeneView via analysis of contig annotation:  

View more variation on this gene (click to hide).
Include clinically associated: in gene region cSNP has frequency double hit
Assembly SNP to Chr Chr Chr position Contig Contig position Allele
Function mRNA Protein
mRNA to Chr Accession Position Allele change Accession Position Residue change
on assembly: is labeled at position on chromosome .

GeneView via analysis of contig annotation: N/A.

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

Function Chr mRNA Protein
SNP to mRNA Accession Position Allele change Accession Position Residue change
on assembly: is labeled at position on chromosome .

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


  Integrated Maps: back to top
Genome Build Chr Chr Pos Contig Contig Pos SNP to
Chr		 Contig
allele		 Group term Group label Contig label Neighbor
SNP		 Map Method
doesn't map to any assembly.

  NCBI Resource Links back to top
Resource
Submitter-Referenced
GenBank
NT_034880
dbSNP Blast Analysis

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source C/C
 C/T
 T/T
 HWP C
 T
ss75529 TSC_42_AA 82 AF 0.659 0.341
TSC_42_C 68 AF 0.397 0.603
TSC_42_A 82 AF 0.476 0.524
HapMap-CEU European 104 IG 0.077 0.500 0.423 0.343 0.327 0.673
HapMap-HCB Asian 76 IG 0.211 0.500 0.289 1.000 0.461 0.539
HapMap-JPT Asian 82 IG 0.244 0.439 0.317 0.479 0.463 0.537
HapMap-YRI Sub-Saharan African 100 IG 0.520 0.460 0.020 0.150 0.750 0.250

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.500+/-0.003 525 409 0 0

  Validation Summary: back to top
Validation status Marker displays
Mendelian segregation		 PCR results confirmed
in multiple reactions		 Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
DoubleHit found by:  BCM_SSAHASNP, NCBI
 UNKNOWN UNKNOWN UNKNOWN

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
HAPLOTYPE:Submission | Specifications | Sample HapSet | Sample Individual
NCBI: PubMed | Entrez | BLAST | OMIM | Taxonomy | Structure

Disclaimer     Privacy statement

Revised: May 25, 2006 1:38 PM .