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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs2300938          
refSNP ID: rs2300938
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:100/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/G/T
Ancestral Allele:Not available
Clinical Association:unknown
HGVS Names
NM_001735.2:c.65+1477A>C
NM_001735.2:c.65+1477A>T
NT_008470.18:g.31132188T>A
NT_008470.18:g.31132188T>G
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 ss10497609 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2300938 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
ss3246730YUSUKE|IMS-JST056815fwd/BG/Tttggttcttattgacttatcagtagcataactatccatataaataatttcatagttttct09/05/0110/10/03100Genomicunknown
ss10497609BCM_SSAHASNP|chr9.NT_008470.15_25633609fwd/TA/Tttggttcttattgacttatcagtagcataactatccatataaataatttcatagttttct06/29/0310/10/03116Genomicunknown
ss13595631BCM_SSAHASNP|chr9.NT_008470.16_25468718fwd/TA/Tttggttcttattgacttatcagtagcataactatccatataaataatttcatagttttct11/05/0311/22/03119Genomicunknown
ss35315259SSAHASNP|TA-079.chr9_120890537fwd/A/Tttggttcttattgacttatcagtagcataactatccatataaataatttcatagttttct03/11/05125Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2300938|allelePos=542|totalLen=1075|taxid=9606|snpclass=1|alleles='A/G/T'|mol=Genomic|build=125
 TATAAAGCTA CTTTAATTTC AGTATTTATA GAAGCTTTAT GTTTTTAAGT TTAGTATTGC
 TTTAATTTTG AATTGTGTAT GGTaggggtc cccaacccct gggccatgga caaataccag
 tccatggctt gttaggaacc aggctacaca gcaggaggtg agcagtgggg caaaggagca
 ttaccacctg agctctgcct cctgtcagat cagtggtggc attagattct cctaggagca
 tgaactctat tgtgaaccgc acatgcgagg gatctagatt gcaagctcct tatgagaata
 taatgcctga tgatctgaag tggaacagtt tcattctgaa accatcccca ccccaatcct
 ggtccatgga aacattgtct tccacaaaac ctgtccctag tgccaaaatg gttggggact
 gctgGTCTAT GTGATGGTAG CCGTCAAGCA AAAATACATA GTGTTTAGAA GCCCCTAAAA
 GAATATTCTG GAACCACCCT TTATAAAGAT TTTGGTTCTT ATTGACTTAT CAGTAGCATA
 A
 D
 CTATCCATAT AAATAATTTC ATAGTTTTCT TTGTCTTTCA ATTGCTGCAG AGGAGCAGGA
 GCTTGCAGAG AGGCAAGAAT GTTATTTTGG cctctatctg gaatgctctt tcctcaaata
 tttgcatggt ttgcttcctc acttccttca ggctctgttt gagtgcagcc tccttaagag
 aacctttcct ggccacattt taaaatagtg ccccataatt attttttaat tctcatactc
 tgctttattt ttttcttcat aatactacct acctgacctt acacattctt tcattggttc
 attcattcat tacttgcttc tcccactaga atgcaagctc taggaattgt cttaccgttt
 gctatatctg cagtgcctat catatgttta gatgctcaat aaatatttgt tgaatcaatc
 aatCAACCAA TTAATTAAAG TGATTGATTG CCATGTTGTA AATGGTACAC TCTGACTTCT
 TCAGAGAAAG TGAGGAAATA ATTTTTATTA AGGGCTAGTA GAAAGAATTC AGA

  GeneView back to top
GeneView via analysis of contig annotation: C5 complement component 5
View variations for gene:
Include clinically associated: in gene region cSNP has frequency double hit
Group
Label		Contig->mRNAGene Model (contig mRNA transcript) Color Legend
referenceNT_008470->NM_001735
svfunction
HuRefNW_001839237->NM_001735
svfunction
CeleraNW_924573->NM_001735
svfunction
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_008470->NM_001735->NP_00172631132188reverseintron
HuRefNW_001839237->NM_001735->NP_001726755805forwardintron
CeleraNW_924573->NM_001735->NP_0017267947266reverseintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs2300938 maps exactly once on NCBI human chromosome 9
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
9NW_001839237.275580593428876minusAalt_assembly_8HuRefHuRefview541
9NW_924573.1794726694459435plusTalt_assembly_1CeleraCeleraview541
9NT_008470.1831132188122850804plusTref_assemblyreferencereferenceview541

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_008470
dbSNP Blast Analysis
GenBank HTGS Finished:
AC006430.22 NC_000009.10

  Population Diversity back to top
There is no frequency data.

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byClusterwith2hit
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .