NCBI

NLM

PubMed Nucleotide Protein Genome Structure PopSet Taxonomy OMIM Books SNP
Search for SNP on NCBI Reference Assembly
Spacer gif
BUILD 129
Have a question about dbSNP? Try searching the SNP FAQ Archive!

Spacer gif
Reference SNP(refSNP) Cluster Report: rs2410429          
refSNP ID: rs2410429
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/C
Ancestral Allele:A
Clinical Association:unknown
HGVS Names
NM_005656.2:c.446-3519T>G
NT_011512.10:g.28517918A>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 ss10982273 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2410429 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
ss3376814TSC-CSHL|TSC1653222fwd/TA/Cactgggtgacagaaggagaccttgtctcaaaaaacccaattgtacatgtttaatgtgtac09/20/0110/10/03100Genomicunknown
ss10982273BCM_SSAHASNP|chr21.NT_011512.8_28516884byFreqfwd/TA/Cactgggtgacagaaggagaccttgtctcaaaaaacccaattgtacatgtttaatgtgtac06/30/0304/07/04116Genomicunknown
ss16911586CSHL-HAPMAP|CSHL-HuAA-200402.chr21.NT_011512.9_28516444fwd/TA/Cactgggtgacagaaggagaccttgtctcaaaaaacccaattgtacatgtttaatgtgtac02/17/0403/04/04120Genomicunknown
ss17708525CSHL-HAPMAP|CSHL-HuCC-200402.chr21.NT_011512.9_28516444fwd/TA/Cactgggtgacagaaggagaccttgtctcaaaaaacccaattgtacatgtttaatgtgtac02/19/0403/04/04120Genomicunknown
ss21804661SSAHASNP|WGSA-200403-chr21.chr21.NT_011512.9_28516444fwd/TA/Cactgggtgacagaaggagaccttgtctcaaaaaacccaattgtacatgtttaatgtgtac03/20/0403/20/04121Genomicunknown
ss41495935ABI|hCV2688337fwd/TA/Cactgggtgacagaaggagaccttgtctcaaaaaacccaattgtacatgtttaatgtgtac07/17/0507/17/05126Genomicunknown
ss77157104HGSV|Cor12156_SNV_20070510.chr21_41777918fwd/TA/Cactgggtgacagaaggagaccttgtctcaaaaaacccaattgtacatgtttaatgtgtac10/09/0710/11/07129Genomicunknown
ss81193634HGSV|Cor18507_SNV_20070510.chr21_41777918fwd/TA/Cactgggtgacagaaggagaccttgtctcaaaaaacccaattgtacatgtttaatgtgtac11/26/0711/28/07130Genomicunknown
ss84284577HGSV|Cor19129_SNV_20070510.chr21_41777918fwd/TA/Cactgggtgacagaaggagaccttgtctcaaaaaacccaattgtacatgtttaatgtgtac12/06/0712/06/07130Genomicunknown
ss84326951HGSV|Cor18517_SNV_20070510.chr21_41777918fwd/TA/Cactgggtgacagaaggagaccttgtctcaaaaaacccaattgtacatgtttaatgtgtac12/06/0712/07/07130Genomicunknown
ss91847927BCMHGSC_JDW|JWB-1500023fwd/TA/Cactgggtgacagaaggagaccttgtctcaaaaaacccaattgtacatgtttaatgtgtac02/26/0803/02/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2410429|allelePos=1422|totalLen=1740|taxid=9606|snpclass=1|alleles='A/C'|mol=Genomic|build=130
 TACAtgaatg gataaacatt gtgctacatc tggacaacgg aatattattt ggtgctaaaa
 agaaatgagc tatcaagcca tgaaaaggca tggaggaaac ttgaatgcat attactaagt
 aaaggaagcc aacaaagtga aggaaggtgt atgtggtgaa ggctacatac tccatgattc
 caacgctaca acatcctgaa aagaccaaaa cttcggaggc actaagaaga tcagatagct
 ggggtgagtg gggagagaga aacaggtgca gcaaaagagg ttttaaggca ggagaactac
 tctggacgat actatcattg tggctgtaca gcattatgca tttgtcaaat cccacagaac
 tgtacaagag aaagggtgaa gtccaggact tcagttcatc ataatgtatg catcaggttc
 atcggtgtta atgaacgcac agcactgatg tgggatgttc ataacagggc aactgtgtgc
 tggggaggag tacaaggagc tcgctgccct gtctgtttca ttttctgtaa acctaaaacc
 gctctaaaat ataaagtctg ttcacttttt taaaaGTAAC TGAAATGAAT ACACTTCTTC
 TTCTTCTTCT TTTTTTTtct tgttcccagg ctggagtgca atggcatgat ctcagctcac
 cgcaacctcc acctcctggg ttcaagagat tctcctgact cagcctcatg agtagctggg
 attacaggca tgcaccacca cgccggctaa ttttgtattt ttagtagaga cggggtttct
 ccatgttggt caggctggtc tcgaactcct gacctcaggc gatccccacc ccctccgccc
 cccacctcgg cctcccaaag tgcggggatt acaggcgtga gccagcacac ccggctCAAA
 ATACACTTCT ATGATTAAAA ACAAAACTGC CACTGTGGCT CAAAGGGAGA CACTTCATTC
 TTGGCTTGTG GGTAATTTTA GGGATTTTCT TTCCCTTCCA GCTATCTGCA CCCGGAAGAG
 ACGGCAGCTG ATAAGCCAGA GAGCTGGAAA AGGTCTCAAG CTAGTCCttt tttttttttt
 tttaaatatt aGGATTTttt ttctcagctt tgtcaaagta tagttgacaa ataaaaattt
 tacatgtagg cctggtgctg tggttcatgc ctgtaatctc agcactttgg aagggcaagg
 cgggaggatc acttgagccc agagttcgag accaacccca tctccaccaa aaaatataaa
 tatatatgca ttagcctggc atgatggtac atgcctgtgg ccccagcttt tcaggaggct
 gagggggaag gatggattga gcccaggagg tcgaggctgc aatgagccat gactgagcca
 ctgcactcca gactgggtga cagaaggaga ccttgtctca a
 M
 aaaacccaat tgtacatgtt taatgtgtac agcgtgatga ctggatatcc gctgtgaaat
 gctcaccata ataaagctag ttaacatgtc caccacgtca cataattacc attttcttTT
 CTCTTTTCTG TGGTGAGAAT ACTTAAAATC TGCCCTTTTA GCAAATTCCA GGTATAGAGT
 ACAGCATTGA TAACTAGAGT GAACAATTTA GTTTCTTTTC TGAGATTCTG AGAAAGACTC
 ACAGAAAGGA TAGCAACGGA AGTAGAAAGT GAATTAGTGT TAAAATATGC GCACACACAC
 CCTTGGGAAG AAAGCGCT

  GeneView back to top
GeneView via analysis of contig annotation: TMPRSS2 transmembrane protease, serine 2
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_011512->NM_005656
function
HuRefNW_001838710->NM_005656
function
CeleraNW_927384->NM_005656
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_011512->NM_005656->NP_00564728517918reverseintron
HuRefNW_001838710->NM_005656->NP_005647100095forwardintron
CeleraNW_927384->NM_005656->NP_00564727539551reverseintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs2410429 maps exactly once on NCBI human chromosome 21
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
21NW_927384.12753955128054428plusCalt_assembly_1CeleraCeleraview1421
21NW_001838710.210009528325331minusTalt_assembly_8HuRefHuRefview1421
21NT_011512.102851791841777918plusAref_assemblyreferencereferenceview1421

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_011512
dbSNP Blast Analysis
GenBank HTGS Finished:
AL773571.1 AP001609.1 AP001610.1

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceA/A
A/C
C/C
HWPA
C
ss10982273HapMap-CEUEuropean 120IG 0.050 0.333 0.617 1.000 0.217 0.783
HapMap-HCBAsian 88IG 0.386 0.409 0.205 0.317 0.591 0.409
HapMap-JPTAsian 88IG 0.409 0.409 0.182 0.371 0.614 0.386
HapMap-YRISub-Saharan African 120IG 0.083 0.317 0.600 0.294 0.242 0.758

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.474+/-0.11027021000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hitwithHapMapFreq
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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 .