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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs605588          
refSNP ID: rs605588
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:83/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/T
Ancestral Allele:T
Clinical Association:unknown
HGVS Names
NM_014600.1:c.1081-786G>A
NT_022184.14:g.10304190G>A
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 ss1954134 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs605588 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
ss777653SC_JCM|AL121657.2_36779rev/TA/Gcatcaccacaaacacataatgcgttgtgtttgtacagtagctacaatgtcaccaggcaac07/27/0010/10/0383Genomicunknown
ss1039221KWOK|OVLP-000804-526815fwd/BC/Tgttgcctggtgacattgtagctactgtacaaacacaacgcattatgtgtttgtggtgatg09/02/0010/10/0386Genomic97 %
ss1954134KWOK|OVLP-000925-345890byFreqfwd/BC/Tgttgcctggtgacattgtagctactgtacaaacacaacgcattatgtgtttgtggtgatg10/06/0010/25/0687Genomic97 %
ss9966783BCM_SSAHASNP|chr2.NT_022184.12_10304190rev/TA/Gcatcaccacaaacacataatgcgttgtgtttgtacagtagctacaatgtcaccaggcaac06/27/0310/10/03116Genomicunknown
ss11487725WI_SSAHASNP|chr2.NT_022184.12_10304190rev/TA/Gcatcaccacaaacacataatgcgttgtgtttgtacagtagctacaatgtcaccaggcaac07/03/0310/10/03116Genomicunknown
ss14506273WUGSC_SSAHASNP|chr2.NT_022184.13_10304190rev/TA/Gcatcaccacaaacacataatgcgttgtgtttgtacagtagctacaatgtcaccaggcaac11/05/0311/22/03119Genomicunknown
ss19455394CSHL-HAPMAP|CSHL-HuDD-200402.chr2.NT_022184.13_10304190rev/TA/Gcatcaccacaaacacataatgcgttgtgtttgtacagtagctacaatgtcaccaggcaac02/20/0403/04/04120Genomicunknown
ss20108688CSHL-HAPMAP|CSHL-HuFF-200402.chr2.NT_022184.13_10304190rev/TA/Gcatcaccacaaacacataatgcgttgtgtttgtacagtagctacaatgtcaccaggcaac02/21/0403/04/04120Genomicunknown
ss21668583SSAHASNP|WGSA-200403-chr2.chr2.NT_022184.13_10304190rev/TA/Gcatcaccacaaacacataatgcgttgtgtttgtacagtagctacaatgtcaccaggcaac03/20/0403/20/04121Genomicunknown
ss78255659HGSV|Cor12878_SNV_20070510.chr2_31399908rev/TA/Gcatcaccacaaacacataatgcgttgtgtttgtacagtagctacaatgtcaccaggcaac10/17/0710/18/07129Genomicunknown
ss78869842HGSV|Cor18507_SNV_20070510.chr2_31399908rev/TA/Gcatcaccacaaacacataatgcgttgtgtttgtacagtagctacaatgtcaccaggcaac10/19/0710/21/07129Genomicunknown
ss80755234KRIBB_YJKIM|KHS1001313fwd/BC/Tgttgcctggtgacattgtagctactgtacaaacacaacgcattatgtgtttgtggtgatg11/26/0711/26/07130Genomicunknown
ss83061843HGSV|Cor19240_SNV_20070510.chr2_31399908rev/TA/Gcatcaccacaaacacataatgcgttgtgtttgtacagtagctacaatgtcaccaggcaac11/30/0712/04/07130Genomicunknown
ss85031025HGSV|Cor19129_SNV_20070510.chr2_31399908rev/TA/Gcatcaccacaaacacataatgcgttgtgtttgtacagtagctacaatgtcaccaggcaac12/06/0712/08/07130Genomicunknown
ss91105867BCMHGSC_JDW|JWB-1219575rev/TA/Gcatcaccacaaacacataatgcgttgtgtttgtacagtagctacaatgtcaccaggcaac02/26/0803/01/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs605588|allelePos=451|totalLen=2003|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 TCTCTTTAAG TCAGTTTTGG CTATTGAATC ATGTCTCTTG AATGCTGTAC CTCTGAGACT
 GGGTCATGTG GGCCTCTACT TTAATAAGGG TTATACTGTA CTTGAAAATC ACCGCAAGTG
 CCTTCACTAC ATTACCTCGT TCACTCCCCC AGCGCCCTTC TGAGGTAGGA AAATCACATT
 CTATCCCCAC TTAGTGAAAA CAAAAACAAA AACCAAACAG GGCACAGGGT ACTAAAACCA
 AATCATAACA GAAGCCAAAG GTCATCCCCA AATTATGGTT CTTAATCAGG ATGCTCATCG
 GAGTCACCTG AGGAGAGTTT TCAAAATAca gtcatgtgct gcattacaat gtttcagtca
 atgagggacc acacgtatga cgagggtccc agaagacaat aagggagctg ggaaattcct
 gttgcctggt gacattgtag ctactgtaca
 Y
 aacacaacgc attatgtgtt tgtggtgatg ctggtgtaaa caaacctact gtgctgccag
 tggtataaaa atctagcaca cacatttcca tagagtacat aataccggat aatgataacg
 gctatgttac tggtttatgt aaatatttac tatactgtac tttttattgt tattttaggg
 tgtattcttt ctacttattt aaaaaaaatg ttaacagtaa aacaacctca ggcaggccct
 tcaggaggaa ttccagaaga aggcattgtt attacaggag atgacacctc catgtgtatt
 actatctctc aagaccttcc agtgggacaa gatgtggagg tgaagacagc gaaactgatg
 atgctgaccc tgtgtaggcc tagactagca tgggtgtttg catcttagtt tttagcacac
 acaaaaataa aaaagtaaaa aataaatttt tttaaataga aaaaacttat agaataagga
 tataaagaaa atatttgtgt atagatatac aatgtacatt ttaagctaat tgttacaaca
 agagtcaaaa actttgtagg ctaggcgcgg tggctcatgc ctgtaatccc agcactttgg
 gaggctgagg caggcggatc acgaggtcaa gagatcgaga ccatcctggc caacatggtg
 aaaaccccgt ctctactaaa attacaaaaa aaatttagct gggcatggtg gcacatgcct
 gtggtcccag ctactcggga ggctgaggag aatcgcttga acccagagtt ggaggttgca
 gtgagccgag atcgcgccac tgcactctag cctagcaaca gagtgagact ctgtatcaaa
 aaaaaaaaaa aaaaaaagtc tgtaaagtag aaatgttaat ttattattga agaaagaaaa
 tgtttctaaa aataaatata gtgtagccta agtgtacagt gtttctaaag aagtctacag
 cagtgtacag tgatgtccta ggccttcaca ctcactcacc actcactcac tggcccaccc
 aaagcaactt ccagttctgc aagctccatt catggtaagt gccctgtaca agtataccac
 tgtttatctt tcatactgta tttttactgt accatttcta tgtttagata cacaaataca
 tggtgttaca attgcctaca gccttcagta cagtcacatg ctaggtctgt ggcctagaag
 caataggtca tcataccata tagtccaggt gtgtggtagg ccctaccatg caggtttgtg
 tatatacatt ctatggtgtt cacacacaat gacaaaatca cctaacaatg cattactgag
 gatgtgtccc tgtcattagc aaggcatgac tgTCCCCGAG GGTTTGACAC AGCAGGCACA
 GGCAGGCAGG TGGGCATGCC GATTTTGAAA GAGCTCCTCT TGCCTTCACA TGACAACCCA
 CACCACACCA TAAAAGAAAT ATCTTCCACT TTGCAGGTCT CTGCAATTTT GAAAGTTTTC
 GAGTCTAGAA CACCAACTTC TCCATGGCCT GTAGAGGGTG ATAGGGTGAC AG

  GeneView back to top
GeneView via analysis of contig annotation: EHD3 EH-domain containing 3
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_022184->NM_014600
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_022184->NM_014600->NP_05541510304190forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs605588 maps exactly once on NCBI human chromosome 2
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
2NW_001838769.1132216231225918minusAalt_assembly_8HuRefHuRefview450
2NW_927719.13126290231330967minusAalt_assembly_1CeleraCeleraview450
2NT_022184.141030419031341761minusGref_assemblyreferencereferenceview450

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_022184 AC015980 AL121657.2
dbSNP Blast Analysis

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
T
ss1954134HapMap-CEUEuropean 114IG 0.070 0.281 0.649 0.251 0.211 0.789
HapMap-HCBAsian 86IG 0.023 0.093 0.884 0.100 0.070 0.930
HapMap-JPTAsian 76IG 0.053 0.947 1.000 0.026 0.974
HapMap-YRISub-Saharan African 110IG 0.018 0.982 1.000 0.009 0.991

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.156+/-0.23227021000

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

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Revised: May 25, 2006 1:38 PM .