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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs1024997          
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:T
Clinical Association:unknown
HGVS Names
NT_023133.12:g.9489846C>T
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 ss1489796 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1024997 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
ss1489796TSC-CSHL|TSC0248350byFreqfwd/BC/Tggtacttgatggcaagaggtaactcaatcatagcttaaagcactctatccaaatagtaag09/07/0004/07/0486Genomic95 %
ss5790691SC_JCM|NT_023133.8_2314294fwd/BC/Tggtacttgatggcaagaggtaactcaatcatagcttaaagcactctatccaaatagtaag01/10/0310/10/03111Genomicunknown
ss17079303CSHL-HAPMAP|CSHL-HuAA-200402.chr5.NT_023133.11_9489846fwd/BC/Tggtacttgatggcaagaggtaactcaatcatagcttaaagcactctatccaaatagtaag02/17/0403/04/04120Genomicunknown
ss24438006PERLEGEN|afd3341659byFreqfwd/BC/Tggtacttgatggcaagaggtaactcaatcatagcttaaagcactctatccaaatagtaag08/10/0409/13/04123Genomicunknown
ss44669945ABI|hCV1992795fwd/BC/Tggtacttgatggcaagaggtaactcaatcatagcttaaagcactctatccaaatagtaag07/19/0507/19/05126Genomicunknown
ss86027424HGSV|Cor18956_SNV_20070510.chr5_164612866fwd/BC/Tggtacttgatggcaagaggtaactcaatcatagcttaaagcactctatccaaatagtaag11/30/0712/11/07130Genomicunknown
ss93322121BCMHGSC_JDW|JWB-2069221fwd/BC/Tggtacttgatggcaagaggtaactcaatcatagcttaaagcactctatccaaatagtaag02/26/0803/04/08129Genomicunknown
ss98784673HUMANGENOME_JCVI|1103654282614fwd/BC/Tggtacttgatggcaagaggtaactcaatcatagcttaaagcactctatccaaatagtaag04/01/0804/01/08130Genomicunknown
ss1095921041000GENOMES|CEU.trio.12.15.2008_1408133_chr5_164612866fwd/BC/Tggtacttgatggcaagaggtaactcaatcatagcttaaagcactctatccaaatagtaag12/15/0812/16/08130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1024997|allelePos=219|totalLen=1103|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 AGCAAGGGGT GAGTGGGCAG AGCTGCAGGT GCTTTCCATC CTACTGAATT CCACGTGGGC
 ACAGGCAAGG CAGGTCTGGA AGCCACGCCA AATTTCACAT GGGCATCTGC GATGAGGCAT
 GTCTGGTCTA TCTGGGGCCT AGCTCAAACC CTGTCATTAC TGTGGATTCT AACACCTGCC
 AGTAAAGGGG TACTTGATGG CAAGAGGTAA CTCAATCA
 Y
 TAGCTTAAAG CACTCTATCC AAATAGTAAG TTTGGTGGAT TGAATCTGTG TGTGACTCTG
 TTTTCAGAAC TAAGCAACCA CATGATGAAT TCATTTGGAG TGTTTGTTGT TTACTGCATA
 AGACAAGATG AATTCTAGTA GTGCCAAAGG GAGGGATTGA ATCATTTATT AAGTACAGTC
 TTGGACAGGT GTCTCAAATG TCAATTCTAG GATTTAATCT AAACTAATCT TCAGAAAAGT
 TAGATTTAAT GGAAATGAGA ACCCAGAGGA ATTCGAAGTA GAGGTAGCTG GATGCTAAAT
 CTCAAACGCT GCTGCTTGTG ACAATCTTTT AAATAAACTT TCTACTTGGC TCTTATCCTT
 CTGTGTTCTG AGGTAGAAAA CGTTTGGAAA ACTGATGCTA GCTCATCGGT AGGTAGGATT
 TATACAAAAC AAGTTGTTTT CTCTTTATTT CTGATGCTGG CATATAGTCA GTTATTTGCA
 AATAAGCTAC ATGGTCATAT CTGAGATCAG ACCACAGAGA TTTTGGCCTC TGTAGGTGTC
 ACTGCAGAGT TTATACATAT AGGATATACT TATATCCTGC TAAAGTAGGT CATATTTTCT
 GATCACAAAT TATGAAGCCA CAGGCAGAGT TTGAAATTGA TAAGGAAAAA CTGCCTAAAT
 GGCTACCACT CATTATATCT AAATATTGGC AGGTCaaaaa aaaaaaaaaa aaaaaTGGGA
 GTTATCTATC ACTGAATGCA ATTTGGAAAA TAAGCTGTAG TAGTTGTCTC ATCTTCAAGC
 CACTGTATTT CTAACTAAAT AATAAAAATA TTTTAGTCGT GGATAATATT TTTGCCATAT
 GCGTGTGCAT GGGTGTGTGT GTGTAAATTT AAAAACCTTG GCTT

  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_023133.8 ABBA01044173
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
ss1489796 HapMap-CEU European 118 IG 0.203 0.576 0.220 0.251 0.492 0.508
HapMap-HCB Asian 90 IG 0.356 0.489 0.156 1.000 0.600 0.400
HapMap-JPT Asian 86 IG 0.488 0.465 0.047 0.317 0.721 0.279
HapMap-YRI Sub-Saharan African 120 IG 0.450 0.450 0.100 1.000 0.675 0.325
CHMJ Asian 74 IG 0.703 0.297
ss24438006 AFD_EUR_PANEL European 48 IG 0.292 0.458 0.250 0.752 0.521 0.479
AFD_AFR_PANEL African American 46 IG 0.261 0.522 0.217 1.000 0.522 0.478
AFD_CHN_PANEL Asian 48 IG 0.417 0.375 0.208 0.294 0.604 0.396

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict		 Additional Freq. Data
0.480+/-0.097 582 459 15 0 ALFRED: The Allele Frequency Database

  Validation Summary: back to top
Validation status Marker displays
Mendelian segregation		 PCR results confirmed
in multiple reactions		 Homozygotes detected
in individual genotype data
byClusterbyFreqbySubmitterwith2hitwithHapMapFreqWith1000GenomeData
Validated by: PERLEGEN
DoubleHit found by:  BCM_SSAHASNP, NCBI
 UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .