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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs761100          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:86/130
Map to Genome Build:36.3
Citation: PubMed
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:G/T
Ancestral Allele:T
Clinical Association:unknown
HGVS Names
NM_014809.3:c.-106+13322G>T
NT_007592.14:g.15490893A>C
Links

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 ss134274 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs761100 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
ss134274TSC-CSHL|TSC0111850byFreqfwd/BG/Tccttactcattgatacttagaaaattgtttggagaaactggaaacttaacttctgaatgg09/06/0010/25/0686Genomic95 %
ss12893988SC_SNP|NT_007592.13_15490893rev/TA/Cccattcagaagttaagtttccagtttctccaaacaattttctaagtatcaatgagtaagg10/21/0311/17/03119Genomicunknown
ss24649551PERLEGEN|afd4058051byFreqrev/TA/Cccattcagaagttaagtttccagtttctccaaacaattttctaagtatcaatgagtaagg08/10/0409/13/04123Genomicunknown
ss44690718ABI|hCV2221339rev/TA/Cccattcagaagttaagtttccagtttctccaaacaattttctaagtatcaatgagtaagg07/19/0507/19/05126Genomicunknown
ss67806534ILLUMINA|HumanHap550v1.1_rs761100fwd/BG/Tccttactcattgatacttagaaaattgtttggagaaactggaaacttaacttctgaatgg11/14/0611/14/06127Genomicunknown
ss67976266ILLUMINA|HumanHap650Yv1.0_rs761100fwd/BG/Tccttactcattgatacttagaaaattgtttggagaaactggaaacttaacttctgaatgg11/14/0611/15/06127Genomicunknown
ss68281328ILLUMINA|HumanHap250Sv1.0_rs761100fwd/BG/Tccttactcattgatacttagaaaattgtttggagaaactggaaacttaacttctgaatgg12/06/0612/07/06127Genomicunknown
ss68969024PERLEGEN|PGP04058051byFreqrev/TA/Cccattcagaagttaagtttccagtttctccaaacaattttctaagtatcaatgagtaagg01/30/0708/14/07127Genomicunknown
ss70937705ILLUMINA|HumanHap550v3.0__rs761100rev/TA/Cccattcagaagttaagtttccagtttctccaaacaattttctaagtatcaatgagtaagg04/20/0703/31/08130Genomicunknown
ss71540770ILLUMINA|HumanHap650Yv3.0_rs761100fwd/BG/Tccttactcattgatacttagaaaattgtttggagaaactggaaacttaacttctgaatgg04/23/0704/23/07127Genomicunknown
ss75548728ILLUMINA|ILMN_Human_1M_rs761100fwd/BG/Tccttactcattgatacttagaaaattgtttggagaaactggaaacttaacttctgaatgg08/28/0708/29/07129Genomicunknown
ss83554915KRIBB_YJKIM|KHS488692fwd/BG/Tccttactcattgatacttagaaaattgtttggagaaactggaaacttaacttctgaatgg12/04/0712/05/07130Genomicunknown
ss1098381591000GENOMES|CEU.trio.12.15.2008_1470962_chr6_24740621rev/TA/Cccattcagaagttaagtttccagtttctccaaacaattttctaagtatcaatgagtaagg12/15/0812/16/08130Genomicunknown
ss1140432631000GENOMES|NA19240_2008_12_16_1322537_chr6_24740621rev/TA/Cccattcagaagttaagtttccagtttctccaaacaattttctaagtatcaatgagtaagg12/18/0812/18/08130Genomicunknown
ss116357564ILLUMINA-UK|NA18507_000036174_NCBI36.1_chr6_24740621rev/TA/Cccattcagaagttaagtttccagtttctccaaacaattttctaagtatcaatgagtaagg01/17/0901/17/09130Genomic99 %

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs761100|allelePos=146|totalLen=602|taxid=9606|snpclass=1|alleles='G/T'|mol=Genomic|build=130
 CAGGCCCAGG CAGTAAGGAG TGGAGAAGTG TGCCTCATGA ATGATTTATC AACTGCTTTG
 GCGAGAGAAA GTGCTGAAAT TAAGAAAGAC CAGACTCATT TTCATCTTTT ATATTCCTTA
 CTCATTGATA CTTAGAAAAT TGTTT
 K
 GGAGAAACTG GAAACTTAAC TTCTGAATGG TGAGCCACAG AGCTTCAACC GATTCAGCTA
 GAATATTCTA TATACCTGTT GGAGATAACA ATATTTGTCT TACCTCTGGC GGTATTGGGA
 TGCTCAACTA ATGCGATATA TGTAAAATTG CCTTGTGATA CAAAGAACTA TTATAAATGA
 CTATTATTTT GATAATGGCG ATGATGAATA TTATAAACCA CTTATTTCCT GATTATTAAT
 AGGATGGATT GTTAATTGAC AATATTCTAC CTTCTTTCCA TTTTGCTCCT CTTCCTTCAT
 AGGGAAAAAG CAAACAATTA TTTACTTAAT GCCTGAAAGT TAAATTCTAA AGGAAAACTT
 TTTACTAGCT GATCATAGGT CTGCTGATAA GAATTGAAAG ATGGGACAAT CTCAGGTTTA
 TGAACAGTTG CCTGATACTA AAGGTTAGTA ATCACC

  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_007592
dbSNP Blast Analysis

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source G/G
 G/T
 T/T
 HWP G
 T
ss134274 CEPH 184 AF 1.000
HapMap-CEU European 118 IG 0.271 0.576 0.153 0.200 0.559 0.441
HapMap-HCB Asian 88 IG 0.773 0.227 0.403 0.886 0.114
HapMap-JPT Asian 90 IG 0.778 0.200 0.022 0.878 0.122
HapMap-YRI Sub-Saharan African 118 IG 0.508 0.407 0.085 1.000 0.712 0.288
CHMJ Asian 74 IG 0.892 0.108
ss24649551 AFD_EUR_PANEL European 48 IG 0.375 0.500 0.125 0.752 0.625 0.375
AFD_AFR_PANEL African American 46 IG 0.478 0.391 0.130 0.655 0.674 0.326
AFD_CHN_PANEL Asian 48 IG 0.792 0.208 0.584 0.896 0.104
ss68969024 HapMap-CEU European 120 GF 0.267 0.567 0.167 0.550 0.450
HapMap-HCB Asian 90 GF 0.778 0.222 0.889 0.111
HapMap-JPT Asian 90 GF 0.778 0.200 0.022 0.878 0.122
HapMap-YRI Sub-Saharan African 120 GF 0.500 0.417 0.083 0.708 0.292

Summary Average
Het.+/- std err:		 Individual
Count		 Founders
Count		 Individual
Overlap		 Genotype
Conflict
0.386+/-0.210 1263 1052 276 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

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Revised: May 25, 2006 1:38 PM .