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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs2291157          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:100/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:G/T
Ancestral Allele:T
Clinical Association:unknown
HGVS Names
NG_008843.1:g.13098A>C
NM_153717.2:c.221A>C
NP_714928.1:p.Gln74Pro
NT_006051.17:g.1808466A>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 ss76891033 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2291157 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
ss3233347YUSUKE|IMS-JST043432byFreqfwd/BG/Tcttgatggggagccagtttccgagggggtcgcgcattagactccaaattcttgagcagat09/05/0110/10/03100Genomicunknown
ss48404350APPLERA_GI|hCV15964702byFreqfwd/BG/Tcttgatggggagccagtttccgagggggtcgcgcattagactccaaattcttgagcagat09/28/0511/03/06126Genomicunknown
ss66367677AFFY|SNP_A-2009539byFreqrev/TA/Cttggagtctaatgcgcgaccccctcggaaact10/29/0608/14/07127Genomicunknown
ss66581228ILLUMINA|HumanHap300v1.1_rs2291157fwd/TG/Tcttgatggggagccagtttccgagggggtcgcgcattagactccaaattcttgagcagat11/09/0611/09/06127Genomicunknown
ss67243117ILLUMINA|HumanHap550v1.1_rs2291157fwd/BG/Tcttgatggggagccagtttccgagggggtcgcgcattagactccaaattcttgagcagat11/14/0611/14/06127Genomicunknown
ss67639958ILLUMINA|HumanHap650Yv1.0_rs2291157fwd/BG/Tcttgatggggagccagtttccgagggggtcgcgcattagactccaaattcttgagcagat11/14/0611/14/06127Genomicunknown
ss68889083PERLEGEN|PGP03395024byFreqrev/TA/Catctgctcaagaatttggagtctaatgcgcgaccccctcggaaactggctccccatcaag01/30/0708/14/07127Genomicunknown
ss70721459ILLUMINA|HumanHap550v3.0__rs2291157rev/TA/Catctgctcaagaatttggagtctaatgcgcgaccccctcggaaactggctccccatcaag04/20/0703/30/08130Genomicunknown
ss71289880ILLUMINA|HumanHap650Yv3.0_rs2291157fwd/BG/Tcttgatggggagccagtttccgagggggtcgcgcattagactccaaattcttgagcagat04/23/0704/23/07127Genomicunknown
ss74906287ILLUMINA|ILMN_Human_1M_rs2291157fwd/BG/Tcttgatggggagccagtttccgagggggtcgcgcattagactccaaattcttgagcagat08/28/0708/29/07129Genomicunknown
ss76091836AFFY|AFFY_6_1M_SNP_A-2009539rev/TA/Cttggagtctaatgcgcgaccccctcggaaact08/28/0708/30/07129Genomicunknown
ss76891033SI_EXO|NT_006051.17_1808466rev/TA/Catctgctcaagaatttggagtctaatgcgcgaccccctcggaaactggctccccatcaag09/20/0709/20/07129Genomicunknown
ss79127255ILLUMINA|HumanHap300v2.0_rs2291157fwd/BG/Tcttgatggggagccagtttccgagggggtcgcgcattagactccaaattcttgagcagat04/18/0711/18/07130Genomicunknown
ss84024351KRIBB_YJKIM|KHS605235fwd/BG/Tcttgatggggagccagtttccgagggggtcgcgcattagactccaaattcttgagcagat12/04/0712/06/07130Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2291157|allelePos=401|totalLen=801|taxid=9606|snpclass=1|alleles='G/T'|mol=Genomic|build=130
 ATCAATGGAA ATCCCACGCA TGGGCACCTC TGGAAGTGTG TGGGGGCGGG AAGTGACCAG
 AAAGGGGCAC TAGAGGACTT GCTGGGTGAT GAAAACATTC TCAGGGGGGT ATTTGTTCTA
 AGGGGCATGC AATTGTCAAA ACTCATCAAA CTGTAAAACC TAAAGTCTGC GCATTTGACT
 GTATGTAAAT TATGCCTCAG AAAAGCAGCC CATTGGGAAA CTATATCTGT CAGAGGCTTG
 TCTACATGAC ACCCGGCTTC CAGGGGGAAT ACCCCACCTC CCACATGTGC CTCCACAAAC
 AAACATCAAC ACCAAGCTTA CATCAACAGC TTCCTTGTCC TTCGACATCT GCACTTCTCT
 CTTCCTCCTC CTTGATGGGG AGCCAGTTTC CGAGGGGGTC
 K
 GCGCATTAGA CTCCAAATTC TTGAGCAGAT TTTGAGTGTC GTCTTTCTAA AACCCGAAGG
 TCAGGAGTTG GGGGTGGATA GAAACACAAC ATTGAGGTCA GTCGGCCTGG TCCCCACCGT
 GACTTTTGCC AGTCAACTCC CCCAGTCCAG CAGCCACTTC TGCTCGCCTC TGTGCTTCTC
 AAGCTTGGTC TTCTGTGTGT GACGCCTCCC ACCCCACGTG GGGTCCGCTA CATGTCCTTC
 AAGACTGCAC AGGTCACCTT CCTGAGCGGT TCCCCTAAGG CCTCCAGGAT GCCCCATTTC
 AGTGCACCCT CAGGACTTGA GGCAAGAGGC AGAGCAAAGC TCGTTCCATT TTTCTTCTAG
 GTTGGGGACC CCATTGGACT GGGAGCTCTT TGGATTTAAC

  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_006051.17
dbSNP Blast Analysis
UniGene Cluster ID
552571

  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
ss3233347 JBIC-allele 1494 AF 0.122 0.878
ss48404350 HapMap-CEU European 120 IG 0.017 0.117 0.867 0.251 0.075 0.925
HapMap-HCB Asian 90 IG 0.022 0.222 0.756 1.000 0.133 0.867
HapMap-JPT Asian 88 IG 0.273 0.727 0.294 0.136 0.864
HapMap-YRI Sub-Saharan African 120 IG 0.067 0.933 1.000 0.033 0.967
AGI_ASP population multiple 74 IG 0.216 0.784 0.479 0.108 0.892
ss66367677 HapMap-CEU European 118 GF 0.017 0.119 0.864 0.076 0.924
HapMap-HCB Asian 90 GF 0.044 0.200 0.756 0.144 0.856
HapMap-JPT Asian 90 GF 0.289 0.711 0.144 0.856
HapMap-YRI Sub-Saharan African 120 GF 0.067 0.933 0.033 0.967
ss68889083 HapMap-CEU European 120 GF 0.017 0.117 0.867 0.075 0.925
HapMap-HCB Asian 90 GF 0.022 0.222 0.756 0.133 0.867
HapMap-JPT Asian 90 GF 0.289 0.711 0.144 0.856
HapMap-YRI Sub-Saharan African 120 GF 0.067 0.933 0.033 0.967
ss76091836 ICMHP 10 IG 0.200 0.800 0.100 0.900
Concordant Genotype Total Sample G/G G/T T/T
ss48404350 38 8 29
ss66367677 268
ss68889083 269
ss76091836 5
ss76891033 1206
RefSNP Genotype Summary Total Individual G/G G/T T/T
rs2291157 1250 8 29
Discordant Genotypes:
Indiviudal
SampleID		 SubSNP(ss) Genotype Population
Handle		 Submitter
Population		 Submitter
SampleID		 SampleID
Alias		 Submission
Batch		 NCBI
ProbeID
5157 ss66367677 C/C CSHL-HAPMAP HapMap-HCB NA18540 CH18540 chr4-HapMap-HCB
5157 ss68889083 A/C CSHL-HAPMAP HapMap-HCB NA18540 CH18540 chr4-HapMap-HCB
5157 ss76891033 N/N CSHL-HAPMAP HapMap-HCB NA18540 CH18540 r27_ch4_CHB_illumina:human_1m_beadchip
Genotype data submitted for1250 samples from1250 individualsIndividual with multiple genotypes submission:270

  Validation Summary: back to top
Validation status Marker displays
Mendelian segregation		 PCR results confirmed
in multiple reactions		 Homozygotes detected
in individual genotype data
byClusterbyFreqbySubmitterwithHapMapFreq
Validated by: PERLEGEN
 UNKNOWN UNKNOWN UNKNOWN

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Revised: May 25, 2006 1:38 PM .