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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs5948          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:52/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/T
Ancestral Allele:T
Clinical Association:unknown
HGVS Names
NM_005139.2:c.656T>A
NP_005130.1:p.Ile219Asn
NT_016354.18:g.4066215T>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 ss10111987 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs5948 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
ss7557WIAF-CSNP|WIAF-11210byFreqfwd/TA/Ttctttttagcatttgatgaatacagaaatacagccaaaaggacattgtggacagcataaa07/15/9904/07/0452Genomicunknown
ss10111987BCM_SSAHASNP|chr4.NT_016354.15_4013199byFreqfwd/TA/Ttctttttagcatttgatgaatacagaaatacagccaaaaggacattgtggacagcataaa06/27/0310/25/06116Genomicunknown
ss23166719PERLEGEN|afd3499314byFreqfwd/TA/Ttctttttagcatttgatgaatacagaaatacagccaaaaggacattgtggacagcataaa08/10/0409/13/04123Genomicunknown
ss68390741CSHL-HAPMAP|sanger:assay:4244095:1byFreqfwd/A/Ttctttttagcatttgatgaatacagaaatacagccaaaaggacattgtggacagcataaa01/11/0701/16/07127NAunknown
ss68902915PERLEGEN|PGP03499314byFreqfwd/A/Ttctttttagcatttgatgaatacagaaatacagccaaaaggacattgtggacagcataaa01/30/0708/14/07127Genomicunknown
ss74820525AFFY|SNP_M-323603fwd/TA/Ttctttttagcatttgatgaatacagaaatacagccaaaaggacattgtggacagcataaa08/09/0708/09/07128Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs5948|allelePos=201|totalLen=401|taxid=9606|snpclass=1|alleles='A/T'|mol=Genomic|build=128
 TGATTTCCTT AAAAAGGAAC AAAAGAAAAA CAAAAACTTC TGTGCCCAGA TTTTCATGGT
 TTAAAGAGGG AGTTTTTTAG CTTGCTACTT GATCTTCTGC ATATCAAATA AAAAACTAGA
 ATATATTCAA ATGTGCTCAA CTGCGTTGCT TTAAATAATT TTGTGGTGCT TCTTTTTAGC
 ATTTGATGAA TACAGAAATA
 W
 CAGCCAAAAG GACATTGTGG ACAGCATAAA AGGAGAATTA TCTGGGCATT TTGAAGACTT
 ACTGTTGGCC ATAGGTAAGA CTTCGAGTGC TGGTAAACTA AGTTACTTTG CACTTGCTTT
 AACTCAGTGC CGAGGCCTGC TCCTTTTGGG CAAGAATCCT GACTGATCCA TTTTTTTTGC
 TCCCTACAGC CCCCAACATG

  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_016354
dbSNP Blast Analysis
UniGene Cluster ID
480042

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source A/T
 T/T
 HWP A
 T
ss10111987 HapMap-CEU European 120 IG 1.000 1.000
HapMap-HCB Asian 90 IG 1.000 1.000
HapMap-JPT Asian 90 IG 1.000 1.000
HapMap-YRI Sub-Saharan African 120 IG 0.250 0.750 0.273 0.125 0.875
ss23166719 AFD_EUR_PANEL European 48 IG 1.000 1.000
AFD_AFR_PANEL African American 46 IG 0.087 0.913 1.000 0.043 0.957
AFD_CHN_PANEL Asian 48 IG 1.000 1.000
ss68902915 HapMap-CEU European 120 GF 1.000 1.000
HapMap-HCB Asian 90 GF 1.000 1.000
HapMap-JPT Asian 90 GF 1.000 1.000
HapMap-YRI Sub-Saharan African 120 GF 0.233 0.767 0.117 0.883
ss7557 WIAF-CSNP-POP1 108 AF 0.025 0.975
Concordant Genotype Total Sample A/T T/T
ss10111987 524 21 248
ss23166719 71 2 69
ss68902915 269 19 250
RefSNP Genotype Summary Total Individual A/T T/T
rs5948 581 23 310
Discordant Genotypes:
Indiviudal
SampleID		 SubSNP(ss) Genotype Population
Handle		 Submitter
Population		 Submitter
SampleID		 SampleID
Alias		 Submission
Batch		 NCBI
ProbeID
5139 ss10111987 A/A CSHL-HAPMAP HapMap-YRI NA19100 YOR105.01 r27_ch4_YRI_illumina:golden_gate_1.0.0
5139 ss68902915 A/T CSHL-HAPMAP HapMap-YRI NA19100 YOR105.01 chr4-HapMap-YRI
Genotype data submitted for596 samples from581 individualsIndividual with multiple genotypes submission:276

  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 YES UNKNOWN

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Revised: May 25, 2006 1:38 PM .