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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs11552197          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:120/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/G
Ancestral Allele:G
Clinical Association:unknown
HGVS Names
NM_001745.2:c.298G>A
NP_001736.1:p.Gly100Ser
NT_034772.5:g.36491891G>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 ss74815259 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs11552197 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
ss16253986CGAP-GAI|1507604byFreqfwd/TA/Gtcagtcagtacaggaacaactgaccagcaggtggtgtggccgaggtaaaggggacccaac11/18/0303/31/08120cDNAunknown
ss68950528PERLEGEN|PGP04785290byFreqfwd/TA/Gtcagtcagtacaggaacaactgaccagcaggtggtgtggccgaggtaaaggggacccaac01/30/0703/31/08127Genomicunknown
ss74815259AFFY|SNP_M-308956byFreqfwd/TA/Gtcagtcagtacaggaacaactgaccagcaggtggtgtggccgaggtaaaggggacccaac08/09/0703/31/08128Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs11552197|allelePos=101|totalLen=201|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=128
 GCAGCAGGAC AGTGATAAAC TGAACTCCCT CAGCGTTCCT TCCGTTTCAA AGCGAGTAGT
 GCTGGGTGAT TCAGTCAGTA CAGGAACAAC TGACCAGCAG
 R
 GTGGTGTGGC CGAGGTAAAG GGGACCCAAC TGGGAGACAA ATTGGACTCG TTCATTAAAC
 CACCTGAGTG CAGTAGTGAT GTCAACCTTG AGCTCCGGCA

  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
NC_000005.8 BI598790
dbSNP Blast Analysis
UniGene Cluster ID
529846

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source A/A
 A/G
 G/G
 HWP A
 G
ss16253986 HapMap-CEU European 116 IG 1.000 1.000
HapMap-HCB Asian 88 IG 0.068 0.932 0.034 0.966
HapMap-JPT Asian 86 IG 0.023 0.977 0.012 0.988
HapMap-YRI Sub-Saharan African 116 IG 1.000 1.000
ss68950528 HapMap-CEU European 120 GF 0.083 0.917 0.042 0.958
HapMap-HCB Asian 90 GF 0.067 0.200 0.733 0.167 0.833
HapMap-JPT Asian 90 GF 0.022 0.222 0.756 0.133 0.867
HapMap-YRI Sub-Saharan African 120 GF 0.083 0.917 0.042 0.958
ss74815259 HapMap-CEU European 116 IG 1.000 1.000
HapMap-HCB Asian 88 IG 0.068 0.932 0.034 0.966
HapMap-JPT Asian 86 IG 0.023 0.977 0.012 0.988
HapMap-YRI Sub-Saharan African 116 IG 1.000 1.000
Concordant Genotype Total Sample A/A A/G G/G
ss74815259 486 223
RefSNP Genotype Summary Total Individual A/A A/G G/G
rs11552197 525 223
Discordant Genotypes:
Indiviudal
SampleID		 SubSNP(ss) Genotype Population
Handle		 Submitter
Population		 Submitter
SampleID		 SampleID
Alias		 Submission
Batch		 NCBI
ProbeID
172 ss74815259 G/G CSHL-HAPMAP HapMap-CEU NA07056 CEPH1340.12 r27_ch5_CEU_bcm:genotype_0002
187 ss74815259 G/G CSHL-HAPMAP HapMap-CEU NA06985 CEPH1341.14 r27_ch5_CEU_bcm:genotype_0002
229 ss74815259 G/G CSHL-HAPMAP HapMap-CEU NA10859 CEPH1347.02 r27_ch5_CEU_bcm:genotype_0002
252 ss74815259 G/G CSHL-HAPMAP HapMap-CEU NA11839 CEPH1349.13 r27_ch5_CEU_bcm:genotype_0002
253 ss74815259 G/G CSHL-HAPMAP HapMap-CEU NA11840 CEPH1349.14 r27_ch5_CEU_bcm:genotype_0002
399 ss74815259 G/G CSHL-HAPMAP HapMap-CEU NA10830 CEPH1408.01 r27_ch5_CEU_bcm:genotype_0002
546 ss74815259 G/G CSHL-HAPMAP HapMap-CEU NA12761 CEPH1447.10 r27_ch5_CEU_bcm:genotype_0002
565 ss74815259 G/G CSHL-HAPMAP HapMap-CEU NA12801 CEPH1454.01 r27_ch5_CEU_bcm:genotype_0002
566 ss74815259 G/G CSHL-HAPMAP HapMap-CEU NA12802 CEPH1454.02 r27_ch5_CEU_bcm:genotype_0002
5132 ss74815259 G/G CSHL-HAPMAP HapMap-YRI NA18500 YOR004.01 r27_ch5_YRI_bcm:genotype_0002
5136 ss74815259 G/G CSHL-HAPMAP HapMap-YRI NA19132 YOR101.01 r27_ch5_YRI_bcm:genotype_0002
5147 ss74815259 G/G CSHL-HAPMAP HapMap-YRI NA19239 YOR117.03 r27_ch5_YRI_bcm:genotype_0002
5156 ss74815259 G/G CSHL-HAPMAP HapMap-HCB NA18603 CH18603 r27_ch5_CHB_bcm:genotype_0002
5161 ss74815259 G/G CSHL-HAPMAP HapMap-HCB NA18572 CH18572 r27_ch5_CHB_bcm:genotype_0002
5162 ss74815259 G/G CSHL-HAPMAP HapMap-HCB NA18547 CH18547 r27_ch5_CHB_bcm:genotype_0002
5163 ss74815259 A/G CSHL-HAPMAP HapMap-HCB NA18609 CH18609 r27_ch5_CHB_bcm:genotype_0002
5164 ss74815259 A/G CSHL-HAPMAP HapMap-HCB NA18550 CH18550 r27_ch5_CHB_bcm:genotype_0002
5166 ss74815259 G/G CSHL-HAPMAP HapMap-HCB NA18552 CH18552 r27_ch5_CHB_bcm:genotype_0002
5169 ss74815259 G/G CSHL-HAPMAP HapMap-HCB NA18564 CH18564 r27_ch5_CHB_bcm:genotype_0002
5176 ss74815259 G/G CSHL-HAPMAP HapMap-HCB NA18621 CH18621 r27_ch5_CHB_bcm:genotype_0002
5178 ss74815259 G/G CSHL-HAPMAP HapMap-HCB NA18622 CH18622 r27_ch5_CHB_bcm:genotype_0002
5185 ss74815259 G/G CSHL-HAPMAP HapMap-HCB NA18632 CH18632 r27_ch5_CHB_bcm:genotype_0002
5189 ss74815259 G/G CSHL-HAPMAP HapMap-HCB NA18592 CH18592 r27_ch5_CHB_bcm:genotype_0002
5192 ss74815259 A/G CSHL-HAPMAP HapMap-HCB NA18637 CH18637 r27_ch5_CHB_bcm:genotype_0002
5194 ss74815259 G/G CSHL-HAPMAP HapMap-JPT NA18940 JA18940 r27_ch5_JPT_bcm:genotype_0002
5199 ss74815259 G/G CSHL-HAPMAP HapMap-JPT NA18945 JA18945 r27_ch5_JPT_bcm:genotype_0002
5200 ss74815259 G/G CSHL-HAPMAP HapMap-JPT NA18949 JA18949 r27_ch5_JPT_bcm:genotype_0002
5201 ss74815259 G/G CSHL-HAPMAP HapMap-JPT NA18948 JA18948 r27_ch5_JPT_bcm:genotype_0002
5205 ss74815259 G/G CSHL-HAPMAP HapMap-JPT NA18953 JA18953 r27_ch5_JPT_bcm:genotype_0002
5210 ss74815259 G/G CSHL-HAPMAP HapMap-JPT NA18961 JA18961 r27_ch5_JPT_bcm:genotype_0002
5217 ss74815259 G/G CSHL-HAPMAP HapMap-JPT NA18976 JA18976 r27_ch5_JPT_bcm:genotype_0002
5222 ss74815259 G/G CSHL-HAPMAP HapMap-JPT NA18981 JA18981 r27_ch5_JPT_bcm:genotype_0002
5223 ss74815259 G/G CSHL-HAPMAP HapMap-JPT NA18971 JA18971 r27_ch5_JPT_bcm:genotype_0002
5228 ss74815259 A/G CSHL-HAPMAP HapMap-JPT NA18994 JA18994 r27_ch5_JPT_bcm:genotype_0002
5232 ss74815259 G/G CSHL-HAPMAP HapMap-JPT NA19000 JA19000 r27_ch5_JPT_bcm:genotype_0002
5254 ss74815259 G/G CSHL-HAPMAP HapMap-YRI NA18870 YOR017.02 r27_ch5_YRI_bcm:genotype_0002
5272 ss74815259 G/G CSHL-HAPMAP HapMap-YRI NA19102 YOR042.02 r27_ch5_YRI_bcm:genotype_0002
5279 ss74815259 G/G CSHL-HAPMAP HapMap-YRI NA19200 YOR045.03 r27_ch5_YRI_bcm:genotype_0002
5288 ss74815259 G/G CSHL-HAPMAP HapMap-YRI NA19210 YOR050.03 r27_ch5_YRI_bcm:genotype_0002
Genotype data submitted for525 samples from525 individualsIndividual with multiple genotypes submission:0

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

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Revised: May 25, 2006 1:38 PM .