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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs11663441          
refSNP ID: rs11663441
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:120/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:G/T
Ancestral Allele:G
Clinical Association:unknown
HGVS Names
NM_004163.3:c.240-1965G>T
NT_025028.13:g.340463G>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 ss16777508 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs11663441 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
ss16777508CSHL-HAPMAP|CSHL-HuAA-200402.chr18.NT_025028.13_340463byFreqfwd/BG/Ttaccaggttctgagccatgaaaatatgatgatagcaagttagaaacacagctcccttccc02/17/0410/26/06120Genomicunknown
ss40881614ABI|hCV1727924fwd/BG/Ttaccaggttctgagccatgaaaatatgatgatagcaagttagaaacacagctcccttccc07/17/0507/17/05126Genomicunknown
ss69215311PERLEGEN|PGP06012599byFreqfwd/BG/Ttaccaggttctgagccatgaaaatatgatgatagcaagttagaaacacagctcccttccc01/30/0703/31/08127Genomicunknown
ss76767029AFFY|AFFY_6_1M_SNP_A-8628471fwd/BG/Tccatgaaaatatgatgatagcaagttagaaac08/28/0708/30/07129Genomicunknown
ss90802298BCMHGSC_JDW|JWB-1104012fwd/BG/Ttaccaggttctgagccatgaaaatatgatgatagcaagttagaaacacagctcccttccc02/26/0803/01/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs11663441|allelePos=251|totalLen=751|taxid=9606|snpclass=1|alleles='G/T'|mol=Genomic|build=129
 TTTTGGTATT TCTGCTCTAC AGTTTTAGAT CATGATGATG CCCTACAGAC AAATCCTACT
 TTGGAAATAA ATAGCAGTGA AAATATCTCT TCTCCCATCT TTTGGTATGA AAAGTATCAT
 TCTCTGTTGC AGTCATTTAA AATATTTAAT AATTGTATAT CTTTTACTGT TTCTTTCTTT
 CACTTGCACT GTTTAACTTC acaaatattt agtgagcaaa taccaggttc tgagccatga
 aaatatgatg
 K
 atagcaagtt agaaacacag ctcccttccc cttagagctt acagtctagG GTAGAATTTG
 GATGAATAAA CAATCGCAAT GGAGCCTTAG GATACTAACA GGAAAACAAA GACATAGGCA
 GGCCCACCAG GAGGAGCGCA TAGCCCACAT GCAGTGTTGG GAAGGCCCCT TCGGGAAGTG
 TTATTTCCTC TGATACCATT ATGTATTTGC TCATGCACAA TGTATGAGTG AGTGCTATCC
 AGGCTCAACG AAGGGGTAGG AAGAAAAGGA AGCACTAAGA CTAAGTAACC CACAGAAAGA
 CCAGCATGTG TGAAAGCCCA GGGGAGCAGA GTGAACTTTC TAAGAACTAA AAGAAGATCA
 GCATGTCTGT GGGTAGTCAA AGGGATGAAG TTGGATAGAT GAACAAAGAT CACTTCCTGC
 AGAGCCTTGC CAGCTTTGTA AGGAGTTTGT GCATTACCTT ACGAGTGATG TCTAATCATT
 AAAATGTCGT TAGTAGAGCA

  GeneView back to top
GeneView via analysis of contig annotation: RAB27B RAB27B, member RAS oncogene family
View variations for gene:
Include clinically associated: in gene region cSNP has frequency double hit
Group
Label		Contig->mRNAGene Model (contig mRNA transcript) Color Legend
referenceNT_025028->NM_004163
svfunction
HuRefNW_001838469->NM_004163
svfunction
CeleraNW_927106->NM_004163
svfunction
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_025028->NM_004163->NP_004154340463forwardintron
HuRefNW_001838469->NM_004163->NP_004154342168forwardintron
CeleraNW_927106->NM_004163->NP_0041547860764forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs11663441 maps exactly once on NCBI human chromosome 18
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
18NW_001838469.134216849258819plusGalt_assembly_8HuRefHuRefview250
18NW_927106.1786076449267181plusGalt_assembly_1CeleraCeleraview250
18NT_025028.1334046350700597plusGref_assemblyreferencereferenceview250

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_025028
dbSNP Blast Analysis
GenBank HTGS Finished:GenBank HTGS Draft:
AC007673.7 AC098848.7 NC_000018.8 AP001910.2

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceG/G
G/T
T/T
HWPG
T
ss16777508HapMap-CEUEuropean 120IG 0.467 0.483 0.050 0.200 0.708 0.292
HapMap-HCBAsian 88IG 0.750 0.250 0.371 0.875 0.125
HapMap-JPTAsian 90IG 0.778 0.200 0.022 0.655 0.878 0.122
HapMap-YRISub-Saharan African 120IG 0.833 0.133 0.033 0.050 0.900 0.100
ss69215311HapMap-CEUEuropean 120GF 0.450 0.517 0.033 0.708 0.292
HapMap-HCBAsian 90GF 0.711 0.267 0.022 0.844 0.156
HapMap-JPTAsian 88GF 0.727 0.250 0.023 0.852 0.148
HapMap-YRISub-Saharan African 120GF 0.750 0.217 0.033 0.858 0.142
Concordant GenotypeTotal SampleG/GG/TT/T
ss167775082571737211
ss692153112571727212
RefSNP Genotype SummaryTotal IndividualG/GG/TT/T
rs116634412701737212
Discordant Genotypes:
Indiviudal
SampleID		SubSNP(ss)GenotypePopulation
Handle		Submitter
Population		Submitter
SampleID		SampleID
Alias		Submission
Batch		NCBI
ProbeID
161ss16777508G/GCSHL-HAPMAPHapMap-CEUNA07029CEPH1340.01r23_ch18_CEU_perlegen:genotyping_1.0.05541455
161ss69215311G/TCSHL-HAPMAPHapMap-CEUNA07029CEPH1340.01chr18-HapMap-CEU
362ss16777508T/TCSHL-HAPMAPHapMap-CEUNA11994CEPH1362.15r23_ch18_CEU_perlegen:genotyping_1.0.05541455
362ss69215311G/TCSHL-HAPMAPHapMap-CEUNA11994CEPH1362.15chr18-HapMap-CEU
618ss16777508G/GCSHL-HAPMAPHapMap-CEUNA12872CEPH1459.09r23_ch18_CEU_perlegen:genotyping_1.0.05541455
618ss69215311G/TCSHL-HAPMAPHapMap-CEUNA12872CEPH1459.09chr18-HapMap-CEU
5141ss16777508G/GCSHL-HAPMAPHapMap-YRINA19098YOR105.03r23_ch18_YRI_perlegen:genotyping_1.0.05541455
5141ss69215311G/TCSHL-HAPMAPHapMap-YRINA19098YOR105.03chr18-HapMap-YRI
5142ss16777508G/GCSHL-HAPMAPHapMap-YRINA19194YOR112.01r23_ch18_YRI_perlegen:genotyping_1.0.05541455
5142ss69215311G/TCSHL-HAPMAPHapMap-YRINA19194YOR112.01chr18-HapMap-YRI
5146ss16777508G/GCSHL-HAPMAPHapMap-YRINA19238YOR117.02r23_ch18_YRI_perlegen:genotyping_1.0.05541455
5146ss69215311G/TCSHL-HAPMAPHapMap-YRINA19238YOR117.02chr18-HapMap-YRI
5167ss16777508G/GCSHL-HAPMAPHapMap-HCBNA18611CH18611r23_ch18_HCB_perlegen:genotyping_1.0.05541455
5167ss69215311G/TCSHL-HAPMAPHapMap-HCBNA18611CH18611chr18-HapMap-HCB
5224ss16777508G/GCSHL-HAPMAPHapMap-JPTNA18974JA18974r23_ch18_JPT_perlegen:genotyping_1.0.05541455
5224ss69215311G/TCSHL-HAPMAPHapMap-JPTNA18974JA18974chr18-HapMap-JPT
5234ss16777508G/GCSHL-HAPMAPHapMap-JPTNA18999JA18999r23_ch18_JPT_perlegen:genotyping_1.0.05541455
5234ss69215311G/TCSHL-HAPMAPHapMap-JPTNA18999JA18999chr18-HapMap-JPT
5253ss16777508G/GCSHL-HAPMAPHapMap-YRINA18872YOR017.01r23_ch18_YRI_perlegen:genotyping_1.0.05541455
5253ss69215311G/TCSHL-HAPMAPHapMap-YRINA18872YOR017.01chr18-HapMap-YRI
5260ss16777508G/GCSHL-HAPMAPHapMap-YRINA18855YOR023.02r23_ch18_YRI_perlegen:genotyping_1.0.05541455
5260ss69215311G/TCSHL-HAPMAPHapMap-YRINA18855YOR023.02chr18-HapMap-YRI
5278ss16777508G/GCSHL-HAPMAPHapMap-YRINA19201YOR045.02r23_ch18_YRI_perlegen:genotyping_1.0.05541455
5278ss69215311G/TCSHL-HAPMAPHapMap-YRINA19201YOR045.02chr18-HapMap-YRI
5290ss16777508G/GCSHL-HAPMAPHapMap-YRINA19206YOR051.02r23_ch18_YRI_perlegen:genotyping_1.0.05541455
5290ss69215311G/TCSHL-HAPMAPHapMap-YRINA19206YOR051.02chr18-HapMap-YRI
Genotype data submitted for270 samples from270 individualsIndividual with multiple genotypes submission:270

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byClusterbyFreqwithHapMapFreqUNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .