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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs5978246          
refSNP ID: rs5978246
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:114/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:G/T
Ancestral Allele:Not available
Clinical Association:unknown
HGVS Names
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 ss8268465 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs5978246 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
ss8268465SC_SNP|NT_011812.10_1620645fwd/BG/Taaaacaatataaatgtcttctcttctggagtctgaaatgggtgtcactggtctaaaatca04/17/0310/10/03114Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs5978246|allelePos=401|totalLen=801|taxid=9606|snpclass=1|alleles='G/T'|mol=Genomic|build=114
 CAGCTCCCAA ATGTCTACTT TCACCTGAGC TAGTCCCTTG AAGAGCTGAT GCTCCCTCCT
 TCCTCTCCCA TGTGGAGGCT TTCCAAACTC AACTTTGCTG TAGCTACCAT GTTGATTTCT
 GCACCTCAAC TGCTCCTTGC ATTCACACTT TTCTTTCTGG CTGTAGGATG CAGAATTTTG
 ACCCCACACA TAACCTTCGA GGAAGGTGGG CTTCAGCAAG CAACTCCAAC AGCCTCAGTG
 AGCCTCATTC ACTGTATCTG AGAATAAGGA TACTAATTCA GCCAATGCAA TAGGTTTGGT
 GTGTTTTAAA TCAGTTCAtg tactggtttt ctacagctgc tgtgacaaat taccttgagt
 gtagatgctt aaaacaatat aaatgtcttc tcttctggag
 K
 tctgaaatgg gtgtcactgg tctaaaatca aggcaggcct gtactccttt ctggaggctc
 cagggaagaa tgtattttca tgacttttca ggtttctaga ggcttctgga attctttggc
 tggtggtgcc cttccaccag cttcaaagtc aacaacactg ggctgagtcc ttcgcaccat
 gccatctctc tgattcttgc actctgcttc cctattctac ttttaaggac ttttgtgatt
 gtattcgttt ccacccaaat aattaagggt aatatcccca tctcaaggtT GGCTTTGAGT
 CATTGAATGG CTTTTCTCTG CCCTCTGAAT AAAGACACTA ATACTCAGCC TGGCTTCCAG
 GTCTCCACTG CCTCTACATA TTCATCTCAT GCAGACACTC

  GeneView back to top
GeneView via analysis of contig annotation: KAL1 Kallmann syndrome 1 sequence
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
HuRefNW_001842360->NM_000216
function
CeleraNW_927700->NM_000216
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
HuRefNW_001842360->NM_000216->NP_000207129083reverseintron
CeleraNW_927700->NM_000216->NP_0002077086595reverseintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer: rs5978246 was not linked to the human genome 36.3 because it aligned to more than 2 locations on the genome.
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
XNW_001842360.11290836338122plusGalt_assembly_8HuRefHuRefview400
XNT_011757.1563423758470613plusGref_assemblyreferencereferenceview400
XNW_927700.1708659512688313plusGalt_assembly_1CeleraCeleraview400
YNT_011875.11221276414521342minusCref_assemblyreferencereferenceview400

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_011812
dbSNP Blast Analysis

  Population Diversity back to top
There is no frequency data.

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

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Revised: May 25, 2006 1:38 PM .