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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs2591593          
refSNP ID: rs2591593
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:100/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/T
Ancestral Allele:C
Clinical Association:unknown
HGVS Names
NM_024690.2:c.11477G>A
NP_078966.2:p.G3826E
NT_011295.10:g.338770C>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 ss90899775 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2591593 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
ss3642743SC_JCM|AC016584.4_234607byFreqfwd/BC/Tagagttgttgctgctgatctgggcacctgcctggatgtgcagaagtggtggtgggaagct09/24/0110/25/06100Genomicunknown
ss6631378WI_SSAHASNP|NT_011176.13_2176219fwd/BC/Tagagttgttgctgctgatctgggcacctgcctggatgtgcagaagtggtggtgggaagct02/12/0310/10/03111Genomicunknown
ss24552896PERLEGEN|afd1597440byFreqfwd/BC/Tagagttgttgctgctgatctgggcacctgcctggatgtgcagaagtggtggtgggaagct08/10/0409/13/04123Genomicunknown
ss65727054ILLUMINA|Human1-rs2591593fwd/BC/Tagagttgttgctgctgatctgggcacctgcctggatgtgcagaagtggtggtgggaagct10/10/0610/10/06127Genomicunknown
ss66557681ILLUMINA|HumanHap300v1.1_rs2591593fwd/BC/Tagagttgttgctgctgatctgggcacctgcctggatgtgcagaagtggtggtgggaagct11/09/0611/09/06127Genomicunknown
ss67262507ILLUMINA|HumanHap550v1.1_rs2591593fwd/BC/Tagagttgttgctgctgatctgggcacctgcctggatgtgcagaagtggtggtgggaagct11/14/0611/14/06127Genomicunknown
ss67661870ILLUMINA|HumanHap650Yv1.0_rs2591593fwd/BC/Tagagttgttgctgctgatctgggcacctgcctggatgtgcagaagtggtggtgggaagct11/14/0611/14/06127Genomicunknown
ss70740890ILLUMINA|HumanHap550v3.0__rs2591593fwd/BC/Tagagttgttgctgctgatctgggcacctgcctggatgtgcagaagtggtggtgggaagct04/20/0703/30/08130Genomicunknown
ss71311818ILLUMINA|HumanHap650Yv3.0_rs2591593fwd/BC/Tagagttgttgctgctgatctgggcacctgcctggatgtgcagaagtggtggtgggaagct04/23/0704/23/07127Genomicunknown
ss74814914AFFY|SNP_M-308483fwd/BC/Tagagttgttgctgctgatctgggcacctgcctggatgtgcagaagtggtggtgggaagct08/09/0708/09/07128Genomicunknown
ss75276228ILLUMINA|ILMN_Human_1M_rs2591593fwd/BC/Tagagttgttgctgctgatctgggcacctgcctggatgtgcagaagtggtggtgggaagct08/28/0708/29/07129Genomicunknown
ss77571593HGSV|Cor12156_SNV_20070510.chr19_8936969fwd/BC/Tagagttgttgctgctgatctgggcacctgcctggatgtgcagaagtggtggtgggaagct10/09/0710/13/07129Genomicunknown
ss79140261ILLUMINA|HumanHap300v2.0_rs2591593fwd/BC/Tagagttgttgctgctgatctgggcacctgcctggatgtgcagaagtggtggtgggaagct04/18/0711/18/07130Genomicunknown
ss84060929KRIBB_YJKIM|KHS622296fwd/BC/Tagagttgttgctgctgatctgggcacctgcctggatgtgcagaagtggtggtgggaagct12/04/0712/06/07130Genomicunknown
ss90899775BCMHGSC_JDW|JWB-1142707fwd/BC/Tagagttgttgctgctgatctgggcacctgcctggatgtgcagaagtggtggtgggaagct02/26/0803/01/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2591593|allelePos=251|totalLen=501|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 CGTATTCAGG GTCCTTAATA CACTGGAGGA GCTGGTAACC TCCTTGATGG TATCTTCTGA
 GACAGAATTC ATCATCTCAG TGATCCAAGG TGCACTTGGG GTTGATTTTT CTTTCTCATT
 CCAGGAGTCA GATGTAGCTC TTGCCTCTGT TGTAAGAGCT GTCTGCCCTT GTCTCTGAAA
 AGTTGCATCT GGAGTTTTTG CTGTGTGTGG GATCACATCC AGAGTTGTTG CTGCTGATCT
 GGGCACCTGC
 Y
 CTGGATGTGC AGAAGTGGTG GTGGGAAGCT GAGTGGAAGT CTGCTCTGCC TTTTTGCTTG
 TGGGATCTGG TCTTGAAAAA GTAACTCCAG AGCTCCTTGC CATTGCAGCT GGTGTGACTG
 CACTTGTAAT GTGCCCTATA GAGAAGGGCA ACTGTGAGGT AGCTGGGCTG ATCATGGTTT
 CCAAAGTGAG TTCCTGGGGA GTTGTGGCCC CCTGAGGAGC TGAGGTAGTG GCTGTGGCTG
 ATGACAGAGA

  GeneView back to top
GeneView via analysis of contig annotation: MUC16 mucin 16, cell surface associated
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_011295->NM_024690
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_011295->NM_024690->NP_078966338771reverse11681missenseAGlu [E]23826
contig referenceGGly [G]23826

GeneView via BLAST analysis of mRNAs: MUC16 mucin 16, cell surface associated
   Variations are assigned to a gene if mapped within 2 kb of mRNA sequence feature.
Accession
class		Nucleotide
accession		Nucleotide
Position		Hit
orientation		Protein
accession		Function
NCBI RefSeqNM_024690.211680minus strandNP_078966.2unclassified

  Integrated Maps: back to top
NCBI MapViewer:  rs2591593 maps exactly once on NCBI human chromosome 19
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
19NW_001838483.256180518657470minusGalt_assembly_8HuRefHuRefview200
19NT_011295.103387718936969plusCref_assemblyreferencereferenceview200
19NW_927195.11893478973101plusCalt_assembly_1CeleraCeleraview200

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000019.6 AC008734
dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):GenBank mRNA:
NM_024690.2 AF414442.2
UniGene Cluster ID
432676

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
T
ss24552896AFD_EUR_PANELEuropean 48IG 0.417 0.375 0.208 0.294 0.604 0.396
AFD_AFR_PANELAfrican American 46IG 0.696 0.217 0.087 0.150 0.804 0.196
AFD_CHN_PANELAsian 48IG 0.500 0.458 0.042 0.439 0.729 0.271
ss3642743HapMap-CEUEuropean 118IG 0.356 0.525 0.119 0.403 0.619 0.381
HapMap-HCBAsian 88IG 0.591 0.341 0.068 0.752 0.761 0.239
HapMap-JPTAsian 90IG 0.711 0.244 0.044 0.833 0.167
HapMap-YRISub-Saharan African 120IG 0.650 0.283 0.067 0.294 0.792 0.208

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.388+/-0.20833226090

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byClusterbyFreqbySubmitterwith2hitwithHapMapFreq
Validated by: PERLEGEN
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .