Reference SNP(refSNP) Cluster Report: rs4085842

Reference SNP(refSNP) Cluster Report: rs4085842

refSNP ID: rs4085842
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	108/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	C/G
Ancestral Allele:	C
Clinical Association:	unknown

HGVS Names
NM_005433.3:c.-9+8537G>C
NT_010859.14:g.793578C>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss5485675 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs4085842 during BLAST analysis for the current build.

NCBI Assay ID	Handle\|Submitter ID	ss to rs Orientation /Strand	Alleles	5' Near Seq 30 bp	3' Near Seq 30 bp	Entry Date	Update Date	Build Added	Molecule Type	Success Rate
ss5485675	TSC-CSHL\|TSC1009758	fwd/T	C/G	ttccctaggtttccccacctgcttgctagt	gcagtgaaacctgcctcatactctaaccct	09/21/02	03/31/08	108	Genomic	unknown
ss6106343	SC_JCM\|NT_011005.10_873790	fwd/T	C/G	ttccctaggtttccccacctgcttgctagt	gcagtgaaacctgcctcatactctaaccct	01/10/03	10/10/03	111	Genomic	unknown
ss10907839	BCM_SSAHASNP\|chr18.NT_010859.12_793578	rev/B	C/G	agggttagagtatgaggcaggtttcactgc	actagcaagcaggtggggaaacctagggaa	06/30/03	10/10/03	116	Genomic	unknown
ss14416192	WI_SSAHASNP\|chr18.NT_010859.13_793578	rev/B	C/G	agggttagagtatgaggcaggtttcactgc	actagcaagcaggtggggaaacctagggaa	11/05/03	11/22/03	119	Genomic	unknown
ss40866319	ABI\|hCV29230300	rev/	C/G	agggttagagtatgaggcaggtttcactgc	actagcaagcaggtggggaaacctagggaa	07/17/05	07/17/05	126	Genomic	unknown
ss66251727	AFFY\|SNP_A-4281546	rev/B	C/G	aggcaggtttcactgc	actagcaagcaggtgg	10/27/06	03/31/08	127	Genomic	unknown
ss76397130	AFFY\|AFFY_6_1M_SNP_A-4281546	rev/	C/G	aggcaggtttcactgc	actagcaagcaggtgg	08/28/07	08/30/07	130	Genomic	unknown
ss83938688	HGSV\|Cor19240_SNV_20070510.chr18_793578	rev/	C/G	agggttagagtatgaggcaggtttcactgc	actagcaagcaggtggggaaacctagggaa	11/30/07	12/06/07	130	Genomic	unknown

Fasta sequence (Legend)

 CTTATAAAAG CCTCACAAAT AGGTAAAATA ATACTTTGGT GGTAAAATAT TTTCTGACTG
 ATTATCAGTT TTTGCCTGGT TTTTGTTAAC TGCTGAGCTC TTTGAACAAA TAAAATATTT
 GGCCTACAAG TGCTCTGATT ATGAGGTGGG TGAACCTGTA GCCTTGCCAG TCACCCTCCT
 TTCCCACCTT ACCAGCTCCT CACTATTTAA AAATCACTGT TTTGAGTTCC CTGTTAGGAG
 ACTCAGATTC TCCCAATAAG GCATTGCTAT TAAGCTTAAT TTAAGTACAG AAACTTCCCT
 AGGTTTCCCC ACCTGCTTGC TAGT
 S
 GCAGTGAAAC CTGCCTCATA CTCTAACCCT ATAGGACAGT ATGAGGTATA GAAAAGCTTC
 AAAAGATTGG GGGTAATAAA CAAAAATAGT AGAAAAGGGT TTGGGAAAAT GAGGAGTGTT
 ACAATATGGA GTTTGTAACT TCTTTACCTT CTCTGTGCTT TTTTTATTTC CCACCCATTC
 ACCTCACTTT GGCATTGGGT AGGGAAAGAA GAAAGCCTGT CCTATGATAG GTGCTATGCC
 ATACTTTTAT ATGCATTATC ACATTTGACT TGAATCTTTG AAA

GeneView

GeneView via analysis of contig annotation: YES1 v-yes-1 Yamaguchi sarcoma viral oncogene homolog 1

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

Group
Label

Contig->mRNA

Gene Model (contig mRNA transcript) Color Legend

reference

NT_010859->NM_005433

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	Function


reference	NT_010859->NM_005433->NP_005424	793578	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs4085842 maps exactly once on NCBI human chromosome 18

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
18	NW_926940.1	678512	678512	minus	C	alt_assembly_1	Celera	Celera	view	324
18	NW_001838461.1	752073	763713	minus	C	alt_assembly_8	HuRef	HuRef	view	324
18	NT_010859.14	793578	793578	minus	C	ref_assembly	reference	reference	view	324

NCBI Resource Links

Submitter-Referenced
GenBank
NT_011005.10

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AP000894.6	AP000931.3 AP000938.3

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/G	G/G	HWP	C	G
ss5485675	HapMap-CEU	European	120	IG	0.117	0.483	0.400		0.358	0.642

	HapMap-HCB	Asian	90	IG	0.200	0.356	0.444		0.378	0.622

	HapMap-JPT	Asian	90	IG	0.267	0.422	0.311		0.478	0.522

	HapMap-YRI	Sub-Saharan African	118	IG	0.525	0.407	0.068		0.729	0.271

ss66251727	HapMap-CEU	European	118	GF	0.119	0.492	0.390		0.364	0.636

	HapMap-HCB	Asian	90	GF	0.200	0.356	0.444		0.378	0.622

	HapMap-JPT	Asian	90	GF	0.267	0.422	0.311		0.478	0.522

	HapMap-YRI	Sub-Saharan African	120	GF	0.550	0.383	0.067		0.742	0.258

Concordant Genotype	Total Sample	C/C	C/G	G/G
ss5485675	269	79	111	77
ss66251727	268	76	111	81

RefSNP Genotype Summary	Total Individual	C/C	C/G	G/G
rs4085842	270	155	111	158

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
5263	ss5485675	C/G	CSHL-HAPMAP	HapMap-YRI	NA18861	YOR024.02	r23_ch18_YRI_affymetrix:genotype_protocol_1
5263	ss66251727	G/G	CSHL-HAPMAP	HapMap-YRI	NA18861	YOR024.02	chr18-HapMap-YRI

Genotype data submitted for	270	samples from	270	individuals	Individual with multiple genotypes submission:	269

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

DoubleHit found by: BCM_SSAHASNP, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .