Reference SNP(refSNP) Cluster Report: rs160284

Reference SNP(refSNP) Cluster Report: rs160284

refSNP ID: rs160284
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	79/129
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_004385.2:c.9735+8144C>T
NT_006713.14:g.33453359C>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss5384574 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs160284 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
ss325583	KWOK\|OVLP-000621-37239	rev/T	A/G	ctgctgtcttttagttgaacagggtaattc	ttgaccgacaactgaaaagaaaagagcagc	06/30/00	10/10/03	79	Genomic	99 %
ss397824	KWOK\|OVLP-000621-236602	rev/T	A/G	ctgctgtcttttagttgaacagggtaattc	ttgaccgacaactgaaaagaaaagagcagc	06/30/00	10/10/03	79	Genomic	99 %
ss398919	KWOK\|OVLP-000621-239779	rev/T	A/G	ctgctgtcttttagttgaacagggtaattc	ttgaccgacaactgaaaagaaaagagcagc	06/30/00	10/10/03	85	Genomic	99 %
ss658204	SC_JCM\|AC020921.4_49060	fwd/B	C/T	gctgctcttttcttttcagttgtcggtcaa	gaattaccctgttcaactaaaagacagcag	07/27/00	10/10/03	85	Genomic	unknown
ss1139864	KWOK\|OVLP-000804-403844	rev/T	A/G	ctgctgtcttttagttgaacagggtaattc	ttgaccgacaactgaaaagaaaagagcagc	09/02/00	10/10/03	86	Genomic	99 %
ss1140440	KWOK\|OVLP-000804-409053	fwd/B	C/T	gctgctcttttcttttcagttgtcggtcaa	gaattaccctgttcaactaaaagacagcag	09/02/00	10/10/03	86	Genomic	99 %
ss1683494	KWOK\|OVLP-000925-256777	rev/T	A/G	ctgctgtcttttagttgaacagggtaattc	ttgaccgacaactgaaaagaaaagagcagc	10/05/00	10/10/03	87	Genomic	99 %
ss1683754	KWOK\|OVLP-000925-259315	fwd/B	C/T	gctgctcttttcttttcagttgtcggtcaa	gaattaccctgttcaactaaaagacagcag	10/05/00	10/10/03	87	Genomic	99 %
ss5384574	TSC-CSHL\|TSC1470010	fwd/B	C/T	gctgctcttttcttttcagttgtcggtcaa	gaattaccctgttcaactaaaagacagcag	09/20/02	05/16/04	110	Genomic	unknown
ss5488064	TSC-CSHL\|TSC1020705	fwd/B	C/T	gctgctcttttcttttcagttgtcggtcaa	gaattaccctgttcaactaaaagacagcag	09/21/02	10/10/03	110	Genomic	unknown
ss81160724	HGSV\|Cor18555_SNV_20070510.chr5_82894757	fwd/B	C/T	gctgctcttttcttttcagttgtcggtcaa	gaattaccctgttcaactaaaagacagcag	11/27/07	11/28/07	130	Genomic	unknown

Fasta sequence (Legend)

 ATGAGCTTTG GCAGTCTCTC CTTACATTTG GATCGTCAGC CCTTCATGAC TGGAGACCTG
 TGCAAATAAG CTTGGGGTAA AGGAGCCTAC TGGCACCATT CATTCTATGG ATTAAATGCA
 AGTTGCTCTC TGGGCCTCTG CCTGAGGCCC CCTCTCTCAC AGTGGTCTCA CAGTGCGAGT
 AACTCACATC CTTCTGAAAA TGCTGTTGAT AATTGCTGCT TTGTAGGGCA GTGAGCTCAC
 ACTATTACAC AAGATTAGTG CTGTTCTCAA GAGCTGGCCA GATTGTCTTT CCCGCACAGA
 GGTTTGCCAG CTAGGAAAAT AATGGGCATA TTGCCACTTT AACAACTATC AGGAGACCCC
 AAGTTAGTTT TTCTTCCCTT CAGCATATTC ATGTTTGTAG GATCCAACTC CAGGCTGCCA
 GCATAGGGTA GTGACACCAA AACAAACGTC TCTTTCTCCT TTAAAACAAA GCTGCTCTTT
 TCTTTTCAGT TGTCGGTCAA
 Y
 GAATTACCCT GTTCAACTAA AAGACAGCAG CAAAACCATA ACCTCCCTTA AAACATAAAT
 AAAGAAGGAC CCAGACTAGA CTAACCTTAA GCAAGTACAA GGATCAGAAG AAGGTTTATC
 TTTACCTTGC AGGGAAGTCA TTTGCCCCTA ACAAACAAGA CAAAGTTAAA TGCACCACTC
 CCCCTCCAGA CTGCAAACAA ATGCCTATTG TGTACACCAG CCATCTAGGG ATAAAAAAGT
 CATTTTAAAG GTACCAAATG TTTTGATTTC TGTAATAAGT AGTCCTCATA GCCTCTTTTC
 AGATAACCAT TTGACCTGTG TTCTGAAAGG CTGAGGCTAA CCCCAAGTGG TTATTCTGTT
 TGTTATTTAG TGAAAAGATG GTTTCTTATC GGCATATGTT TCAAACAGGT ACCTGTCCTC
 TTGGGAAAGT GTTTTCTGTT TGGAATTTGC TTTCCTACTT CGGTGGTTAT CTGCTTGCCC
 TTGGTATCCA GTG

GeneView

GeneView via analysis of contig annotation: VCAN versican

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_006713->NM_004385

function

HuRef

NW_001838951->NM_004385

function

Celera

NW_922729->NM_004385

function

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


reference	NT_006713->NM_004385->NP_004376	33453359	forward	intron

HuRef	NW_001838951->NM_004385->NP_004376	12149174	forward	intron

Celera	NW_922729->NM_004385->NP_004376	12163900	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs160284 maps exactly once on NCBI human chromosome 5

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
5	NW_001838951.1	12149174	78067283	plus	C	alt_assembly_8	HuRef	HuRef	view	500
5	NW_922729.1	12163900	78764056	plus	C	alt_assembly_1	Celera	Celera	view	500
5	NT_006713.14	33453359	82894757	plus	C	ref_assembly	reference	reference	view	500

NCBI Resource Links

Submitter-Referenced
GenBank
AC020921.4 AC007554 AC020921.4 AC026696.3

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC020921.6 AC026696.5 NC_000005.8	AC007554.4 AC008908.5

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	HWP	C	T
ss5384574	CEPH		184	AF				0.970	0.030

	HapMap-CEU	European	120	IG	1.000			1.000

	HapMap-HCB	Asian	90	IG	0.889	0.111	0.752	0.944	0.056

	HapMap-JPT	Asian	90	IG	0.956	0.044	1.000	0.978	0.022

	HapMap-YRI	Sub-Saharan African	120	IG	1.000			1.000

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.033+/-0.124	270	210	0	0

Validation Summary:

Validation status	Marker displays Mendelian segregation	PCR results confirmed in multiple reactions	Homozygotes detected in individual genotype data
	UNKNOWN	UNKNOWN	UNKNOWN

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Revised: May 25, 2006 1:38 PM .