Reference SNP(refSNP) Cluster Report: rs600097

Reference SNP(refSNP) Cluster Report: rs600097

refSNP ID: rs600097
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	83/129
Map to Genome Build:	36.3

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

HGVS Names
NM_001048209.1:c.167+21837A>G
NM_016522.2:c.167+21837A>G
NT_033899.7:g.35365795A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss38755425 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs600097 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
ss772044	SC_JCM\|AP000932.3_14824	fwd/B	C/T	agcagctagagtggaaaacagtgcgtttcg	acctttaacctagataaatgaatgtcttat	07/27/00	10/25/06	83	Genomic	unknown
ss1593277	KWOK\|OVLP-000925-280451	rev/T	A/G	ataagacattcatttatctaggttaaaggt	cgaaacgcactgttttccactctagctgct	10/04/00	10/10/03	87	Genomic	99 %
ss1595421	KWOK\|OVLP-000925-301650	rev/T	A/G	ataagacattcatttatctaggttaaaggt	cgaaacgcactgttttccactctagctgct	10/04/00	10/10/03	87	Genomic	99 %
ss1595966	KWOK\|OVLP-000925-308517	fwd/B	C/T	agcagctagagtggaaaacagtgcgtttcg	acctttaacctagataaatgaatgtcttat	10/04/00	10/10/03	87	Genomic	99 %
ss1656242	KWOK\|OVLP-000925-287059	fwd/B	C/T	agcagctagagtggaaaacagtgcgtttcg	acctttaacctagataaatgaatgtcttat	10/05/00	10/10/03	87	Genomic	93 %
ss1656268	KWOK\|OVLP-000925-310110	fwd/B	C/T	agcagctagagtggaaaacagtgcgtttcg	acctttaacctagataaatgaatgtcttat	10/05/00	10/10/03	87	Genomic	93 %
ss1656283	KWOK\|OVLP-000925-315234	fwd/B	C/T	agcagctagagtggaaaacagtgcgtttcg	acctttaacctagataaatgaatgtcttat	10/05/00	10/10/03	87	Genomic	93 %
ss16161916	SC_SNP\|NT_033899.6_35347166	rev/T	A/G	ataagacattcatttatctaggttaaaggt	cgaaacgcactgttttccactctagctgct	11/18/03	11/22/03	120	Genomic	unknown
ss20763520	SSAHASNP\|WGSA-200403-chr11.chr11.NT_033899.6_35347166	rev/T	A/G	ataagacattcatttatctaggttaaaggt	cgaaacgcactgttttccactctagctgct	03/19/04	03/19/04	121	Genomic	unknown
ss38755425	ABI\|hCV633500	rev/T	A/G	ataagacattcatttatctaggttaaaggt	cgaaacgcactgttttccactctagctgct	07/16/05	11/02/06	126	Genomic	unknown
ss66686617	ILLUMINA\|HumanHap300v1.1_rs600097	fwd/B	C/T	agcagctagagtggaaaacagtgcgtttcg	acctttaacctagataaatgaatgtcttat	11/09/06	11/09/06	127	Genomic	unknown
ss67432948	ILLUMINA\|HumanHap550v1.1_rs600097	fwd/B	C/T	agcagctagagtggaaaacagtgcgtttcg	acctttaacctagataaatgaatgtcttat	11/14/06	11/14/06	127	Genomic	unknown
ss67788868	ILLUMINA\|HumanHap650Yv1.0_rs600097	fwd/B	C/T	agcagctagagtggaaaacagtgcgtttcg	acctttaacctagataaatgaatgtcttat	11/14/06	11/14/06	127	Genomic	unknown
ss69334467	PERLEGEN\|PGP13181860	rev/T	A/G	ataagacattcatttatctaggttaaaggt	cgaaacgcactgttttccactctagctgct	01/30/07	08/14/07	127	Genomic	unknown
ss70853430	ILLUMINA\|HumanHap550v3.0__rs600097	fwd/B	C/T	agcagctagagtggaaaacagtgcgtttcg	acctttaacctagataaatgaatgtcttat	04/20/07	03/31/08	130	Genomic	unknown
ss71439285	ILLUMINA\|HumanHap650Yv3.0_rs600097	fwd/B	C/T	agcagctagagtggaaaacagtgcgtttcg	acctttaacctagataaatgaatgtcttat	04/23/07	04/23/07	127	Genomic	unknown
ss75559267	ILLUMINA\|ILMN_Human_1M_rs600097	fwd/B	C/T	agcagctagagtggaaaacagtgcgtttcg	acctttaacctagataaatgaatgtcttat	08/28/07	08/29/07	129	Genomic	unknown
ss79213762	ILLUMINA\|HumanHap300v2.0_rs600097	fwd/B	C/T	agcagctagagtggaaaacagtgcgtttcg	acctttaacctagataaatgaatgtcttat	04/18/07	11/18/07	130	Genomic	unknown
ss83494181	KRIBB_YJKIM\|KHS474856	fwd/B	C/T	agcagctagagtggaaaacagtgcgtttcg	acctttaacctagataaatgaatgtcttat	12/04/07	12/05/07	130	Genomic	unknown
ss111305397	1000GENOMES\|CEU.trio.12.15.2008_2654094_chr11_131308589	rev/T	A/G	ataagacattcatttatctaggttaaaggt	cgaaacgcactgttttccactctagctgct	12/15/08	12/17/08	130	Genomic	unknown

Fasta sequence (Legend)

 AGCTAGATTT CATCTATTTC AATAACCCAA ATTCATCGCC CACGGGACTT TGATATTAAG
 ACAGATTCTT CCTCTCCTTA TTCTGCTTGG GTATAGGTTA AGAAGCTTTG AGATAGAGTC
 TTTCCAGGAA GAGGACACTA AAGCACTAAC TTAATAAAAC TTTGTGATTA AACCTGGGAG
 ACCTAAGGCA CAGTCCAGAG CCATTAGTTT CAAGTTCAGG AGCAAACCAC AGCACAAGGA
 AACTGGCTGC ATAACCTTAA ATAATCACCC AGCAGCTAGA GTGGAAAACA GTGCGTTTCG
 Y
 ACCTTTAACC TAGATAAATG AATGTCTTAT TTAGAAAGAG CAAATCCTTG GCGGGGAAAC
 TAGATGGTCA GGCACATGGA ACTCCCAGCT GAAACACAAG GTGTTTGGAA AACAATAGTC
 TCATTTTTGA TGGAAGCACC TTACAAACCG GCCAAGTGCA CCAGAAAGAG CTGAGCCCAG
 GTGATGCCTG CGGGTGTAGG GGAGTGAGGT CTCTAGGGCA GGCACCCACC TCCCTGCCCC
 AGGGCCCCAC GCACTCCCTG ACAGTCCCAG GACCAGGAGC CAATTGGCAG TGCTGGCTGC

GeneView

GeneView via analysis of contig annotation: HNT neurotrimin

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_033899->NM_001048209

function

reference

NT_033899->NM_016522

function

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


reference	NT_033899->NM_001048209->NP_001041674	35365795	forward	intron

reference	NT_033899->NM_016522->NP_057606	35365795	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs600097 maps exactly once on NCBI human chromosome 11

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
11	NW_001838044.1	5144074	127759221	minus	A	alt_assembly_8	HuRef	HuRef	view	300
11	NW_925173.1	41843761	128974861	minus	A	alt_assembly_1	Celera	Celera	view	300
11	NT_033899.7	35365795	131308589	minus	A	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_033899 AC012134 AP000762 AP000762.3 AP000844 AP000844.2 AP000932.3 AP001811 AP001811.2 AP002341

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AP000844.4	AP000762.3 AP000932.3 AP001811.2 AP002831.1

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss38755425	HapMap-CEU	European	120	IG	0.100	0.550	0.350	0.200	0.375	0.625

	HapMap-HCB	Asian	90	IG	0.422	0.444	0.133	1.000	0.644	0.356

	HapMap-JPT	Asian	90	IG	0.533	0.356	0.111	0.403	0.711	0.289

	HapMap-YRI	Sub-Saharan African	120	IG		0.117	0.883	0.655	0.058	0.942

ss69334467	HapMap-CEU	European	120	GF	0.100	0.550	0.350		0.375	0.625

	HapMap-HCB	Asian	90	GF	0.422	0.444	0.133		0.644	0.356

	HapMap-JPT	Asian	90	GF	0.533	0.356	0.111		0.711	0.289

	HapMap-YRI	Sub-Saharan African	120	GF		0.117	0.883		0.058	0.942

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.485+/-0.084	270	210	270	0

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

UNKNOWN

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Revised: May 25, 2006 1:38 PM .