Reference SNP(refSNP) Cluster Report: rs629176

Reference SNP(refSNP) Cluster Report: rs629176

refSNP ID: rs629176
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:	A/T
Ancestral Allele:	A
Clinical Association:	unknown

HGVS Names
NM_033063.1:c.1317-8630A>T
NT_033927.7:g.5530608T>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss1779771 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs629176 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
ss82267	TSC-CSHL\|TSC0029022	fwd/B	A/T	agggagtgaactgtgtagatcaaactcagc	tctctgaccttcttgtgactcattttccat	09/06/00	04/07/04	92	Genomic	95 %
ss801707	SC_JCM\|AP000584.3_18852	rev/T	A/T	atggaaaatgagtcacaagaaggtcagaga	gctgagtttgatctacacagttcactccct	07/27/00	10/10/03	83	Genomic	unknown
ss1779771	KWOK\|OVLP-000925-344991	rev/T	A/T	atggaaaatgagtcacaagaaggtcagaga	gctgagtttgatctacacagttcactccct	10/05/00	04/07/04	89	Genomic	99 %
ss1780873	KWOK\|OVLP-000925-365129	fwd/B	A/T	agggagtgaactgtgtagatcaaactcagc	tctctgaccttcttgtgactcattttccat	10/05/00	10/10/03	92	Genomic	99 %
ss1781263	KWOK\|OVLP-000925-372726	fwd/B	A/T	agggagtgaactgtgtagatcaaactcagc	tctctgaccttcttgtgactcattttccat	10/05/00	10/10/03	87	Genomic	99 %
ss1858743	KWOK\|OVLP-000925-357938	fwd/B	A/T	agggagtgaactgtgtagatcaaactcagc	tctctgaccttcttgtgactcattttccat	10/06/00	10/10/03	92	Genomic	87 %
ss10651426	BCM_SSAHASNP\|chr11.NT_033927.5_5506888	fwd/B	A/T	agggagtgaactgtgtagatcaaactcagc	tctctgaccttcttgtgactcattttccat	06/29/03	10/10/03	116	Genomic	unknown
ss16163444	SC_SNP\|NT_033927.6_5506888	fwd/B	A/T	agggagtgaactgtgtagatcaaactcagc	tctctgaccttcttgtgactcattttccat	11/18/03	11/22/03	120	Genomic	unknown
ss16526545	CSHL-HAPMAP\|CSHL-HuAA-200402.chr11.NT_033927.6_5506888	fwd/B	A/T	agggagtgaactgtgtagatcaaactcagc	tctctgaccttcttgtgactcattttccat	02/17/04	03/04/04	120	Genomic	unknown
ss17423696	CSHL-HAPMAP\|CSHL-HuCC-200402.chr11.NT_033927.6_5506888	fwd/B	A/T	agggagtgaactgtgtagatcaaactcagc	tctctgaccttcttgtgactcattttccat	02/19/04	03/04/04	120	Genomic	unknown
ss19910811	CSHL-HAPMAP\|CSHL-HuFF-200402.chr11.NT_033927.6_5506888	fwd/B	A/T	agggagtgaactgtgtagatcaaactcagc	tctctgaccttcttgtgactcattttccat	02/21/04	03/04/04	120	Genomic	unknown
ss20776525	SSAHASNP\|WGSA-200403-chr11.chr11.NT_033927.6_5506888	fwd/B	A/T	agggagtgaactgtgtagatcaaactcagc	tctctgaccttcttgtgactcattttccat	03/19/04	03/19/04	121	Genomic	unknown
ss38757896	ABI\|hCV1029817	fwd/	A/T	agggagtgaactgtgtagatcaaactcagc	tctctgaccttcttgtgactcattttccat	07/16/05	11/02/06	126	Genomic	unknown
ss65841857	KRIBB_YJKIM\|KHS17651	fwd/	A/T	agggagtgaactgtgtagatcaaactcagc	tctctgaccttcttgtgactcattttccat	10/17/06	12/16/06	127	Genomic	unknown
ss83125689	HGSV\|Cor18555_SNV_20070510.chr11_74985507	fwd/	A/T	agggagtgaactgtgtagatcaaactcagc	tctctgaccttcttgtgactcattttccat	11/27/07	12/04/07	130	Genomic	unknown
ss83427658	HGSV\|Cor18956_SNV_20070510.chr11_74985507	fwd/	A/T	agggagtgaactgtgtagatcaaactcagc	tctctgaccttcttgtgactcattttccat	11/30/07	12/05/07	130	Genomic	unknown
ss88642834	BCMHGSC_JDW\|JWB-0444069	fwd/	A/T	agggagtgaactgtgtagatcaaactcagc	tctctgaccttcttgtgactcattttccat	02/26/08	02/27/08	129	Genomic	unknown

Fasta sequence (Legend)

 GCCCATCCAC ATTCACACCT GGAAGCCCTA CCTGTGCAGC TGCCAATCAG TCTACCAGCC
 CAGGGCCACA CTGAGTCCGC CAGATGTGGC TCATCACACA GAAACACCAG CTAGGACCAC
 AGTTAGGAGA AATGCTGCCT CCACAAGACT TAATTCTGGG TTAGGGGTGG AGGGAGTGAA
 CTGTGTAGAT CAAACTCAGC
 W
 TCTCTGACCT TCTTGTGACT CATTTTCCAT AGACGAGAGT ATGGAGAGTC ATTGAACGTT
 TCAGAGCAAG CGAGGGACAG AGGAGGAGGC TGCTGTTTCA GGCGATGCAC ATCTCTGCAA
 CAGGAATCCT ACAGATAGTC CCAAGTGCTG GACAAGGAAT GGGTTTTAGG GTCACCCAAA
 cctgggttca catcctggct caccacttac aagttgtgtg actttgttcc ttaatcaccg
 agttctgatt tgtttatctg taaatgggag tgacacctgc agactctaac cttactgtga
 ggattaaatg agacgaagtg tgtaaagGCC AAGTAAAGGT TCATTCCCTC CCCCTAGGCT
 GTGGCAACTC TGCATTTTAC AAAAGTCGAA TCAAGATCTG GGGCCAGCCC CTAGTTCAGG
 TCTTTCCCTG CCACTCTGGG TTCCCTCCAG GCAGACATGT TCTTCTGAAA TACAGGGAAA
 TGGTTGCACT TAGGTGGGTA AGTGGCTAGG TGGTTATGTT TTCTTTGTGG TTATTTACCT
 AT

GeneView

GeneView via analysis of contig annotation: MAP6 microtubule-associated protein 6

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_033927->NM_033063

function

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


reference	NT_033927->NM_033063->NP_149052	5530608	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs629176 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_001838028.2	12370701	71604936	minus	T	alt_assembly_8	HuRef	HuRef	view	200
11	NW_925106.1	20963720	72615644	plus	A	alt_assembly_1	Celera	Celera	view	200
11	NT_033927.7	5530608	74985507	plus	T	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_033927 AC011256 AP000584.2 AP000588 AP000588.2 AP001142 AP001142.1 AP001922 AP001922.2 AP002386 AP002815.1

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AP001922.4	AP000584.3 AP000588.3 AP001142.2 AP002386.1

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/T	T/T	HWP	A	T
ss1779771	HapMap-CEU	European	120	IG	0.467	0.450	0.083	0.752	0.692	0.308

	HapMap-HCB	Asian	88	IG	0.477	0.523		0.020	0.739	0.261

	HapMap-JPT	Asian	88	IG	0.659	0.295	0.045	0.752	0.807	0.193

	HapMap-YRI	Sub-Saharan African	120	IG	0.650	0.300	0.050	0.655	0.800	0.200

ss38757896	AoD_African_American		90	AF					0.760	0.240

	AoD_Caucasian		92	AF					0.720	0.280

	AoD_Chinese		90	AF					0.760	0.240

	AoD_Japanese		90	AF					0.760	0.240

ss65841857	KHP1		180	AF	0.644	0.278	0.078	0.100	0.783	0.217

ss82267	TSC_42_AA		80	AF					0.790	0.210

	TSC_42_C		84	AF					0.655	0.345

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.359+/-0.225	270	210	0	0

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: ILLUMINA

DoubleHit found by: BCM_SSAHASNP, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .