Reference SNP(refSNP) Cluster Report: rs604139

Reference SNP(refSNP) Cluster Report: rs604139

refSNP ID: rs604139
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_001105566.1:c.220+5301C>T
NM_001105567.1:c.220+5301C>T
NM_001105568.1:c.220+5301C>T
NM_022113.4:c.220+5301C>T
NT_007592.14:g.8726558G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44742728 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs604139 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
ss776170	SC_JCM\|AL138724.4_179535	rev/T	A/G	ctgagttgcagggcattaacaatgctcgaa	acacatggcttcagcacatttgagcaacat	07/27/00	10/10/03	83	Genomic	unknown
ss1219210	KWOK\|OVLP-000804-216763	fwd/B	C/T	atgttgctcaaatgtgctgaagccatgtgt	ttcgagcattgttaatgccctgcaactcag	09/02/00	10/10/03	86	Genomic	97 %
ss1733378	KWOK\|OVLP-000925-378671	fwd/B	C/T	atgttgctcaaatgtgctgaagccatgtgt	ttcgagcattgttaatgccctgcaactcag	10/05/00	10/10/03	87	Genomic	97 %
ss10308649	BCM_SSAHASNP\|chr6.NT_007592.13_8726558	rev/T	A/G	ctgagttgcagggcattaacaatgctcgaa	acacatggcttcagcacatttgagcaacat	06/29/03	10/10/03	116	Genomic	unknown
ss11805523	WI_SSAHASNP\|chr6.NT_007592.13_8726558	rev/T	A/G	ctgagttgcagggcattaacaatgctcgaa	acacatggcttcagcacatttgagcaacat	07/04/03	10/10/03	116	Genomic	unknown
ss12901856	SC_SNP\|NT_007592.13_8726558	rev/T	A/G	ctgagttgcagggcattaacaatgctcgaa	acacatggcttcagcacatttgagcaacat	10/21/03	11/17/03	119	Genomic	unknown
ss22440699	SSAHASNP\|WGSA-200403-chr6.chr6.NT_007592.13_8726558	rev/T	A/G	ctgagttgcagggcattaacaatgctcgaa	acacatggcttcagcacatttgagcaacat	03/21/04	03/21/04	121	Genomic	unknown
ss44742728	ABI\|hCV3115780	rev/T	A/G	ctgagttgcagggcattaacaatgctcgaa	acacatggcttcagcacatttgagcaacat	07/19/05	11/03/06	126	Genomic	unknown
ss76694370	AFFY\|AFFY_6_1M_SNP_A-8555810	rev/T	A/G	attaacaatgctcgaa	acacatggcttcagca	08/28/07	08/30/07	129	Genomic	unknown
ss93406529	BCMHGSC_JDW\|JWB-2103679	rev/T	A/G	ctgagttgcagggcattaacaatgctcgaa	acacatggcttcagcacatttgagcaacat	02/26/08	03/04/08	129	Genomic	unknown

Fasta sequence (Legend)

 TCACTGCTGA TTGCAATTAA AGCATTCTTG ACAATGAATC AATACATTTT TTAACATTTC
 TAAAATGTGC CATGTTAGTA GATAACAGTG ACTTCCAGTA ACTTTGGTTT TTATTTTCTT
 CCCAGCTCTA CAGAAATCTT CATATCAAAA ATAAAAAAAA AGCAGTCTGG TAGTGGCATA
 TCTGGGGTCA GTGTGGATGT GAACATTCCC TGGCCTGAGA GATTCTAAAC TGTTGACTCA
 GAAATTATAT AACAGTTCTT GCCATATGGC ATGTTGCTCA AATGTGCTGA AGCCATGTGT
 Y
 TTCGAGCATT GTTAATGCCC TGCAACTCAG GAGAAAGGTT GTACATCTGC CTCTTATTCT
 GCTAGCATTG CTTTATACTG TGAGGGGACA GAAGAGCACC TCCAATCTGT GGACTAATGC
 AGTGGGAAGA GCAGCCATGT TTGATTCTGT TCCCATCATG GGGGATTTTA TGTGCTCAGA
 GCTAGAAATG ATTTCTGCTT CATATTGCTT AACTAAATAT TAACTTAACT AACCAGAATC
 GTAATGAGAC AAAACATTTG TGCAGCAAAA TTTACATTCT AAAAGCCAAC AGTAGCCAAA

GeneView

GeneView via analysis of contig annotation: KIF13A kinesin family member 13A

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_007592->NM_001105566

function

reference

NT_007592->NM_001105567

function

reference

NT_007592->NM_001105568

function

reference

NT_007592->NM_022113

function

HuRef

NW_001838973->NM_001105566

function

HuRef

NW_001838973->NM_001105567

function

HuRef

NW_001838973->NM_001105568

function

HuRef

NW_001838973->NM_022113

function

Celera

NW_922984->NM_001105566

function

Celera

NW_922984->NM_001105567

function

Celera

NW_922984->NM_001105568

function

Celera

NW_922984->NM_022113

function

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


reference	NT_007592->NM_001105566->NP_001099036	8726558	reverse	intron

reference	NT_007592->NM_001105567->NP_001099037	8726558	reverse	intron

reference	NT_007592->NM_001105568->NP_001099038	8726558	reverse	intron

reference	NT_007592->NM_022113->NP_071396	8726558	reverse	intron

HuRef	NW_001838973->NM_001105566->NP_001099036	14158363	reverse	intron

HuRef	NW_001838973->NM_001105567->NP_001099037	14158363	reverse	intron

HuRef	NW_001838973->NM_001105568->NP_001099038	14158363	reverse	intron

HuRef	NW_001838973->NM_022113->NP_071396	14158363	reverse	intron

Celera	NW_922984->NM_001105566->NP_001099036	17501575	reverse	intron

Celera	NW_922984->NM_001105567->NP_001099037	17501575	reverse	intron

Celera	NW_922984->NM_001105568->NP_001099038	17501575	reverse	intron

Celera	NW_922984->NM_022113->NP_071396	17501575	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs604139 maps exactly once on NCBI human chromosome 6

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
6	NW_001838973.1	14158363	17813326	minus	A	alt_assembly_8	HuRef	HuRef	view	300
6	NT_007592.14	8726558	17976286	minus	G	ref_assembly	reference	reference	view	300
6	NW_922984.1	17501575	19106319	minus	A	alt_assembly_1	Celera	Celera	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_007592 AL023807 AL138724.5 AL138724.7

dbSNP Blast Analysis
GenBank HTGS Finished:
AL023807.6 NC_000006.10

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss44742728	HapMap-CEU	European	120	IG	0.700	0.300			0.850	0.150

	HapMap-HCB	Asian	90	IG	0.556	0.289	0.156		0.700	0.300

	HapMap-JPT	Asian	90	IG	0.444	0.511	0.044		0.700	0.300

	HapMap-YRI	Sub-Saharan African	120	IG	0.700	0.250	0.050		0.825	0.175

	AoD_African_American		90	AF					0.140	0.860

	AoD_Caucasian		92	AF					0.180	0.820

	AoD_Chinese		90	AF					0.210	0.790

	AoD_Japanese		90	AF					0.120	0.880

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.345+/-0.231	270	210	0	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 .