Reference SNP(refSNP) Cluster Report: rs613440

Reference SNP(refSNP) Cluster Report: rs613440

refSNP ID: rs613440
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_001083592.1:c.91+104205G>A
NM_005012.2:c.91+104205G>A
NT_032977.8:g.34316303G>A

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss1967461 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs613440 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
ss785665	SC_JCM\|AC025544.3_104561	fwd/B	C/T	ggatgagagtaaccagggcagcagatggag	agacagggctccacctttaggttttctgga	07/27/00	10/10/03	83	Genomic	unknown
ss1150177	KWOK\|OVLP-000804-456171	fwd/B	C/T	ggatgagagtaaccagggcagcagatggag	agacagggctccacctttaggttttctgga	09/02/00	10/10/03	86	Genomic	99 %
ss1244246	KWOK\|OVLP-000804-465098	fwd/B	C/T	ggatgagagtaaccagggcagcagatggag	agacagggctccacctttaggttttctgga	09/02/00	10/10/03	86	Genomic	97 %
ss1934217	KWOK\|OVLP-000925-727318	fwd/B	C/T	ggatgagagtaaccagggcagcagatggag	agacagggctccacctttaggttttctgga	10/06/00	10/10/03	87	Genomic	99 %
ss1934503	KWOK\|OVLP-000925-728486	fwd/B	C/T	ggatgagagtaaccagggcagcagatggag	agacagggctccacctttaggttttctgga	10/06/00	10/10/03	87	Genomic	99 %
ss1967461	KWOK\|OVLP-000925-729136	fwd/B	C/T	ggatgagagtaaccagggcagcagatggag	agacagggctccacctttaggttttctgga	10/06/00	10/10/03	87	Genomic	97 %
ss2427187	SC_JCM\|AL353713.7_67025	fwd/B	C/T	ggatgagagtaaccagggcagcagatggag	agacagggctccacctttaggttttctgga	11/03/00	10/10/03	92	Genomic	unknown
ss11340694	WI_SSAHASNP\|chr1.NT_032977.5_16793295	rev/T	A/G	tccagaaaacctaaaggtggagccctgtct	ctccatctgctgccctggttactctcatcc	07/03/03	10/10/03	116	Genomic	unknown
ss16411058	CSHL-HAPMAP\|CSHL-HuAA-200402.chr1.NT_032977.6_25907454	rev/T	A/G	tccagaaaacctaaaggtggagccctgtct	ctccatctgctgccctggttactctcatcc	02/17/04	03/04/04	120	Genomic	unknown
ss20498046	SSAHASNP\|WGSA-200403-chr1.chr1.NT_032977.6_25907454	rev/T	A/G	tccagaaaacctaaaggtggagccctgtct	ctccatctgctgccctggttactctcatcc	03/18/04	03/18/04	121	Genomic	unknown
ss41164972	ABI\|hCV587298	rev/T	A/G	tccagaaaacctaaaggtggagccctgtct	ctccatctgctgccctggttactctcatcc	07/16/05	07/17/05	126	Genomic	unknown
ss87490929	BCMHGSC_JDW\|JWB-0056702	rev/T	A/G	tccagaaaacctaaaggtggagccctgtct	ctccatctgctgccctggttactctcatcc	02/26/08	02/26/08	129	Genomic	unknown

Fasta sequence (Legend)

 TCTGGGGCTT CTATCTCTCC CTCTTCTAAC AGTTTATTTT CCTTTAAATT GTCCTTTCAA
 CATAAGCCTT AATAGTTGGG GTTTCAAACC CTTTAGAGGA aattaattaa ttggttaatt
 aattaatGAA ATTATTCAAC AAATGGAGGC TCAGGACCTG TAATGCAACA GGCTTCATAT
 ACCATGAGGA CTGAACAGGC TGCGGTCTGC ACTCTCCTGA AGTTTGCAGC CTTGTGAGGG
 AGACTGGCAA GAAATAAGTA CATAACTATG CAGTAGTAAC AAATTGTGAA AAGGCCTCAC
 AGTACTTATA AAAAGAGAAT GAATGCCCTG GATGAGAGTA ACCAGGGCAG CAGATGGAG
 Y
 AGACAGGGCT CCACCTTTAG GTTTTCTGGA AAGAGGGAAG GATGAAAGAT GAATAGGTTG
 GTGCTGAGGA GCAAAGTCAG CAGAGGCTAG ACCCACAGAG TCCTGTAAGC CAAGCCATGG
 CAAGGATTTC AGCCCTAAAC CTGTAAGCAA ATGGCAGCCG TGAAGGAGTT TTAAACCAAG
 AAAGCTCATG ATCAGATTTC TGTTTAAAAA AAAAAAAATC ACTCCAGCTA CAATGTGGTG
 AATAGATTAG AAGGGGACAG AGAAAATGTA CAGAGACCGT CAGGAGACTG CTGCAAGTTG
 CAGGTCTTGA AACTGTTAAG CAAATAACAA TTAGGTTTAT TTCCGATCAG TTCCTCATCG
 TCAAGGAATG GTAATGGTGT TGTCAAAGCA AAATGGAAGT AAAGGTATAT AAAAACGCTT
 GCAAATACTC AGGGATATTT GGAAATAATG CATTCACAAG CATTCCACAT

GeneView

GeneView via analysis of contig annotation: ROR1 receptor tyrosine kinase-like orphan receptor 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_032977->NM_001083592

function

reference

NT_032977->NM_005012

function

HuRef

NW_001838579->NM_001083592

function

HuRef

NW_001838579->NM_005012

function

Celera

NW_921351->NM_001083592

function

Celera

NW_921351->NM_005012

function

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


reference	NT_032977->NM_001083592->NP_001077061	34316303	forward	intron

reference	NT_032977->NM_005012->NP_005003	34316303	forward	intron

HuRef	NW_001838579->NM_001083592->NP_001077061	19342473	reverse	intron

HuRef	NW_001838579->NM_005012->NP_005003	19342473	reverse	intron

Celera	NW_921351->NM_001083592->NP_001077061	38495103	forward	intron

Celera	NW_921351->NM_005012->NP_005003	38495103	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs613440 maps exactly once on NCBI human chromosome 1

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
1	NW_001838579.2	19342473	62452249	plus	T	alt_assembly_8	HuRef	HuRef	view	359
1	NW_921351.1	38495103	62634245	minus	A	alt_assembly_1	Celera	Celera	view	359
1	NT_032977.8	34316303	64116972	minus	G	ref_assembly	reference	reference	view	359

NCBI Resource Links

Submitter-Referenced
GenBank
NT_032977 AC025544 AL161742 AL161742.3 AL161742.4 AL353713.7 AL356914 AL356914.2

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AL353713.7 NC_000001.9	AC025544.4 AL356914.2

Population Diversity

There is no frequency data.

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 .