Reference SNP(refSNP) Cluster Report: rs849557

Reference SNP(refSNP) Cluster Report: rs849557

refSNP ID: rs849557
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	86/129
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_003872.2:c.251+578G>A
NM_018534.3:c.251+578G>A
NM_201264.1:c.251+578G>A
NM_201266.1:c.251+578G>A
NM_201267.1:c.251+578G>A
NM_201279.1:c.251+578G>A
NT_005403.16:g.56772440G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss41630871 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs849557 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
ss1217061	KWOK\|OVLP-000804-189758	fwd/B	C/T	agtgtttgttaaataaatccatgacactga	tttgagactctacttgtgtagcacagctat	09/02/00	10/10/03	86	Genomic	97 %
ss1738397	KWOK\|OVLP-000925-520834	fwd/B	C/T	agtgtttgttaaataaatccatgacactga	tttgagactctacttgtgtagcacagctat	10/05/00	10/10/03	87	Genomic	97 %
ss3868346	SC_JCM\|AF281074.1_18515	rev/T	A/G	atagctgtgctacacaagtagagtctcaaa	tcagtgtcatggatttatttaacaaacact	09/25/01	10/10/03	100	Genomic	unknown
ss6438058	WI_SSAHASNP\|NT_005403.11_7011962	rev/T	A/G	atagctgtgctacacaagtagagtctcaaa	tcagtgtcatggatttatttaacaaacact	02/12/03	10/10/03	111	Genomic	unknown
ss20084042	CSHL-HAPMAP\|CSHL-HuFF-200402.chr2.NT_005403.14_56772439	rev/T	A/G	atagctgtgctacacaagtagagtctcaaa	tcagtgtcatggatttatttaacaaacact	02/21/04	03/04/04	120	Genomic	unknown
ss21657714	SSAHASNP\|WGSA-200403-chr2.chr2.NT_005403.14_56772439	rev/T	A/G	atagctgtgctacacaagtagagtctcaaa	tcagtgtcatggatttatttaacaaacact	03/20/04	03/20/04	121	Genomic	unknown
ss23710829	PERLEGEN\|afd0780663	rev/T	A/G	atagctgtgctacacaagtagagtctcaaa	tcagtgtcatggatttatttaacaaacact	08/10/04	09/13/04	123	Genomic	unknown
ss41630871	ABI\|hCV2186516	rev/T	A/G	atagctgtgctacacaagtagagtctcaaa	tcagtgtcatggatttatttaacaaacact	07/17/05	11/03/06	126	Genomic	unknown
ss66432919	AFFY\|SNP_A-2170345	rev/T	A/G	caagtagagtctcaaa	tcagtgtcatggattt	10/29/06	08/14/07	127	Genomic	unknown
ss68840741	PERLEGEN\|PGP00780663	rev/T	A/G	atagctgtgctacacaagtagagtctcaaa	tcagtgtcatggatttatttaacaaacact	01/30/07	08/14/07	127	Genomic	unknown
ss76207314	AFFY\|AFFY_6_1M_SNP_A-2170345	rev/T	A/G	caagtagagtctcaaa	tcagtgtcatggattt	08/28/07	08/30/07	129	Genomic	unknown
ss77213096	HGSV\|Cor12156_SNV_20070510.chr2_206388529	rev/T	A/G	atagctgtgctacacaagtagagtctcaaa	tcagtgtcatggatttatttaacaaacact	10/09/07	10/11/07	129	Genomic	unknown
ss78107023	HGSV\|Cor12878_SNV_20070510.chr2_206388529	rev/T	A/G	atagctgtgctacacaagtagagtctcaaa	tcagtgtcatggatttatttaacaaacact	10/17/07	10/17/07	129	Genomic	unknown
ss82243843	HGSV\|Cor19240_SNV_20070510.chr2_206388529	rev/T	A/G	atagctgtgctacacaagtagagtctcaaa	tcagtgtcatggatttatttaacaaacact	11/30/07	12/02/07	130	Genomic	unknown
ss91519393	BCMHGSC_JDW\|JWB-1373058	rev/T	A/G	atagctgtgctacacaagtagagtctcaaa	tcagtgtcatggatttatttaacaaacact	02/26/08	03/01/08	129	Genomic	unknown

Fasta sequence (Legend)

 CCAACCTTAA CTTTTAGGGA CCTCGGTAGT AACATGGCAT TTCTAAAGTA CTCCCAAGTG
 TCTAAGTGTC CACTTGGGAG TTCCTAAGCC ACACATTTCC AGGGTGGCAG AACCAATGTT
 GTAAGACCAG CTGAGTCACC TTGGGTGACT GACCTAACCT CTCTGTGCTT CGGTTTTCTC
 TCTTTTGCAA AATGGAGATC ATAATGGCAC TAACTTCCCA GGGCCCACTG TGCAAAGTAA
 ATGGATTAAT ATTTGTAATG CAATTAGAAG AGTGTTTGTT AAATAAATCC ATGACACTGA
 Y
 TTTGAGACTC TACTTGTGTA GCACAGCTAT CAAGAACCAA TGTGAATCTT AGAACTACTT
 AGATTTTTTT TTTTTTTACC CTTTTTTTTT TCTATAAGAA AACCAGTTAC CGCTATATAA
 GGTAACAGGC TGATCCTGCG TGGCTGGATG CGAGGGAAGT CTCCACTTGG GGATACAGCT
 ACTATCTTAT TAAGGAAGTG GGTGGGGTTT ATACATGTAG CAGCTGTGGA AATGGGGAGA
 TCTCCAAGTG CAAGGTAACC CAAAGTCAAG AGTAGAGTTT TGTAGTCCAG CCCCTGCCAC

GeneView

GeneView via analysis of contig annotation: NRP2 neuropilin 2

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_005403->NM_003872

function

reference

NT_005403->NM_018534

function

reference

NT_005403->NM_201264

function

reference

NT_005403->NM_201266

function

reference

NT_005403->NM_201267

function

reference

NT_005403->NM_201279

function

HuRef

NW_001838863->NM_003872

function

HuRef

NW_001838863->NM_018534

function

HuRef

NW_001838863->NM_201264

function

HuRef

NW_001838863->NM_201266

function

HuRef

NW_001838863->NM_201267

function

HuRef

NW_001838863->NM_201279

function

Celera

NW_921618->NM_003872

function

Celera

NW_921618->NM_018534

function

Celera

NW_921618->NM_201264

function

Celera

NW_921618->NM_201266

function

Celera

NW_921618->NM_201267

function

Celera

NW_921618->NM_201279

function

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


reference	NT_005403->NM_003872->NP_003863	56772440	forward	intron

reference	NT_005403->NM_018534->NP_061004	56772440	forward	intron

reference	NT_005403->NM_201264->NP_957716	56772440	forward	intron

reference	NT_005403->NM_201266->NP_957718	56772440	forward	intron

reference	NT_005403->NM_201267->NP_957719	56772440	forward	intron

reference	NT_005403->NM_201279->NP_958436	56772440	forward	intron

HuRef	NW_001838863->NM_003872->NP_003863	31967854	forward	intron

HuRef	NW_001838863->NM_018534->NP_061004	31967854	forward	intron

HuRef	NW_001838863->NM_201264->NP_957716	31967854	forward	intron

HuRef	NW_001838863->NM_201266->NP_957718	31967854	forward	intron

HuRef	NW_001838863->NM_201267->NP_957719	31967854	forward	intron

HuRef	NW_001838863->NM_201279->NP_958436	31967854	forward	intron

Celera	NW_921618->NM_003872->NP_003863	11235316	forward	intron

Celera	NW_921618->NM_018534->NP_061004	11235316	forward	intron

Celera	NW_921618->NM_201264->NP_957716	11235316	forward	intron

Celera	NW_921618->NM_201266->NP_957718	11235316	forward	intron

Celera	NW_921618->NM_201267->NP_957719	11235316	forward	intron

Celera	NW_921618->NM_201279->NP_958436	11235316	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs849557 maps exactly once on NCBI human chromosome 2

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
2	NW_001838863.1	31967854	198411548	minus	A	alt_assembly_8	HuRef	HuRef	view	300
2	NW_921618.1	11235316	200320786	minus	G	alt_assembly_1	Celera	Celera	view	300
2	NT_005403.16	56772440	206271268	minus	G	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_005403 AC007362 AC067978 AC067978.2

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC007362.4 NC_000002.10	AC067978.2

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss23710829	AFD_EUR_PANEL	European	48	IG	0.042	0.458	0.500	0.439	0.271	0.729

	AFD_AFR_PANEL	African American	46	IG	0.217	0.609	0.174	0.294	0.522	0.478

	AFD_CHN_PANEL	Asian	46	IG		0.087	0.913	1.000	0.043	0.957

ss41630871	HapMap-CEU	European	120	IG	0.067	0.483	0.450	0.317	0.308	0.692

	HapMap-HCB	Asian	86	IG		0.209	0.791	0.479	0.105	0.895

	HapMap-JPT	Asian	90	IG		0.333	0.667	0.200	0.167	0.833

	HapMap-YRI	Sub-Saharan African	120	IG	0.483	0.367	0.150	0.200	0.667	0.333

ss66432919	HapMap-CEU	European	118	GF	0.068	0.475	0.458		0.305	0.695

	HapMap-HCB	Asian	90	GF		0.200	0.800		0.100	0.900

	HapMap-JPT	Asian	90	GF		0.333	0.667		0.167	0.833

	HapMap-YRI	Sub-Saharan African	120	GF	0.483	0.367	0.150		0.667	0.333

ss68840741	HapMap-CEU	European	120	GF	0.067	0.483	0.450		0.308	0.692

	HapMap-HCB	Asian	90	GF		0.200	0.800		0.100	0.900

	HapMap-JPT	Asian	90	GF		0.333	0.667		0.167	0.833

	HapMap-YRI	Sub-Saharan African	120	GF	0.483	0.367	0.150		0.667	0.333

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.443+/-0.159	332	260	270	0

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: PERLEGEN

DoubleHit found by: BCM_SSAHASNP, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .