Reference SNP(refSNP) Cluster Report: rs2659057

Reference SNP(refSNP) Cluster Report: rs2659057

refSNP ID: rs2659057
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	100/129
Map to Genome Build:	36.3

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

HGVS Names
NT_011109.15:g.23603435A>T

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss16805407 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2659057 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
ss3750420	SC_JCM\|AC027602.4_116170	fwd/T	A/T	gaaaccctgtctctacttaaaaaaaaaaaa	ttccaaaaaattagccgggcacggtggtgg	09/25/01	10/10/03	100	Genomic	unknown
ss16805407	CSHL-HAPMAP\|CSHL-HuAA-200402.chr19.NT_011109.15_23603435	rev/B	A/T	ccaccaccgtgcccggctaattttttggaa	ttttttttttttaagtagagacagggtttc	02/17/04	03/04/04	120	Genomic	unknown
ss21517914	SSAHASNP\|WGSA-200403-chr19.chr19.NT_011109.15_23603435	rev/B	A/T	ccaccaccgtgcccggctaattttttggaa	ttttttttttttaagtagagacagggtttc	03/20/04	03/20/04	121	Genomic	unknown
ss40999430	ABI\|hCV11509599	rev/	A/T	ccaccaccgtgcccggctaattttttggaa	ttttttttttttaagtagagacagggtttc	07/17/05	07/17/05	126	Genomic	unknown
ss78938330	HGSV\|Cor18507_SNV_20070510.chr19_56027057	rev/	A/T	ccaccaccgtgcccggctaattttttggaa	ttttttttttttaagtagagacagggtttc	10/19/07	10/21/07	129	Genomic	unknown

Fasta sequence (Legend)

 ttagctgggc gtggtggcac acacctgtaa tcccaattgc ttgggaggct gaggcaggag
 aatctcttga acccagaagg cagaggttac agtgagcgga gatcacgcca ctccactcca
 acctgggcta cagagccaga ctccgtctca aaaaaaaaaa aaaaaaagaa aaaaaaaGAA
 AGAAAGTGAA TTTGAAGAGC TGGACTTTAT CCTGGTGGTG CCAAGGATCC ATGGAGGGTG
 GTGAGCAGGG GAGGGGCACA GCCAGCTCCA GATGTAGAAA GACCCTTTGG GGTCATGGCT
 GGAGGGCAAG CTGGTGGAGG GGACTGGACT GGAGGGGGAC CCAAAAGGCC AGATAAGAGG
 GTTGAGATAg accaggcgcg gtggctcatg cctgtaatcc cagcactttg ggaggccgag
 gtgggtggat catgaagtca agagattgag gccatcctgg ctaacacggt gaaaccctgt
 ctctacttaa aaaaaaaaaa
 W
 ttccaaaaaa ttagccgggc acggtggtgg gcgcctgtag tcccagctac tcgggaggct
 gaggcgggag aatggtgtga acctgggagg tggagcttgc agtgagccga cattgtgcca
 ctgcactcca gcctgggtga cagagtgaga ctccgtctca aaaaaaaaaa aaaGTTGGGA
 CAGGGGTCCT TGGTGATGAT GGAGAGAGAT CCAGGGGCTG GTAGCATGGT GCTGGAGGCT
 GACAGGTGGA GGAGGTGGGG CAGGGTCTGT CCGAGTGCCT AGAGGAAGAG TAAACCTTCC
 AGAGATGGGG GACCCAGAAG GAAGCGCAGA GTGGGGTTGG GGGAAGGGGA TACCGGTGGT
 CAGAAGAAAT TTA

GeneView

GeneView via analysis of contig annotation: KLK15 kallikrein-related peptidase 15

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_011109->NM_017509

function

reference

NT_011109->NM_138563

function

reference

NT_011109->NM_138564

function

HuRef

NW_001838498->NM_017509

function

HuRef

NW_001838498->NM_138563

function

HuRef

NW_001838498->NM_138564

function

Celera

NW_927284->NM_017509

function

Celera

NW_927284->NM_138563

function

Celera

NW_927284->NM_138564

function

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


reference	NT_011109->NM_017509->NP_059979	23603435	reverse	5' near gene

reference	NT_011109->NM_138563->NP_612630	23603435	reverse	5' near gene

reference	NT_011109->NM_138564->NP_612631	23603435	reverse	5' near gene

HuRef	NW_001838498->NM_017509->NP_059979	4595622	forward	5' near gene

HuRef	NW_001838498->NM_138563->NP_612630	4595622	forward	5' near gene

HuRef	NW_001838498->NM_138564->NP_612631	4595622	forward	5' near gene

Celera	NW_927284->NM_017509->NP_059979	693631	reverse	5' near gene

Celera	NW_927284->NM_138563->NP_612630	693631	reverse	5' near gene

Celera	NW_927284->NM_138564->NP_612631	693631	reverse	5' near gene

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs2659057 maps exactly once on NCBI human chromosome 19

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
19	NW_001838498.2	4595622	47670284	plus	A	alt_assembly_8	HuRef	HuRef	view	500
19	NW_927284.1	693631	48386347	minus	A	alt_assembly_1	Celera	Celera	view	500
19	NT_011109.15	23603435	56027057	minus	A	ref_assembly	reference	reference	view	500

NCBI Resource Links

Submitter-Referenced
GenBank
NT_011109 AC010325 AC011523 AF243527

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC010325.7 AC011523.3 NC_000019.8	AC027602.4

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

DoubleHit found by: BCM_SSAHASNP

UNKNOWN

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Revised: May 25, 2006 1:38 PM .