Reference SNP(refSNP) Cluster Report: rs1688031

Reference SNP(refSNP) Cluster Report: rs1688031

refSNP ID: rs1688031
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	89/129
Map to Genome Build:	36.3

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

HGVS Names
NM_002151.1:c.1050+55T>C
NM_182983.1:c.1050+55T>C
NT_011109.15:g.7824858T>C
XM_001719287.1:c.223-5958A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss90962218 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1688031 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
ss2518470	SC_JCM\|AC024682.3_71780	fwd/T	A/G	gatggggagcccgaccacccactcccctgc	tctccatccctggggtggcagcgaccaggg	11/03/00	10/10/03	89	Genomic	unknown
ss3253058	YUSUKE\|IMS-JST063143	rev/B	C/T	ccctggtcgctgccaccccagggatggaga	gcaggggagtgggtggtcgggctccccatc	09/05/01	10/10/03	100	Genomic	unknown
ss16791976	CSHL-HAPMAP\|CSHL-HuAA-200402.chr19.NT_011109.15_7824858	rev/B	C/T	ccctggtcgctgccaccccagggatggaga	gcaggggagtgggtggtcaggctccccatc	02/17/04	03/04/04	120	Genomic	unknown
ss19398523	CSHL-HAPMAP\|CSHL-HuDD-200402.chr19.NT_011109.15_7824858	rev/B	C/T	ccctggtcgctgccaccccagggatggaga	gcaggggagtgggtggtcaggctccccatc	02/20/04	03/04/04	120	Genomic	unknown
ss21506877	SSAHASNP\|WGSA-200403-chr19.chr19.NT_011109.15_7824858	rev/B	C/T	ccctggtcgctgccaccccagggatggaga	gcaggggagtgggtggtcaggctccccatc	03/20/04	03/20/04	121	Genomic	unknown
ss90962218	BCMHGSC_JDW\|JWB-1165529	rev/B	C/T	ccctggtcgctgccaccccagggatggaga	gcaggggagtgggtggtcaggctccccatc	02/26/08	03/01/08	129	Genomic	unknown

Fasta sequence (Legend)

 TAGACGCCTG GCTTCTGGGC CAGGGCACAG CCAGTGCCCC AACTCACAAT GCCACACAGC
 CGCCAACGTG GCGTCCGAGA GATGCTGTCC TCACACACAA AGGGACCACC GCTGTCGCCC
 TGGGAGGGGA GAGGGAGGTC TGGCTGAAGG CCAAAGTGGT TGGACAGGAG GCCCACCCCG
 GGATGACATG GGCTGTGGCC CCAGAGCCCT CAGGCTTTTA GATGGGGAGC CTGACCACCC
 ACTCCCCTGC
 R
 TCTCCATCCC TGGGGTGGCA GCGACCAGGG GGCTGCCCCT ACAGAGTCCC TCACCTGGCA
 GGCATCAATG CCACCCTCGG GGTAGCCAGC ACAGAACATC TTGGGCTTGA TCTGGTTTCC
 ATAGAAGTCA GCGCCATTGC AGACATCATT GCTGATTATG GGGACTCGAG CCTCCTGGAG
 TACCCCGGCC TGTTGGCCTG GGGGTGTGCA GGCAAGGCTG GCCAGAGCTG GGGGGTGTAC
 ACACCCCCCT

GeneView

GeneView via analysis of contig annotation: LOC100128675 hypothetical LOC100128675

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

GeneView via analysis of contig annotation: HPN hepsin

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->XM_001719287

function

HuRef

NW_001838494->XM_001721961

function

Celera

NW_927206->XM_001719305

function

reference

NT_011109->NM_002151

function

reference

NT_011109->NM_182983

function

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


reference	NT_011109->XM_001719287->XP_001719339	7824858	reverse	intron

HuRef	NW_001838494->XM_001721961->XP_001722013	676719	reverse	intron

Celera	NW_927206->XM_001719305->XP_001719357	7841786	reverse	intron

reference	NT_011109->NM_002151->NP_002142	7824858	forward	intron

reference	NT_011109->NM_182983->NP_892028	7824858	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs1688031 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_001838494.1	676719	32064662	minus	C	alt_assembly_8	HuRef	HuRef	view	200
19	NW_927206.1	7841786	32270218	minus	C	alt_assembly_1	Celera	Celera	view	200
19	NT_011109.15	7824858	40248480	minus	T	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_011109 AC020907

dbSNP Blast Analysis

UniGene Cluster ID
182385

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 .