Reference SNP(refSNP) Cluster Report: rs10420953

Reference SNP(refSNP) Cluster Report: rs10420953

refSNP ID: rs10420953
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	119/129
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_002819.3:c.324C>T
NM_031990.2:c.324C>T
NM_031991.2:c.324C>T
NM_175847.1:c.40-3542C>T
NP_002810.1:p.N108N
NP_114367.1:p.N108N
NP_114368.1:p.N108N
NT_011255.14:g.744326C>T
NT_011255.14:g.744327C>T

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss14720597 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs10420953 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
ss14720597	BCM_SSAHASNP\|chr19.NT_011255.14_744327	fwd/B	C/T	catcgagatgaacacggaggaggctgccaa	accatggtgaactactacacctcggtgacc	11/10/03	03/31/08	119	Genomic	unknown
ss16249875	CGAP-GAI\|1498811	fwd/B	C/T	catcgagatgaacacggaggaggctgccaa	accatggtgaactactacacctcggtgacc	11/18/03	11/22/03	120	cDNA	unknown
ss19400475	CSHL-HAPMAP\|CSHL-HuDD-200402.chr19.NT_011255.14_744327	fwd/B	C/T	catcgagatgaacacggaggaggctgccaa	accatggtgaactactacacctcggtgacc	02/20/04	03/04/04	120	Genomic	unknown
ss65744800	ILLUMINA\|Human1-rs10420953	fwd/T	C/T	catcgagatgaacacggaggaggctgccaa	accatggtgaactactacacctcggtgacc	10/10/06	10/10/06	127	Genomic	unknown
ss86242467	CORNELL\|hCV25474383	fwd/B	C/T	catcgagatgaacacggaggaggctgccaa	accatggtgaactactacacctcggtgacc	01/21/08	01/21/08	129	Genomic	unknown
ss86342614	CANCER-GENOME\|16360	fwd/B	C/T	catcgagatgaacacggaggaggctgccaa	accatggtgaactactacacctcggtgacc	01/25/08	01/25/08	129	Genomic	unknown
ss90878425	BCMHGSC_JDW\|JWB-1134827	fwd/B	C/T	catcgagatgaacacggaggaggctgccaa	accatggtgaactactacacctcggtgacc	02/26/08	03/01/08	129	Genomic	unknown

Fasta sequence (Legend)

 CGTCACGGAG GGGGAAGTCA TCTCCCTGGG GCTGCCCTTT GGGAAGGTCA CCAACCTCCT
 GATGCTGAAG GGGAAAAACC AGGTACCTGA GCCGCGTTTC TCCGGGGTGC TCACACCGTG
 CAGGCGGGGA CGAGGAGGGC CCAGCGCTCA CTGCCTCCCC AACAGGCCTT CATCGAGATG
 AACACGGAGG AGGCTGCCAA
 Y
 ACCATGGTGA ACTACTACAC CTCGGTGACC CCTGTGCTGC GCGGCCAGCC CATCTACATC
 CAGTTCTCCA ACCACAAGGA GCTGAAGACC GACAGCTCTC CCAACCAGGC GGTGCGTGGC
 CCCGCGGCGG ACCCCAGCAG CCCGGGGACC TCGGGGGTGG GCCCAGCCGC AGGGGCCGGG
 GACTCACGGC TGTGCCTCCC

GeneView

GeneView via analysis of contig annotation: PTBP1 polypyrimidine tract binding protein 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_011255->NM_002819

function

reference

NT_011255->NM_031990

function

reference

NT_011255->NM_031991

function

reference

NT_011255->NM_175847

function

HuRef

NW_001838476->NM_002819

function

Celera

NW_927140->NM_002819

function

Celera

NW_927140->NM_031990

function

Celera

NW_927140->NM_031991

function

Celera

NW_927140->NM_175847

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	mRNA pos	Function	dbSNP allele	Protein residue	Codon pos	Amino acid pos


reference	NT_011255->NM_002819->NP_002810	744327	forward	411	synonymous	T	Asn [N]	3	108
					contig reference	C	Asn [N]	3	108

reference	NT_011255->NM_031990->NP_114367	744327	forward	411	synonymous	T	Asn [N]	3	108
					contig reference	C	Asn [N]	3	108

reference	NT_011255->NM_031991->NP_114368	744327	forward	411	synonymous	T	Asn [N]	3	108
					contig reference	C	Asn [N]	3	108

reference	NT_011255->NM_175847->NP_787041	744327	forward		intron

HuRef	NW_001838476->NM_002819->NP_002810	562671	forward	747	synonymous	T	Asn [N]	3	108
					contig reference	C	Asn [N]	3	108

Celera	NW_927140->NM_002819->NP_002810	11882	reverse	411	synonymous	T	Asn [N]	3	108
					contig reference	C	Asn [N]	3	108

Celera	NW_927140->NM_031990->NP_114367	11882	reverse	411	synonymous	T	Asn [N]	3	108
					contig reference	C	Asn [N]	3	108

Celera	NW_927140->NM_031991->NP_114368	11882	reverse	411	synonymous	T	Asn [N]	3	108
					contig reference	C	Asn [N]	3	108

Celera	NW_927140->NM_175847->NP_787041	11882	reverse		intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs10420953 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_927140.1	11882	11882	minus	G	alt_assembly_1	Celera	Celera	view	200
19	NW_001838476.1	562671	573472	plus	C	alt_assembly_8	HuRef	HuRef	view	200
19	NT_011255.14	744327	755327	plus	C	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_011255 BG106617

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC006273.1 NC_000019.8	AC023583.2

UniGene Cluster ID
172550

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	HWP	C	T
ss14720597	HapMap-CEU	European	116	IG	0.845	0.155		0.922	0.078

	HapMap-HCB	Asian	90	IG	0.911	0.089		0.956	0.044

	HapMap-JPT	Asian	88	IG	0.955	0.045		0.977	0.023

	HapMap-YRI	Sub-Saharan African	118	IG	0.898	0.102		0.949	0.051

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.097+/-0.198	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 .