Reference SNP(refSNP) Cluster Report: rs4347731

Reference SNP(refSNP) Cluster Report: rs4347731

refSNP ID: rs4347731
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	111/129
Map to Genome Build:	36.3

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

HGVS Names
NM_003323.1:c.1447+135T>C
NT_011109.15:g.21653344A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss7935961 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs4347731 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
ss5784389	SC_JCM\|NT_011109.12_5525745	fwd/T	A/G	accctgagggtgtgtaaactacaattccca	taggctttgcaatagggtggcatctgccct	01/10/03	10/10/03	111	Genomic	unknown
ss7935961	DEVINE_LAB\|DB_1_590310	fwd/T	A/G	accctgagggtgtgtaaactacaattccca	taggctttgcaatagggtggcatctgccct	03/16/03	10/25/06	113	Genomic	96 %
ss24719445	PERLEGEN\|afd1615138	fwd/T	A/G	accctgagggtgtgtaaactacaattccca	taggctttgcaatagggtggcatctgccct	08/10/04	09/13/04	123	Genomic	unknown
ss44176510	ABI\|hCV26654774	fwd/T	A/G	accctgagggtgtgtaaactacaattccca	taggctttgcaatagggtggcatctgccct	07/18/05	07/18/05	126	Genomic	unknown
ss66051255	AFFY\|SNP_A-1824412	fwd/T	A/G	taaactacaattccca	taggctttgcaatagg	10/27/06	03/31/08	127	Genomic	unknown
ss66586747	ILLUMINA\|HumanHap300v1.1_rs4347731	fwd/B	A/G	accctgagggtgtgtaaactacaattccca	taggctttgcaatagggtggcatctgccct	11/09/06	11/09/06	127	Genomic	unknown
ss67328833	ILLUMINA\|HumanHap550v1.1_rs4347731	fwd/T	A/G	accctgagggtgtgtaaactacaattccca	taggctttgcaatagggtggcatctgccct	11/14/06	11/14/06	127	Genomic	unknown
ss67729574	ILLUMINA\|HumanHap650Yv1.0_rs4347731	fwd/T	A/G	accctgagggtgtgtaaactacaattccca	taggctttgcaatagggtggcatctgccct	11/14/06	11/14/06	127	Genomic	unknown
ss69229865	PERLEGEN\|PGP01615138	fwd/T	A/G	accctgagggtgtgtaaactacaattccca	taggctttgcaatagggtggcatctgccct	01/30/07	03/31/08	127	Genomic	unknown
ss70800906	ILLUMINA\|HumanHap550v3.0__rs4347731	fwd/T	A/G	accctgagggtgtgtaaactacaattccca	taggctttgcaatagggtggcatctgccct	04/20/07	03/30/08	130	Genomic	unknown
ss71379727	ILLUMINA\|HumanHap650Yv3.0_rs4347731	fwd/T	A/G	accctgagggtgtgtaaactacaattccca	taggctttgcaatagggtggcatctgccct	04/23/07	04/23/07	127	Genomic	unknown
ss74947546	ILLUMINA\|ILMN_Human_1M_rs4347731	fwd/T	A/G	accctgagggtgtgtaaactacaattccca	taggctttgcaatagggtggcatctgccct	08/28/07	08/29/07	129	Genomic	unknown
ss75957076	AFFY\|AFFY_6_1M_SNP_A-1824412	fwd/T	A/G	taaactacaattccca	taggctttgcaatagg	08/28/07	08/29/07	129	Genomic	unknown
ss78030213	HGSV\|Cor12878_SNV_20070510.chr19_54076966	fwd/T	A/G	accctgagggtgtgtaaactacaattccca	taggctttgcaatagggtggcatctgccct	10/17/07	10/17/07	129	Genomic	unknown
ss79180018	ILLUMINA\|HumanHap300v2.0_rs4347731	fwd/T	A/G	accctgagggtgtgtaaactacaattccca	taggctttgcaatagggtggcatctgccct	04/18/07	11/18/07	130	Genomic	unknown
ss84254703	KRIBB_YJKIM\|KHS668860	fwd/T	A/G	accctgagggtgtgtaaactacaattccca	taggctttgcaatagggtggcatctgccct	12/04/07	12/06/07	130	Genomic	unknown

Fasta sequence (Legend)

 tcagcctcct gattagctgg gactacaggt gaccaccact acacccagct aattttttct
 gtgtttttag tagagacggg gtttcaccgt gttagtcagg atggtctcaa tctcctgacc
 tcgtatccgc ccgcctcggc ctcccaaagt gctgggatta caggtgtgag ccacagtgcc
 cggcctaatt tttgtatttt tagtagagac agggtttcac catgttggcc aggctgttct
 tgaactcctg acctcagatg atccacccac ctcggtctcc caaagtgcta ggattataag
 cgggagctac cgcgccaggc cGAGAATGGA GACTTTTAAG AGGCTGAGCG GTGCCCTTAC
 TAAGCCAGAA ACCCTGAGGG TGTGTAAACT ACAATTCCCA
 R
 TAGGCTTTGC AATAGGGTGG CATCTGCCCT GCCTAGAAAA ACGCTCAAGT GATGATGGGA
 GATGTAGTTC CCTTCCGTTC ACACCCTAAC CCCCACCCCA CCTGGCCCGG CTAAACTGGT
 TTCCAGGAGC TCACGGTGTT TGGGATCCAC GATTTGGAAG TTCTTCACCG AAGCCCGAGT
 GACTCGACCA TGGAAATTGA GCGTGTAGAC ACCGTTCTCC TTGTCCCACG ACGGGGTTTT
 GTTGTGCAAC AAAAGCAACC CTTGTTTGTC CCCACGTTGG TAACGACTCA GTAGCGACTC
 CTGTTCCTAG AAGGTAAAGA AGGGGCTGTG GTTTTCTCAG AGGCTTTCGA AACTCCATCT
 TGAACAGGGG CGACTCCATC TTGAACAGGG GCGACTCCAT

GeneView

GeneView via analysis of contig annotation: TULP2 tubby like protein 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_011109->NM_003323

function

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


reference	NT_011109->NM_003323->NP_003314	21653344	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs4347731 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_001838497.2	1219773	45761598	minus	T	alt_assembly_8	HuRef	HuRef	view	400
19	NW_927240.1	925862	46252503	plus	A	alt_assembly_1	Celera	Celera	view	400
19	NT_011109.15	21653344	54076966	plus	A	ref_assembly	reference	reference	view	400

NCBI Resource Links

Submitter-Referenced
GenBank
NT_011109.12

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss24719445	AFD_EUR_PANEL	European	48	IG	0.708	0.208	0.083	0.150	0.812	0.188

	AFD_AFR_PANEL	African American	46	IG	0.957	0.043		1.000	0.978	0.022

	AFD_CHN_PANEL	Asian	48	IG	1.000				1.000

ss66051255	HapMap-CEU	European	118	GF	0.797	0.186	0.017		0.890	0.110

	HapMap-HCB	Asian	90	GF	1.000				1.000

	HapMap-JPT	Asian	90	GF	1.000				1.000

	HapMap-YRI	Sub-Saharan African	120	GF	1.000				1.000

ss69229865	HapMap-CEU	European	120	GF	0.800	0.183	0.017		0.892	0.108

	HapMap-HCB	Asian	90	GF	1.000				1.000

	HapMap-JPT	Asian	90	GF	1.000				1.000

	HapMap-YRI	Sub-Saharan African	120	GF	1.000				1.000

ss7935961	HapMap-CEU	European	120	IG	0.800	0.183	0.017	0.752	0.892	0.108

	HapMap-HCB	Asian	90	IG	1.000				1.000

	HapMap-JPT	Asian	90	IG	1.000				1.000

	HapMap-YRI	Sub-Saharan African	120	IG	1.000				1.000

Concordant Genotype	Total Sample	A/A	A/G	G/G
ss24719445	71	63	6	2
ss66051255	268	249	17	2
ss69229865	269	250	17	2
ss7935961	269	250	17	2

RefSNP Genotype Summary	Total Individual	A/A	A/G	G/G
rs4347731	332	307	21	3

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
5286	ss7935961	A/A	CSHL-HAPMAP	HapMap-YRI	NA19211	YOR050.01	r23_ch19_YRI_perlegen:genotyping_1.0.0	5628703
5286	ss66051255	A/A	CSHL-HAPMAP	HapMap-YRI	NA19211	YOR050.01	chr19-HapMap-YRI
5286	ss69229865	A/G	CSHL-HAPMAP	HapMap-YRI	NA19211	YOR050.01	chr19-HapMap-YRI

Genotype data submitted for	341	samples from	332	individuals	Individual with multiple genotypes submission:	270

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 .