Reference SNP(refSNP) Cluster Report: rs339731

Reference SNP(refSNP) Cluster Report: rs339731

refSNP ID: rs339731
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	79/129
Map to Genome Build:	36.3

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

HGVS Names
NM_144719.3:c.1718+4600T>C
NT_022517.17:g.42707363A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss14202381 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs339731 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
ss432982	KWOK\|OVLP-000621-332754	fwd/B	C/T	tctccccttgtagtaaattatttccttgtg	ggtttcaatttttgtgattttatgagctta	06/30/00	10/10/03	79	Genomic	99 %
ss526508	SC_JCM\|AC022064.3_23122	rev/T	A/G	taagctcataaaatcacaaaaattgaaacc	cacaaggaaataatttactacaaggggaga	07/12/00	10/10/03	80	Genomic	unknown
ss1041857	KWOK\|OVLP-000804-560726	fwd/B	C/T	tctccccttgtagtaaattatttccttgtg	ggtttcaatttttgtgattttatgagctta	09/02/00	10/10/03	86	Genomic	97 %
ss1042566	KWOK\|OVLP-000804-569177	fwd/B	C/T	tctccccttgtagtaaattatttccttgtg	ggtttcaatttttgtgattttatgagctta	09/02/00	10/10/03	86	Genomic	97 %
ss1959841	KWOK\|OVLP-000925-568951	fwd/B	C/T	tctccccttgtagtaaattatttccttgtg	ggtttcaatttttgtgattttatgagctta	10/06/00	12/09/03	87	Genomic	97 %
ss1960028	KWOK\|OVLP-000925-573004	fwd/B	C/T	tctccccttgtagtaaattatttccttgtg	ggtttcaatttttgtgattttatgagctta	10/06/00	10/10/03	87	Genomic	97 %
ss14202381	BCM_SSAHASNP\|chr3.NT_022517.16_42692951	rev/T	A/G	taagctcataaaatcacaaaaattgaaacc	cacaaggaaataatttactacaaggggaga	11/05/03	04/07/04	119	Genomic	unknown
ss14648989	WI_SSAHASNP\|chr3.NT_022517.16_42692951	rev/T	A/G	taagctcataaaatcacaaaaattgaaacc	cacaaggaaataatttactacaaggggaga	11/05/03	11/22/03	119	Genomic	unknown
ss22026951	SSAHASNP\|WGSA-200403-chr3.chr3.NT_022517.16_42692951	rev/T	A/G	taagctcataaaatcacaaaaattgaaacc	cacaaggaaataatttactacaaggggaga	03/20/04	03/20/04	121	Genomic	unknown
ss23907739	PERLEGEN\|afd4011092	rev/T	A/G	taagctcataaaatcacaaaaattgaaacc	cacaaggaaataatttactacaaggggaga	08/10/04	09/13/04	123	Genomic	unknown
ss44368355	ABI\|hCV7627551	rev/T	A/G	taagctcataaaatcacaaaaattgaaacc	cacaaggaaataatttactacaaggggaga	07/18/05	07/18/05	126	Genomic	unknown
ss65723108	ILLUMINA\|Human1-rs339731	fwd/B	C/T	tctccccttgtagtaaattatttccttgtg	ggtttcaatttttgtgattttatgagctta	10/10/06	10/10/06	127	Genomic	unknown
ss66234102	AFFY\|SNP_A-4263470	rev/T	A/G	cacaaaaattgaaacc	cacaaggaaataattt	10/27/06	10/28/06	127	Genomic	unknown
ss74900965	ILLUMINA\|ILMN_Human_1M_rs339731	fwd/B	C/T	tctccccttgtagtaaattatttccttgtg	ggtttcaatttttgtgattttatgagctta	08/28/07	08/29/07	129	Genomic	unknown
ss76379990	AFFY\|AFFY_6_1M_SNP_A-4263470	rev/T	A/G	cacaaaaattgaaacc	cacaaggaaataattt	08/28/07	08/30/07	129	Genomic	unknown
ss78072788	HGSV\|Cor12878_SNV_20070510.chr3_42742363	rev/T	A/G	taagctcataaaatcacaaaaattgaaacc	cacaaggaaataatttactacaaggggaga	10/17/07	10/17/07	129	Genomic	unknown

Fasta sequence (Legend)

 ATTTTTCGGT AAAAGCTCCT GTTCTCagcc aggcacagtg gctcatgcct gtaatcccag
 cactttggga ggccgaggtg ggtgaatcac ctgaggtcag gaattcaaga ccaccctggc
 caacgtggtg aaaccccatc tctactaaga atccaaaaat tagccaggtg tggtggcagg
 cacctgtaat cccagcaact tgggaggctg aagcagaatt gcttgaacct gggaggcgga
 ggttgcagtg agccaagatc acgccactcc actccagcct gggcaaaaag agcaaaacac
 ccccgtctca aaaacaaaac aacaacaaca aaaCCCTCTT GTTCTCTTTC TTATAGCATT
 TGTTCTTTCA TTACAATTTT TGCCTTTCTC CTTTAAATAA TTTTGAACTT ATTCCCTTTA
 GAGTTTTCTA CCATCTTCAT TAATTAGGAT CCTAAGTAAT GTCTGTCGGC TCTCCCCTTG
 TAGTAAATTA TTTCCTTGTG
 Y
 GGTTTCAATT TTTGTGATTT TATGAGCTTA TCTTCAGTGG GGCTTTTTTC CTTGTAGGAG
 TTCTTAGGTG ATGACCGTGT TTCTGTGGAG GTGTTCTGCA TTTGTCTCTG TGAAGCTTTT
 AGGGTTTCAG TGGTCTCTGA TTGGTACTTT ATGTGAATTT ATTGGCTTAG ATTCCCTGAA
 CACATGAATG CTGCCCTTGT GTTTCAGTTT CACATGATTG GTGCTTCCTC CCCTCCTCCC
 CATTTCCCAA GGCCCTGATA GACTGCAGGC TTCCTTACTA CTTTCCTGAA CTTGTAGATG
 GATATTATCT TAGTCCTCtt tttttttttt tttgagacag ggtctcactc tgtcacccag
 gctggagtgc agtggtgtga tcacagctca ctgcagcctc aacttcccgg gctccagtga
 tcctcccacc tcagcctctg gagtagctgg gaccacaggc acatgccaac atgcctggct
 aatttttata tttttATAGA

GeneView

GeneView via analysis of contig annotation: CCDC13 coiled-coil domain containing 13

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_022517->NM_144719

function

HuRef

NW_001838877->NM_144719

function

Celera

NW_921651->NM_144719

function

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


reference	NT_022517->NM_144719->NP_653320	42707363	reverse	intron

HuRef	NW_001838877->NM_144719->NP_653320	23454678	forward	intron

Celera	NW_921651->NM_144719->NP_653320	42707750	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs339731 maps exactly once on NCBI human chromosome 3

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
3	NW_921651.1	42707750	42707750	minus	G	alt_assembly_1	Celera	Celera	view	500
3	NT_022517.17	42707363	42742363	minus	A	ref_assembly	reference	reference	view	500
3	NW_001838877.2	23454678	42812984	plus	C	alt_assembly_8	HuRef	HuRef	view	500

NCBI Resource Links

Submitter-Referenced
GenBank
NT_022517 AC006059 AC018471.8 AC018471.9 AC022064.3

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC006059.3 AC092041.2 AC099329.2 NC_000003.10	AC022064.3

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss14202381	CEPH		184	AF					0.340	0.660

	HapMap-CEU	European	120	IG	0.067	0.433	0.500	0.655	0.283	0.717

	HapMap-HCB	Asian	90	IG	0.267	0.467	0.267	0.317	0.500	0.500

	HapMap-JPT	Asian	88	IG	0.250	0.500	0.250	0.403	0.500	0.500

	HapMap-YRI	Sub-Saharan African	120	IG		0.100	0.900	0.752	0.050	0.950

ss23907739	AFD_EUR_PANEL	European	48	IG	0.042	0.375	0.583	1.000	0.229	0.771

	AFD_AFR_PANEL	African American	44	IG		0.227	0.773	0.584	0.114	0.886

	AFD_CHN_PANEL	Asian	48	IG	0.208	0.500	0.292	1.000	0.458	0.542

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.419+/-0.184	332	260	9	0

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: ILLUMINA

DoubleHit found by: BCM_SSAHASNP

UNKNOWN

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Revised: May 25, 2006 1:38 PM .