Reference SNP(refSNP) Cluster Report: rs569732

Reference SNP(refSNP) Cluster Report: rs569732

refSNP ID: rs569732
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	83/129
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_005231.2:c.88-38T>C
NM_138565.1:c.88-38T>C
NT_033927.7:g.476335T>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss88632120 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs569732 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
ss741037	SC_JCM\|AP000405.3_7738	fwd/B	C/T	tgatggggtggtggtttgtctgtgtcacaa	ccaggctgtgagatttactggtcgcttttc	07/27/00	04/07/04	83	Genomic	unknown
ss1703436	KWOK\|OVLP-000925-490590	fwd/B	C/T	tgatggggtggtggtttgtctgtgtcacaa	ccaggctgtgagatttactggtcgcttttc	10/05/00	10/10/03	87	Genomic	99 %
ss3243217	YUSUKE\|IMS-JST053302	fwd/B	C/T	tgatggggtggtggtttgtctgtgtcacaa	ccaggctgtgagatttactggtcgcttttc	09/05/01	10/10/03	100	Genomic	unknown
ss10663727	BCM_SSAHASNP\|chr11.NT_033927.5_452615	fwd/B	C/T	tgatggggtggtggtttgtctgtgtcacaa	ccaggctgtgagatttactggtcgcttttc	06/29/03	10/10/03	116	Genomic	unknown
ss20812959	SSAHASNP\|WGSA-200403-chr11.chr11.NT_033927.6_452615	fwd/B	C/T	tgatggggtggtggtttgtctgtgtcacaa	ccaggctgtgagatttactggtcgcttttc	03/19/04	03/19/04	121	Genomic	unknown
ss24539937	PERLEGEN\|afd4124088	fwd/B	C/T	tgatggggtggtggtttgtctgtgtcacaa	ccaggctgtgagatttactggtcgcttttc	08/10/04	09/13/04	123	Genomic	unknown
ss65719054	ILLUMINA\|Human1-rs569732	fwd/B	C/T	tgatggggtggtggtttgtctgtgtcacaa	ccaggctgtgagatttactggtcgcttttc	10/10/06	10/10/06	127	Genomic	unknown
ss65836102	KRIBB_YJKIM\|KHS11894	fwd/B	C/T	tgatggggtggtggtttgtctgtgtcacaa	ccaggctgtgagatttactggtcgcttttc	10/17/06	12/16/06	127	Genomic	unknown
ss66813800	ILLUMINA\|HumanHap300v1.1_rs569732	fwd/T	C/T	tgatggggtggtggtttgtctgtgtcacaa	ccaggctgtgagatttactggtcgcttttc	11/09/06	11/09/06	127	Genomic	unknown
ss67419029	ILLUMINA\|HumanHap550v1.1_rs569732	fwd/B	C/T	tgatggggtggtggtttgtctgtgtcacaa	ccaggctgtgagatttactggtcgcttttc	11/14/06	11/14/06	127	Genomic	unknown
ss67780582	ILLUMINA\|HumanHap650Yv1.0_rs569732	fwd/B	C/T	tgatggggtggtggtttgtctgtgtcacaa	ccaggctgtgagatttactggtcgcttttc	11/14/06	11/14/06	127	Genomic	unknown
ss70846347	ILLUMINA\|HumanHap550v3.0__rs569732	rev/T	A/G	gaaaagcgaccagtaaatctcacagcctgg	ttgtgacacagacaaaccaccaccccatca	04/20/07	03/31/08	130	Genomic	unknown
ss71430988	ILLUMINA\|HumanHap650Yv3.0_rs569732	fwd/B	C/T	tgatggggtggtggtttgtctgtgtcacaa	ccaggctgtgagatttactggtcgcttttc	04/23/07	04/23/07	127	Genomic	unknown
ss75830459	ILLUMINA\|ILMN_Human_1M_rs569732	fwd/B	C/T	tgatggggtggtggtttgtctgtgtcacaa	ccaggctgtgagatttactggtcgcttttc	08/28/07	08/29/07	129	Genomic	unknown
ss79209199	ILLUMINA\|HumanHap300v2.0_rs569732	fwd/B	C/T	tgatggggtggtggtttgtctgtgtcacaa	ccaggctgtgagatttactggtcgcttttc	04/18/07	11/18/07	130	Genomic	unknown
ss83486247	KRIBB_YJKIM\|KHS473022	fwd/B	C/T	tgatggggtggtggtttgtctgtgtcacaa	ccaggctgtgagatttactggtcgcttttc	12/04/07	12/05/07	130	Genomic	unknown
ss85066668	HGSV\|Cor19240_SNV_20070510.chr11_69931234	fwd/B	C/T	tgatggggtggtggtttgtctgtgtcacaa	ccaggctgtgagatttactggtcgcttttc	11/30/07	12/08/07	130	Genomic	unknown
ss86116823	HGSV\|Cor18517_SNV_20070510.chr11_69931234	fwd/B	C/T	tgatggggtggtggtttgtctgtgtcacaa	ccaggctgtgagatttactggtcgcttttc	12/06/07	12/11/07	130	Genomic	unknown
ss88632120	BCMHGSC_JDW\|JWB-0439829	fwd/B	C/T	tgatggggtggtggtttgtctgtgtcacaa	ccaggctgtgagatttactggtcgcttttc	02/26/08	02/27/08	129	Genomic	unknown
ss110629524	1000GENOMES\|CEU.trio.12.15.2008_2566844_chr11_69931234	fwd/B	C/T	tgatggggtggtggtttgtctgtgtcacaa	ccaggctgtgagatttactggtcgcttttc	12/15/08	12/17/08	130	Genomic	unknown
ss114757568	1000GENOMES\|NA19240_2008_12_16_2312295_chr11_69931234	fwd/B	C/T	tgatggggtggtggtttgtctgtgtcacaa	ccaggctgtgagatttactggtcgcttttc	12/18/08	12/18/08	130	Genomic	unknown

Fasta sequence (Legend)

 GGCTCATCTG CTGGCCTCTG TGGATGGCGC CCTGAGGCCT CCGTAACCCT CCCCGGCTGC
 TCTTTCAGAT GTGGAAAGCT TCAGCAGGCC ACGCTGTGTC CATCGCCCAG GATGACGCGG
 GGGCCGATGA CTGGGAGACC GACCCTGATT TTGTGGTAGG AGCCGCCAGC CTTTGCTTTC
 CTCTTTCATG AAGTGGAAGT GGCTCTCCTG GGTTTTTCTT TGATGGGGTG GTGGTTTGTC
 TGTGTCACAA
 Y
 CCAGGCTGTG AGATTTACTG GTCGCTTTTC TTTTCAGAAT GATGTGAGTG AGAAGGAGCA
 AAGATGGGGT GCCAAGACGG TGCAGGGCTC CGGGCACCAG GAGCATATCA AGTAAGAGGC
 GTCGCCACCA CCCTCCCGAG GGCCCCTCTG CGGATGGAGC CCCAGGTGCA ACAGGGCCCA
 TGGTCATCTG TGGAGGGACA GCCCGTGTGG AAACTGCATT TATCTTCTTG ACCTGATACC
 CATGCAGTAA

GeneView

GeneView via analysis of contig annotation: CTTN cortactin

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_033927->NM_005231

function

reference

NT_033927->NM_138565

function

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


reference	NT_033927->NM_005231->NP_005222	476335	forward	intron

reference	NT_033927->NM_138565->NP_612632	476335	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs569732 maps exactly once on NCBI human chromosome 11

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
11	NW_001838027.1	1082794	66514776	plus	C	alt_assembly_8	HuRef	HuRef	view	200
11	NW_925106.1	15862857	67514781	plus	C	alt_assembly_1	Celera	Celera	view	200
11	NT_033927.7	476335	69931234	plus	T	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_033927 AP000487 AP000487.3

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AP000487.6	AL929539.5 AP000405.3

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss24539937	AFD_EUR_PANEL	European	42	IG	0.333	0.429	0.238	0.584	0.548	0.452

	AFD_AFR_PANEL	African American	36	IG	0.556	0.333	0.111	0.479	0.722	0.278

	AFD_CHN_PANEL	Asian	42	IG	0.048	0.286	0.667	0.752	0.190	0.810

ss3243217	JBIC-allele		1502	AF					0.098	0.902

ss65836102	KHP1		172	AF		0.221	0.779	0.251	0.110	0.890

ss741037	SC_12_A	Asian	22	IG		0.091	0.909	1.000	0.045	0.955

	SC_12_AA	African American	16	IG	0.375	0.500	0.125	1.000	0.625	0.375

	SC_12_C	European	14	IG	0.143	0.429	0.429	1.000	0.357	0.643

	SC_95_C	European	94	IG	0.149	0.532	0.319	0.527	0.415	0.585

	CEPH		93	AF					0.030	0.970

	HapMap-CEU	European	120	IG	0.183	0.550	0.267	0.439	0.458	0.542

	HapMap-HCB	Asian	90	IG	0.044	0.289	0.667	0.752	0.189	0.811

	HapMap-JPT	Asian	88	IG		0.114	0.886	0.752	0.057	0.943

	HapMap-YRI	Sub-Saharan African	120	IG	0.667	0.333		0.150	0.833	0.167

Concordant Genotype	Total Sample	C/C	C/T	T/T
ss24539937	69	17	21	21
ss741037	344	91	117	128

RefSNP Genotype Summary	Total Individual	C/C	C/T	T/T
rs569732	401	105	130	146

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
174	ss741037	C/T	TSC-CSHL	SC_95_C	CEPH1341.01		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE	796095
174	ss741037	T/T	CSHL-HAPMAP	HapMap-CEU	NA07048	CEPH1341.01	r23_ch11_CEU_illumina:golden_gate_1.0.0	796095
215	ss741037	C/T	TSC-CSHL	SC_95_C	CEPH1346.01		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE	796095
215	ss741037	C/C	CSHL-HAPMAP	HapMap-CEU	NA10857	CEPH1346.01	r23_ch11_CEU_illumina:golden_gate_1.0.0	796095
215	ss24539937	C/C	PERLEGEN	AFD_EUR_PANEL	NA10857		71_IND_CHR_11
229	ss741037	C/C	TSC-CSHL	SC_12_C	CEPH1347.02		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE	796095
229	ss741037	C/T	TSC-CSHL	SC_95_C	CEPH1347.02		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE	796095
229	ss741037	C/T	CSHL-HAPMAP	HapMap-CEU	NA10859	CEPH1347.02	r23_ch11_CEU_illumina:golden_gate_1.0.0	796095
230	ss741037	C/C	TSC-CSHL	SC_95_C	CEPH1347.03		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE	796095
230	ss741037	T/T	TSC-CSHL	SC_12_C	CEPH1347.03		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE	796095
399	ss741037	C/C	TSC-CSHL	SC_95_C	CEPH1408.01		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE	796095
399	ss741037	C/T	CSHL-HAPMAP	HapMap-CEU	NA10830	CEPH1408.01	r23_ch11_CEU_illumina:golden_gate_1.0.0	796095
399	ss24539937	N/N	PERLEGEN	AFD_EUR_PANEL	NA10830		71_IND_CHR_11
429	ss741037	C/T	TSC-CSHL	SC_12_C	CEPH1416.01		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE	796095
429	ss741037	T/T	TSC-CSHL	SC_95_C	CEPH1416.01		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE	796095
429	ss741037	C/T	CSHL-HAPMAP	HapMap-CEU	NA10835	CEPH1416.01	r23_ch11_CEU_illumina:golden_gate_1.0.0	796095
430	ss741037	C/T	TSC-CSHL	SC_95_C	CEPH1416.02		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE	796095
430	ss741037	T/T	TSC-CSHL	SC_12_C	CEPH1416.02		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE	796095

Genotype data submitted for	472	samples from	401	individuals	Individual with multiple genotypes submission:	63

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: ILLUMINA

UNKNOWN

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Revised: May 25, 2006 1:38 PM .