Reference SNP(refSNP) Cluster Report: rs880083

Reference SNP(refSNP) Cluster Report: rs880083

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	86/130
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
NT_029289.10:g.15023983C>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss1306048 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs880083 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
ss1306048	TSC-CSHL\|TSC0214907	fwd/B	C/T	tggcaggcaagagatgtgacaggcaagagt	ctggctttccctatctagcacctctttgtt	09/06/00	04/07/04	86	Genomic	95 %
ss11768144	WI_SSAHASNP\|chr5.NT_029289.9_15023984	fwd/B	C/T	tggcaggcaagagatgtgacaggcaagagt	ctggctttccctatctagcacctctttgtt	07/04/03	10/10/03	116	Genomic	unknown
ss24341974	PERLEGEN\|afd4050848	fwd/B	C/T	tggcaggcaagagatgtgacaggcaagagt	ctggctttccctatctagcacctctttgtt	08/10/04	09/13/04	123	Genomic	unknown
ss44647475	ABI\|hCV7507727	fwd/B	C/T	tggcaggcaagagatgtgacaggcaagagt	ctggctttccctatctagcacctctttgtt	07/19/05	11/03/06	126	Genomic	unknown
ss65788224	ILLUMINA\|Human1-rs880083	fwd/B	C/T	tggcaggcaagagatgtgacaggcaagagt	ctggctttccctatctagcacctctttgtt	10/10/06	10/10/06	127	Genomic	unknown
ss66597153	ILLUMINA\|HumanHap300v1.1_rs880083	fwd/T	C/T	tggcaggcaagagatgtgacaggcaagagt	ctggctttccctatctagcacctctttgtt	11/09/06	11/09/06	127	Genomic	unknown
ss67886062	ILLUMINA\|HumanHap550v1.1_rs880083	fwd/B	C/T	tggcaggcaagagatgtgacaggcaagagt	ctggctttccctatctagcacctctttgtt	11/14/06	11/14/06	127	Genomic	unknown
ss68024821	ILLUMINA\|HumanHap650Yv1.0_rs880083	fwd/B	C/T	tggcaggcaagagatgtgacaggcaagagt	ctggctttccctatctagcacctctttgtt	11/14/06	11/15/06	127	Genomic	unknown
ss68954641	PERLEGEN\|PGP04050848	fwd/B	C/T	tggcaggcaagagatgtgacaggcaagagt	ctggctttccctatctagcacctctttgtt	01/30/07	08/14/07	127	Genomic	unknown
ss70977670	ILLUMINA\|HumanHap550v3.0__rs880083	fwd/B	C/T	tggcaggcaagagatgtgacaggcaagagt	ctggctttccctatctagcacctctttgtt	04/20/07	03/31/08	130	Genomic	unknown
ss71589455	ILLUMINA\|HumanHap650Yv3.0_rs880083	fwd/B	C/T	tggcaggcaagagatgtgacaggcaagagt	ctggctttccctatctagcacctctttgtt	04/23/07	04/23/07	127	Genomic	unknown
ss74928428	ILLUMINA\|ILMN_Human_1M_rs880083	fwd/B	C/T	tggcaggcaagagatgtgacaggcaagagt	ctggctttccctatctagcacctctttgtt	08/28/07	08/29/07	129	Genomic	unknown
ss76597453	AFFY\|AFFY_6_1M_SNP_A-8458579	rev/T	A/G	agatagggaaagccag	actcttgcctgtcaca	08/28/07	08/30/07	130	Genomic	unknown
ss79286176	ILLUMINA\|HumanHap300v2.0_rs880083	fwd/B	C/T	tggcaggcaagagatgtgacaggcaagagt	ctggctttccctatctagcacctctttgtt	04/18/07	11/18/07	130	Genomic	unknown
ss83590923	KRIBB_YJKIM\|KHS497083	fwd/B	C/T	tggcaggcaagagatgtgacaggcaagagt	ctggctttccctatctagcacctctttgtt	12/04/07	12/05/07	130	Genomic	unknown
ss109534486	1000GENOMES\|CEU.trio.12.15.2008_1393434_chr5_153841240	fwd/B	C/T	tggcaggcaagagatgtgacaggcaagagt	ctggctttccctatctagcacctctttgtt	12/15/08	12/16/08	130	Genomic	unknown

Fasta sequence (Legend)

 CCATGATGTG GAAAGCACTG TTCCCCAACC TAGAGAAGGG ATTCAGTGTC ATTTTTCAAG
 CGGTGCCCCC ACCAGAAACT CAGCCCTAAG GGATCTCCTG AGGCTTGGGG CTGGGGCAAC
 CCCCAGCAGG ATGACGTCGG GGGAGACTGC AGTACAACTA GGCTCTAGAC TGCCTTCTCA
 GAGACCCCAA AATGCTTTAC TGTAGTCCGT GGAGAGCAGC AGAACTCCCG GGATGGTGGG
 GACCTTGTAA GGTTGTTCTC TATCTCTGCC CAAGCTATAT TGTAGGAGGA GGTCTGAGAC
 CTAGGATTTT GGCTAAAATT GCTTTAGGCT GGCAGGCAAG AGATGTGACA GGCAAGAGT
 Y
 CTGGCTTTCC CTATCTAGCA CCTCTTTGTT CCTTTCCAGT CCGAGCCTCA GTTTCCCCAG
 TTGCAGAAGA AGGGAATAGG ATTGATAGTC TGGAATTCTG GAATTCCCAG CTCCTCACTA
 TTGCAGGGAC CCTGCCCTGG TTCCTCCTGG GACTTAGTGC TCAGCTCAGG GATCCCTACA
 GAAGGACTCC GCTTTCCTCT TGCCTACCTC AACAGACCAA GGACTAGAAC TCCCAGGGTC
 CTAGCCCACA CTGCCCCTGC AGCCTCCTCT TAACGAACCT TGCTCACCTA AAGAGTGCCT
 TCAGGGGGGT TGGCCTTCTT AGTATTTTCA AATGCAGGCT TCTCGTTTCT TCCCCAATTG
 TAGTGGTGAG ACCCCGCAGA AACTCTCTTT ACCCTGTTTA CAAGTAGAAG GCTTATGCAC
 ATAAACACAT TCCACCTTGC TATGGAATCG GCCCATCTGA GTTAAAACTG GCACATCATT
 CTCCTGTGTG AGCTCTACAC TCAGTTTTTT CTCCTGTAAA

GeneView

GeneView via analysis of contig annotation:

View more variation on this gene (click to hide).

Assembly	SNP to Chr	Chr	Chr position	Contig	Contig position	Allele

Function	mRNA				Protein
Function	mRNA to Chr	Accession	Position	Allele change	Accession	Position	Residue change

GeneView via analysis of contig annotation: N/A.

GeneView via direct blast against RefSeq sequences (used when no gene model is available):

Function	Chr	mRNA				Protein
Function	Chr	SNP to mRNA	Accession	Position	Allele change	Accession	Position	Residue change

GeneView via direct blast against RefSeq sequences (used when no gene model is available): N/A

Integrated Maps:

Genome Build	Chr	Chr Pos	Contig	Contig Pos	SNP to Chr	Contig allele	Group term	Group label	Contig label	Neighbor SNP	Map Method

doesn't map to any assembly.

NCBI Resource Links

Resource

Submitter-Referenced
GenBank
NT_029289

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail							Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	C/C	C/T	G/G	T/T	HWP	C	T
ss1306048	TSC_42_AA		74	AF								0.720	0.280

	TSC_42_C		78	AF								0.730	0.270

	TSC_42_A		74	AF								0.720	0.280

	SC_12_A	Asian	20	AF	0.100	0.400			0.500		0.003	0.700	0.300

	SC_12_AA	African American	18	AF		0.444			0.556		0.005	0.780	0.220

	SC_12_C	European	24	AF		0.571			0.429		0.010	0.710	0.290

	SC_95_C	European	86	IG			0.465	0.512		0.023	0.100	0.721	0.279

	HapMap-CEU	European	120	IG			0.417	0.500		0.083	0.343	0.667	0.333

	HapMap-HCB	Asian	90	IG			0.333	0.489		0.178	1.000	0.578	0.422

	HapMap-JPT	Asian	88	IG			0.386	0.432		0.182	0.527	0.602	0.398

	HapMap-YRI	Sub-Saharan African	114	IG			0.614	0.333		0.053	1.000	0.781	0.219

ss24341974	AFD_EUR_PANEL	European	46	IG			0.522	0.435		0.043	0.584	0.739	0.261

	AFD_AFR_PANEL	African American	38	IG			0.684	0.263		0.053	0.655	0.816	0.184

	AFD_CHN_PANEL	Asian	40	IG			0.700	0.200		0.100	0.100	0.800	0.200

ss44647475	AoD_African_American		90	AF								0.770	0.230

	AoD_Caucasian		92	AF								0.680	0.320

ss68954641	HapMap-CEU	European	120	GF			0.417	0.500		0.083		0.667	0.333

	HapMap-HCB	Asian	90	GF			0.333	0.489		0.178		0.578	0.422

	HapMap-JPT	Asian	90	GF			0.400	0.422		0.178		0.611	0.389

	HapMap-YRI	Sub-Saharan African	120	GF			0.633	0.317		0.050		0.792	0.208

Concordant Genotype	Total Sample	A/A	A/G	C/C	C/T	G/G	T/T
ss1306048	1282	1	7	598	515	13	112
ss24341974	67			38	16		4
ss68954641	268			130	112		26

RefSNP Genotype Summary	Total Individual	A/A	A/G	C/C	C/T	G/G	T/T
rs880083	1327	1	7	637	528	13	117

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
114	ss1306048	C/C	TSC-CSHL	SC_95_C	CEPH1331.12		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE	489060
114	ss1306048	G/G	TSC-CSHL	SC_12_C	CEPH1331.12		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE	489060
229	ss1306048	A/G	TSC-CSHL	SC_12_C	CEPH1347.02		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE	489060
229	ss1306048	T/T	TSC-CSHL	SC_95_C	CEPH1347.02		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE	489060
229	ss1306048	T/T	CSHL-HAPMAP	HapMap-CEU	NA10859	CEPH1347.02	r27_ch5_CEU_affymetrix:genomewidesnp_6.0	489060
229	ss68954641	T/T	CSHL-HAPMAP	HapMap-CEU	NA10859	CEPH1347.02	chr5-HapMap-CEU
230	ss1306048	A/G	TSC-CSHL	SC_12_C	CEPH1347.03		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE	489060
230	ss1306048	C/T	TSC-CSHL	SC_95_C	CEPH1347.03		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE	489060
231	ss1306048	A/G	TSC-CSHL	SC_12_C	CEPH1347.04		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE	489060
231	ss1306048	C/T	TSC-CSHL	SC_95_C	CEPH1347.04		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE	489060
429	ss1306048	A/G	TSC-CSHL	SC_12_C	CEPH1416.01		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE	489060
429	ss1306048	N/N	TSC-CSHL	SC_95_C	CEPH1416.01		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE	489060
429	ss1306048	C/T	CSHL-HAPMAP	HapMap-CEU	NA10835	CEPH1416.01	r27_ch5_CEU_affymetrix:genomewidesnp_6.0	489060
429	ss68954641	C/T	CSHL-HAPMAP	HapMap-CEU	NA10835	CEPH1416.01	chr5-HapMap-CEU
430	ss1306048	A/G	TSC-CSHL	SC_12_C	CEPH1416.02		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE	489060
430	ss1306048	C/C	TSC-CSHL	SC_95_C	CEPH1416.02		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE	489060
842	ss1306048	A/G	TSC-CSHL	SC_12_AA	NA17111		TSC-SANGER-SC_12_AA-Sep-18-2003-GENOTYPE	489060
842	ss24341974	C/T	PERLEGEN	AFD_AFR_PANEL	NA17111		71_IND_CHR_5
846	ss1306048	A/G	TSC-CSHL	SC_12_AA	NA17115		TSC-SANGER-SC_12_AA-Sep-18-2003-GENOTYPE	489060
846	ss24341974	C/T	PERLEGEN	AFD_AFR_PANEL	NA17115		71_IND_CHR_5
865	ss1306048	G/G	TSC-CSHL	SC_12_AA	NA17134		TSC-SANGER-SC_12_AA-Sep-18-2003-GENOTYPE	489060
865	ss24341974	C/C	PERLEGEN	AFD_AFR_PANEL	NA17134		71_IND_CHR_5
867	ss1306048	A/G	TSC-CSHL	SC_12_AA	NA17136		TSC-SANGER-SC_12_AA-Sep-18-2003-GENOTYPE	489060
867	ss24341974	C/T	PERLEGEN	AFD_AFR_PANEL	NA17136		71_IND_CHR_5

Genotype data submitted for	1409	samples from	1327	individuals	Individual with multiple genotypes submission:	294

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, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .