Reference SNP(refSNP) Cluster Report: rs2123104

Reference SNP(refSNP) Cluster Report: rs2123104

refSNP ID: rs2123104
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	96/129
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

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss5225875 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2123104 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
ss3045667	TSC-CSHL\|TSC1129169	fwd/B	C/T	gggctgagagaacacttagaagcaaactga	gagtcagggctcaggcctcccttaaaacta	06/07/01	10/10/03	96	Genomic	unknown
ss5225704	TSC-CSHL\|TSC1146404	rev/T	A/G	tagttttaagggaggcctgagccctgactc	tcagtttgcttctaagtgttctctcagccc	09/20/02	10/10/03	108	Genomic	unknown
ss5225875	TSC-CSHL\|TSC1145657	fwd/B	C/T	gggctgagagaacacttagaagcaaactga	gagtcagggctcaggcctcccttaaaacta	09/20/02	04/07/04	108	Genomic	unknown
ss23880457	PERLEGEN\|afd2951616	fwd/B	C/T	gggctgagagaacacttagaagcaaactga	gagtcagggctcaggcctcccttaaaacta	08/10/04	09/13/04	123	Genomic	unknown
ss44596043	ABI\|hCV16129566	fwd/B	C/T	gggctgagagaacacttagaagcaaactga	gagtcagggctcaggcctcccttaaaacta	07/19/05	07/19/05	126	Genomic	unknown
ss68925260	PERLEGEN\|PGP02951616	fwd/B	C/T	gggctgagagaacacttagaagcaaactga	gagtcagggctcaggcctcccttaaaacta	01/30/07	08/14/07	127	Genomic	unknown
ss76803532	AFFY\|AFFY_6_1M_SNP_A-8665033	fwd/B	C/T	cttagaagcaaactga	gagtcagggctcaggc	08/28/07	08/30/07	129	Genomic	unknown
ss82183636	HGSV\|Cor19240_SNV_20070510.chr5_4884687	fwd/B	C/T	gggctgagagaacacttagaagcaaactga	gagtcagggctcaggcctcccttaaaacta	11/30/07	12/02/07	130	Genomic	unknown
ss111346897	1000GENOMES\|NA19240_2008_12_16_1072290_chr5_4884687	fwd/B	C/T	gggctgagagaacacttagaagcaaactga	gagtcagggctcaggcctcccttaaaacta	12/16/08	12/17/08	130	Genomic	unknown

Fasta sequence (Legend)

 AATGCACTTC TTTGAAAAAA AGATATGGAG TTTGAATACA GGTAATGTTT GATGATGAGG
 TTAGACTGGA ATAGGATGTA GGGTGTTTGG AGCTAGAGGT GTTAGCTAAA GTAGGTGCTA
 AGGTTTCAGT CTGGGGTTGG GGTTGAAAGT AGGAGCTGGG CTCACGGGGT GGGGGGTTGA
 TTAGGTCAGA AGCTGAGTTG GTGATGGGCT GAGAGAACAC TTAGAAGCAA ACTGA
 Y
 GAGTCAGGGC TCAGGCCTCC CTTAAAACTA CACAGTTTCC TTATCACCCT CATTGAAGTG
 TTCCTTTCCT GAGAGTTCCT TGTGCAGGGT CAGGCACCAT CCTTGGATCA AGCTTGTGGT
 CCAGTTTGGT GGTTCAGGCA TTTCTTTTAT TTTATAAAGA AAAATCTCTC TTTTCCCTTG
 ACTTCCAGAT AGCCACTTTT CCCCATGTCC ATAGGGAAGG TCCAGCTTTT TCCATTTCTC
 CTTGTAGTTT CTGTTTTTCC TGTGATCTTG GTGAAGAAAA TTAATTTAGT GCTTTCAGTT
 ATCTTAGAGT CTTTGATCCT TACTTAAATA CTGTGATGAA ATATGATTAT TTTCCTCCTT
 TAAGAGAGAT AGAAATAAAG CTTCAGATAT CCCAAGG

GeneView

GeneView: no link established by analysis of contig annotation
GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs2123104 maps exactly once on NCBI human chromosome 5

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
5	NW_001838926.1	642071	4804679	plus	T	alt_assembly_8	HuRef	HuRef	view	235
5	NW_922518.1	3960611	4858179	plus	T	alt_assembly_1	Celera	Celera	view	235
5	NT_006576.15	4821687	4884687	plus	T	ref_assembly	reference	reference	view	235

NCBI Resource Links

Submitter-Referenced
GenBank
NC_000005.8

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/T	T/T	HWP	C	T
ss23880457	AFD_EUR_PANEL	European	48	IG	0.125	0.875	0.752	0.062	0.938

	AFD_AFR_PANEL	African American	46	IG	0.087	0.913	1.000	0.043	0.957

	AFD_CHN_PANEL	Asian	48	IG	0.250	0.750	0.527	0.125	0.875

ss5225875	HapMap-CEU	European	120	IG	0.150	0.850	0.584	0.075	0.925

	HapMap-HCB	Asian	90	IG	0.244	0.756	0.371	0.122	0.878

	HapMap-JPT	Asian	88	IG	0.273	0.727	0.294	0.136	0.864

	HapMap-YRI	Sub-Saharan African	120	IG	0.167	0.833	0.527	0.083	0.917

ss68925260	HapMap-CEU	European	120	GF	0.150	0.850		0.075	0.925

	HapMap-HCB	Asian	90	GF	0.156	0.844		0.078	0.922

	HapMap-JPT	Asian	90	GF	0.267	0.733		0.133	0.867

	HapMap-YRI	Sub-Saharan African	120	GF	0.167	0.833		0.083	0.917

Concordant Genotype	Total Sample	C/T	T/T
ss23880457	71	11	60
ss5225875	266	49	216
ss68925260	266	49	217

RefSNP Genotype Summary	Total Individual	C/T	T/T
rs2123104	332	59	269

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
5154	ss5225875	C/T	CSHL-HAPMAP	HapMap-HCB	NA18562	CH18562	r23_ch5_HCB_imsut-riken:genotyping
5154	ss68925260	T/T	CSHL-HAPMAP	HapMap-HCB	NA18562	CH18562	chr5-HapMap-HCB
5161	ss5225875	C/T	CSHL-HAPMAP	HapMap-HCB	NA18572	CH18572	r23_ch5_HCB_imsut-riken:genotyping
5161	ss68925260	T/T	CSHL-HAPMAP	HapMap-HCB	NA18572	CH18572	chr5-HapMap-HCB
5174	ss5225875	C/T	CSHL-HAPMAP	HapMap-HCB	NA18571	CH18571	r23_ch5_HCB_imsut-riken:genotyping
5174	ss68925260	T/T	CSHL-HAPMAP	HapMap-HCB	NA18571	CH18571	chr5-HapMap-HCB
5180	ss5225875	C/T	CSHL-HAPMAP	HapMap-HCB	NA18623	CH18623	r23_ch5_HCB_imsut-riken:genotyping
5180	ss68925260	T/T	CSHL-HAPMAP	HapMap-HCB	NA18623	CH18623	chr5-HapMap-HCB

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

Validated by: PERLEGEN

UNKNOWN

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Revised: May 25, 2006 1:38 PM .