Reference SNP(refSNP) Cluster Report: rs2162188

Reference SNP(refSNP) Cluster Report: rs2162188

refSNP ID: rs2162188
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:	C
Clinical Association:	unknown

HGVS Names

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss5209205 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2162188 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
ss3094416	TSC-CSHL\|TSC1194165	fwd/B	C/T	tgttacttcacttgagaaagcttcatgatt	cctgactcagagatgccagagattcctggc	06/07/01	10/10/03	96	Genomic	unknown
ss5209205	TSC-CSHL\|TSC1218654	fwd/B	C/T	tgttacttcacttgagaaagcttcatgatt	cctgactcagagatgccagagattcctggc	09/20/02	04/07/04	108	Genomic	unknown
ss10025875	BCM_SSAHASNP\|chr3.NT_005962.15_22603442	fwd/B	C/T	tgttacttcacttgagaaagcttcatgatt	cctgactcagagatgccagagattcctggc	06/27/03	10/10/03	116	Genomic	unknown
ss14206222	BCM_SSAHASNP\|chr3.NT_005612.14_93886137	fwd/B	C/T	tgttacttcacttgagaaagcttcatgatt	cctgactcagagatgccagagattcctggc	11/05/03	11/22/03	119	Genomic	unknown
ss23372982	PERLEGEN\|afd2974369	fwd/B	C/T	tgttacttcacttgagaaagcttcatgatt	cctgactcagagatgccagagattcctggc	08/10/04	09/13/04	123	Genomic	unknown
ss66205367	AFFY\|SNP_A-2295520	rev/T	A/G	gcatctctgagtcagg	aatcatgaagctttct	10/27/06	08/14/07	127	Genomic	unknown
ss76297907	AFFY\|AFFY_6_1M_SNP_A-2295520	rev/T	A/G	gcatctctgagtcagg	aatcatgaagctttct	08/28/07	08/30/07	129	Genomic	unknown

Fasta sequence (Legend)

 CAGGGAGAAT GTTACTTCAC TTGAGAAAGC TTCATGATT
 Y
 CCTGACTCAG AGATGCCAGA GATTCCTGGC CGAGCAGTCT GCAGCCGGGA TACATGCACC
 TCTAGAAGGC ATCCAGGCCT CACCTCTTTC ATGTGCAGCT TTTTCTGGAC AGGATATGAT
 TTCCCACCTC CCTTGTGGAA CGTACATTTT GGAGTGACTA CCTGCCAATA TAAGGAGTAG
 AAACTTATTT TAATAAAAAG CAACATAATC TGTGAATAGA CATAGACATT CAATGTTAAG
 CAATGCAAGG AAGGAGAAAG TGTCTGTACT GGGAGTCAAG AGACCTGGGC TCTAGCCTGA
 TTCTGCCACA ACCAACTGTG GGACATCTTC TCTGGGCCTT GGTTCTTTAT TTGCAAAATA
 AAACTTGGCA GGTCATCTTT GTGGTTCCCT CCAGCTCTGA TAATTAATGA GTATAAATTT
 GAGGAAATAA AAAGGCAAAG TAGAATATAC TATTATGTTA AGATGTTATT ATTCTCTCAA
 GATGAGAATT TTATATTGGA AAAGAACCTG GTTTTTACGT AATATCAGAA AGGAGGCTGA
 GTGCAGAGGA CATTTCCCAG GCCTACTAGA AGATGTATTC TTGACTCTTG CTTCT

GeneView

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

Integrated Maps:

NCBI MapViewer: rs2162188 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_001838884.2	6633739	184795292	minus	G	alt_assembly_8	HuRef	HuRef	view	39
3	NW_921807.1	94007622	185821952	plus	C	alt_assembly_1	Celera	Celera	view	39
3	NT_005612.15	93886129	188873673	plus	C	ref_assembly	reference	reference	view	39

NCBI Resource Links

Submitter-Referenced
GenBank
NT_005962

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss23372982	AFD_EUR_PANEL	European	48	IG	0.875	0.125		0.752	0.938	0.062

	AFD_AFR_PANEL	African American	46	IG	0.565	0.348	0.087	0.655	0.739	0.261

	AFD_CHN_PANEL	Asian	48	IG	0.792	0.208		0.584	0.896	0.104

ss5209205	HapMap-CEU	European	120	IG	0.767	0.233		0.317	0.883	0.117

	HapMap-HCB	Asian	90	IG	0.889	0.111		0.752	0.944	0.056

	HapMap-JPT	Asian	90	IG	0.844	0.156		0.584	0.922	0.078

	HapMap-YRI	Sub-Saharan African	120	IG	0.467	0.400	0.133	0.752	0.667	0.333

ss66205367	HapMap-CEU	European	118	GF	0.763	0.237			0.881	0.119

	HapMap-HCB	Asian	90	GF	0.889	0.111			0.944	0.056

	HapMap-JPT	Asian	90	GF	0.844	0.156			0.922	0.078

	HapMap-YRI	Sub-Saharan African	120	GF	0.467	0.400	0.133		0.667	0.333

Concordant Genotype	Total Sample	C/C	C/T	T/T
ss23372982	71	53	16	2
ss5209205	268	190	67	11
ss66205367	267

RefSNP Genotype Summary	Total Individual	C/C	C/T	T/T
rs2162188	332	234	83	13

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
5132	ss5209205	T/T	CSHL-HAPMAP	HapMap-YRI	NA18500	YOR004.01	r23_ch3_YRI_affymetrix:genechip500k	395836
5132	ss66205367	A/A	CSHL-HAPMAP	HapMap-YRI	NA18500	YOR004.01	chr3-HapMap-YRI
5281	ss5209205	T/T	CSHL-HAPMAP	HapMap-YRI	NA19172	YOR047.02	r23_ch3_YRI_affymetrix:genechip500k	395836
5281	ss66205367	A/A	CSHL-HAPMAP	HapMap-YRI	NA19172	YOR047.02	chr3-HapMap-YRI

Genotype data submitted for	341	samples from	332	individuals	Individual with multiple genotypes submission:	269

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: ILLUMINA, PERLEGEN

DoubleHit found by: BCM_SSAHASNP

UNKNOWN

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Revised: May 25, 2006 1:38 PM .