Reference SNP(refSNP) Cluster Report: rs181168

Reference SNP(refSNP) Cluster Report: rs181168

refSNP ID: rs181168
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

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss240578 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs181168 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
ss240578	KWOK\|OVLP-000621-364901	fwd/B	C/T	cacaaatttccattttccccagtcatctgc	gtcactcagacatcatctagaaattatatg	06/30/00	10/25/06	79	Genomic	94 %
ss1277600	KWOK\|OVLP-000804-642553	fwd/B	C/T	cacaaatttccattttccccagtcatctgc	gtcactcagacatcatctagaaattatatg	09/02/00	10/10/03	86	Genomic	94 %
ss2187141	TSC-CSHL\|TSC0565323	fwd/B	C/T	tttccattttccccagtcatctgc	gtcactcagacatcatctagaaattatatg	10/19/00	04/07/04	88	Genomic	95 %
ss2540373	SC_JCM\|AC044914.3_140152	fwd/B	C/T	cacaaatttccattttccccagtcatctgc	gtcactcagacatcatctagaaattatatg	11/03/00	10/10/03	89	Genomic	unknown
ss6720318	WI_SSAHASNP\|NT_022846.10_2174650	rev/T	A/G	catataatttctagatgatgtctgagtgac	gcagatgactggggaaaatggaaatttgtg	02/12/03	10/10/03	111	Genomic	unknown
ss10112061	BCM_SSAHASNP\|chr4.NT_016354.15_56984770	rev/T	A/G	catataatttctagatgatgtctgagtgac	gcagatgactggggaaaatggaaatttgtg	06/27/03	10/10/03	116	Genomic	unknown
ss23960072	PERLEGEN\|afd4039275	rev/T	A/G	catataatttctagatgatgtctgagtgac	gcagatgactggggaaaatggaaatttgtg	08/10/04	09/13/04	123	Genomic	unknown
ss44499235	ABI\|hCV766702	rev/T	A/G	catataatttctagatgatgtctgagtgac	gcagatgactggggaaaatggaaatttgtg	07/19/05	07/19/05	126	Genomic	unknown
ss66641191	ILLUMINA\|HumanHap300v1.1_rs181168	fwd/B	C/T	cacaaatttccattttccccagtcatctgc	gtcactcagacatcatctagaaattatatg	11/09/06	11/09/06	127	Genomic	unknown
ss67197461	ILLUMINA\|HumanHap550v1.1_rs181168	fwd/B	C/T	cacaaatttccattttccccagtcatctgc	gtcactcagacatcatctagaaattatatg	11/14/06	11/14/06	127	Genomic	unknown
ss67586978	ILLUMINA\|HumanHap650Yv1.0_rs181168	fwd/B	C/T	cacaaatttccattttccccagtcatctgc	gtcactcagacatcatctagaaattatatg	11/14/06	11/14/06	127	Genomic	unknown
ss70675674	ILLUMINA\|HumanHap550v3.0__rs181168	fwd/B	C/T	cacaaatttccattttccccagtcatctgc	gtcactcagacatcatctagaaattatatg	04/20/07	03/30/08	130	Genomic	unknown
ss71238738	ILLUMINA\|HumanHap650Yv3.0_rs181168	fwd/B	C/T	cacaaatttccattttccccagtcatctgc	gtcactcagacatcatctagaaattatatg	04/23/07	04/23/07	127	Genomic	unknown
ss75543019	ILLUMINA\|ILMN_Human_1M_rs181168	fwd/B	C/T	cacaaatttccattttccccagtcatctgc	gtcactcagacatcatctagaaattatatg	08/28/07	08/29/07	129	Genomic	unknown
ss79094550	ILLUMINA\|HumanHap300v2.0_rs181168	fwd/B	C/T	cacaaatttccattttccccagtcatctgc	gtcactcagacatcatctagaaattatatg	04/18/07	11/18/07	130	Genomic	unknown
ss83378925	KRIBB_YJKIM\|KHS447466	fwd/B	C/T	cacaaatttccattttccccagtcatctgc	gtcactcagacatcatctagaaattatatg	12/04/07	12/04/07	130	Genomic	unknown
ss85142030	HGSV\|Cor18517_SNV_20070510.chr4_132847244	rev/T	A/G	catataatttctagatgatgtctgagtgac	gcagatgactggggaaaatggaaatttgtg	12/06/07	12/08/07	130	Genomic	unknown
ss92777690	BCMHGSC_JDW\|JWB-1853166	rev/T	A/G	catataatttctagatgatgtctgagtgac	gcagatgactggggaaaatggaaatttgtg	02/26/08	03/03/08	129	Genomic	unknown

Fasta sequence (Legend)

 TACTAGTGGT ATTTAAAAAA ATAGTTAAAT GTATATTATA ACCACTCCTA TGTGCAAATC
 ACAGTGTTTT TCTGAGTGAG AAAAATCAAT ACATGCATTT cacacaagta caatgctgaa
 gcaaatacag ttcccctgga aacaattatt ggggcctccc aaatgaaaca tacaacagtc
 agatggcgca agttcccagt gatctgtagt accccactgg agcttcctgc aggactgtcc
 atcttccaca agatggtaag ccttagatat tcttattcag tgtaaatgat agaattcagt
 cacgggtttc agagggactg cttcagggta gtcagttcaa tctgccctgc ttgtccatga
 cacaattcaC GAACCCCTCA GAATGACTGA GAATAGAGGT GAAGGCAACA TCTAGAGGTG
 CTTTTAACCT AAGGTGTAGG AGCTGGGACC ATCACCGACT GACTCATGGT CAGAATTATC
 TGGTGAGGGA TGGCAGACTC GGGCtttaag atacttgcaa ctgtatcggg gagcaatact
 agagtatttt ccttctggag aaaagctccc ggggcaattc tgaaacaatg aatattaatg
 ctccttttGT CTGTACCTTT TAGTATTTAC AGAGTTGTCT CCTCATGTGT CGGGATTTTT
 TTTTTTCTTT CTTCACTTTC ACAAAATTAG TCTGTCCTAT TTCAGTAAAC ACAAATTTCC
 ATTTTCCCCA GTCATCTGC
 Y
 GTCACTCAGA CATCATCTAG AAATTATATG AAAATGCTAT TGTCCCTCTT GCAGTAGATC
 TTTCTGGTGC AAAGTCTGAC TTGTAGATCT TTCTGGTGCA AGAAGGACAA ACACATTTTC
 ATCTAATTCA GCC

GeneView

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

Integrated Maps:

NCBI MapViewer: rs181168 maps exactly once on NCBI human chromosome 4

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
4	NW_001838920.1	13067053	128220484	minus	G	alt_assembly_8	HuRef	HuRef	view	739
4	NW_922217.1	12128319	129870840	minus	A	alt_assembly_1	Celera	Celera	view	739
4	NT_016354.18	57037786	132709089	minus	G	ref_assembly	reference	reference	view	739

NCBI Resource Links

Submitter-Referenced
GenBank
NT_016354 AC026537 AC044914.3

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC105424.2 NC_000004.10	AC026537.2

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss2187141	TSC_42_AA		84	AF						1.000

	TSC_42_C		84	AF						1.000

	TSC_42_A		84	AF					0.200	0.800

	AfAm	African American	40	IG	0.100	0.350	0.550	0.655	0.275	0.725

	Caucasian	European	40	IG	0.050	0.200	0.750	0.343	0.150	0.850

	Asian	Asian	40	IG	0.250	0.450	0.300	0.752	0.475	0.525

	CEPH	European	38	IG		0.105	0.895	1.000	0.053	0.947

	PDpanel	Global	32	IG	0.062	0.188	0.750	0.251	0.156	0.844

ss23960072	AFD_EUR_PANEL	European	46	IG		0.304	0.696	0.403	0.152	0.848

	AFD_AFR_PANEL	African American	42	IG	0.190	0.238	0.571	0.050	0.310	0.690

	AFD_CHN_PANEL	Asian	48	IG	0.333	0.625	0.042	0.100	0.646	0.354

ss240578	HapMap-CEU	European	116	IG	0.017	0.328	0.655	0.439	0.181	0.819

	HapMap-HCB	Asian	90	IG	0.311	0.533	0.156	0.584	0.578	0.422

	HapMap-JPT	Asian	88	IG	0.159	0.636	0.205	0.100	0.477	0.523

	HapMap-YRI	Sub-Saharan African	114	IG	0.123	0.404	0.474	0.584	0.325	0.675

Concordant Genotype	Total Sample	C/C	C/T	T/T
ss2187141	95	9	25	61
ss23960072	69
ss240578	269	34	112	114

RefSNP Genotype Summary	Total Individual	C/C	C/T	T/T
rs181168	413	43	137	174

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
215	ss240578	C/T	CSHL-HAPMAP	HapMap-CEU	NA10857	CEPH1346.01	r23_ch4_CEU_wicgr:genotype_protocol_1
215	ss2187141	T/T	AFFY	CEPH	NA10857		AFFY_071103
215	ss23960072	A/G	PERLEGEN	AFD_EUR_PANEL	NA10857		71_IND_CHR_4
838	ss2187141	C/T	AFFY	AfAm	NA17107		AFFY_071103
838	ss23960072	G/G	PERLEGEN	AFD_AFR_PANEL	NA17107		71_IND_CHR_4

Genotype data submitted for	438	samples from	413	individuals	Individual with multiple genotypes submission:	24

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

DoubleHit found by: BCM_SSAHASNP, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .