Reference SNP(refSNP) Cluster Report: rs2071560

Reference SNP(refSNP) Cluster Report: rs2071560

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	96/130
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
NM_002278.3:c.512T>C
NP_002269.3:p.Ile171Thr
NT_010755.15:g.3346681A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss24098677 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2071560 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
ss2985221	YUSUKE\|IMS-JST007092	fwd/B	C/T	aggcagagaatgccaggatggttgtgaaca	tgataatgccaaactggctgccgatgactt	05/24/01	10/10/03	96	Genomic	unknown
ss3186605	HGBASE\|SNP000572189	fwd/B	C/T	gagaatgccaggatggttgtgaaca	tgataatgccaaactggctgccgat	07/09/01	10/10/03	98	Genomic	unknown
ss24098677	PERLEGEN\|afd4528593	rev/T	A/G	aagtcatcggcagccagtttggcattatca	tgttcacaaccatcctggcattctctgcct	08/10/04	09/13/04	123	Genomic	unknown
ss69196310	PERLEGEN\|PGP04528593	rev/T	A/G	aagtcatcggcagccagtttggcattatca	tgttcacaaccatcctggcattctctgcct	01/30/07	08/14/07	127	Genomic	unknown
ss74808556	AFFY\|SNP_M-180408	fwd/B	C/T	aggcagagaatgccaggatggttgtgaaca	tgataatgccaaactggctgccgatgactt	08/09/07	08/09/07	128	Genomic	unknown
ss74899931	ILLUMINA\|ILMN_Human_1M_rs2071560	fwd/B	C/T	aggcagagaatgccaggatggttgtgaaca	tgataatgccaaactggctgccgatgactt	08/28/07	08/29/07	129	Genomic	unknown

Fasta sequence (Legend)

 GTTCTTCTTG CTTCGTCTCA TCCTGAACTA ACCCTCTCCA TGTGCCTTGG CCTACAGATT
 CTGTGTACCA AGGCAGAGAA TGCCAGGA
 TGGTTGTGAA CA
 Y
 TGATAATGCC AA
 ACTGGCTGCC GATGACTTCA GGGCCAAGTG AGTTCAGTCG GGGGGCTGGA GCTGGGGAGG
 ACCTGTCCTC ATAGGCTCTG GGGCAACT

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
X90761.1

dbSNP Blast Analysis

UniGene Cluster ID
41752

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	A	C	G	T
ss24098677	AFD_EUR_PANEL	European	48	IG						1.000					1.000

	AFD_AFR_PANEL	African American	44	IG				0.045		0.955	1.000		0.023		0.977

	AFD_CHN_PANEL	Asian	48	IG				0.333		0.667	0.343		0.167		0.833

	HapMap-CEU	European	120	IG				0.017		0.983	1.000		0.008		0.992

	HapMap-HCB	Asian	90	IG				0.200		0.800	0.479		0.100		0.900

	HapMap-JPT	Asian	88	IG				0.227		0.773	0.403		0.114		0.886

	HapMap-YRI	Sub-Saharan African	118	IG			0.017	0.085		0.898	0.100		0.059		0.941

	EURAME		32	GF					1.000					1.000

	AFRAME		32	GF		0.062			0.938		1.000	0.031		0.969

ss69196310	HapMap-CEU	European	120	GF				0.033		0.967			0.017		0.983

	HapMap-HCB	Asian	90	GF				0.156		0.844			0.078		0.922

	HapMap-JPT	Asian	90	GF				0.178		0.822			0.089		0.911

	HapMap-YRI	Sub-Saharan African	120	GF			0.017	0.083		0.900			0.058		0.942

Concordant Genotype	Total Sample	A/A	A/G	C/C	C/T	G/G	T/T
ss24098677	1085	965	95			1

RefSNP Genotype Summary	Total Individual	A/A	A/G	C/C	C/T	G/G	T/T
rs2071560	1087	965	95			1

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
172	ss24098677	A/A	CSHL-HAPMAP	HapMap-CEU	NA07056	CEPH1340.12	r27_ch17_CEU_illumina:human_1m_beadchip
5158	ss24098677	A/G	CSHL-HAPMAP	HapMap-HCB	NA18605	CH18605	r27_ch17_CHB_illumina:human_1m_beadchip
5170	ss24098677	A/G	CSHL-HAPMAP	HapMap-HCB	NA18566	CH18566	r27_ch17_CHB_illumina:human_1m_beadchip
5216	ss24098677	A/G	CSHL-HAPMAP	HapMap-JPT	NA18967	JA18967	r27_ch17_JPT_illumina:human_1m_beadchip
5217	ss24098677	A/G	CSHL-HAPMAP	HapMap-JPT	NA18976	JA18976	r27_ch17_JPT_illumina:human_1m_beadchip
5295	ss24098677	A/G	CSHL-HAPMAP	HapMap-YRI	NA19221	YOR058.01	r27_ch17_YRI_illumina:human_1m_beadchip

Genotype data submitted for	1102	samples from	1087	individuals	Individual with multiple genotypes submission:	15

Validation Summary:

Validation status	Marker displays Mendelian segregation	PCR results confirmed in multiple reactions	Homozygotes detected in individual genotype data
	UNKNOWN	UNKNOWN	UNKNOWN

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Revised: May 25, 2006 1:38 PM .