Reference SNP(refSNP) Cluster Report: rs2971863

Reference SNP(refSNP) Cluster Report: rs2971863

refSNP ID: rs2971863
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	101/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	A/G
Ancestral Allele:	G
Clinical Association:	unknown

HGVS Names
NM_018218.2:c.3407T>C
NP_060688.1:p.M1136T
NT_005120.15:g.318887A>G

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44191509 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2971863 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
ss4185102	SC_JCM\|AC093109.1_46341	fwd/T	A/G	tgcactggagaggatgtagctgctctgctc	tggagggcttcttggctgcagagacacaga	10/15/01	10/10/03	101	Genomic	unknown
ss23206493	PERLEGEN\|afd4009827	fwd/T	A/G	tgcactggagaggatgtagctgctctgctc	tggagggcttcttggctgcagagacacaga	08/10/04	09/13/04	123	Genomic	unknown
ss44191509	ABI\|hCV15878070	fwd/T	A/G	tgcactggagaggatgtagctgctctgctc	tggagggcttcttggctgcagagacacaga	07/18/05	03/31/08	126	Genomic	unknown
ss48420697	APPLERA_GI\|hCV15878070	fwd/T	A/G	tgcactggagaggatgtagctgctctgctc	tggagggcttcttggctgcagagacacaga	09/28/05	11/03/06	126	Genomic	unknown
ss65746560	ILLUMINA\|Human1-rs2971863	fwd/B	A/G	tgcactggagaggatgtagctgctctgctc	tggagggcttcttggctgcagagacacaga	10/10/06	10/10/06	127	Genomic	unknown
ss74877890	ILLUMINA\|ILMN_Human_1M_rs2971863	fwd/T	A/G	tgcactggagaggatgtagctgctctgctc	tggagggcttcttggctgcagagacacaga	08/28/07	08/29/07	129	Genomic	unknown

Fasta sequence (Legend)

 GCACCAGCCC CCGTGGCTGC CACGTGTTGC AGAGCTAAGT GACTACATGC ACTGGCCAGG
 CCTCAGAGGA GCCGTCCCTG TGCTCAAAGG AAGCAGAGGA TTTGGGATTG GAGGCGCCAG
 GCAGCCAGTC CCCATGCCCA GGAAACCCAC GTTTGTGGCA TCAGCCGGAG AGTTCATCGG
 GAGTAGAGCC GTGCAGCGGC GCGGTTATCT GAAGCTCCCC ACGTGGATGG AGAGAGAAGT
 TTCCGGGGCT CGGGGCCGGG CAGGCGTCTC TGCACTGGAG AGGATGTAGC TGCTCTGCTC
 R
 TGGAGGGCTT CTTGGCTGCA GAGACACAGA CACTGTCATT GACTCATGGA TGCAGTGGGT
 GTCAGGGTGA GGGGTTCACG AAGACCCCAA AATACACTCC AATTTTATAG GCCACAAGGA
 CGTGCATTTG CAATTGCACA GACAGATCTC AGCCACCTGC CAGAGGGCCC CATTTTGCCC
 TGCCACCAGC CCTGTGCCAG GCCAGCTGCC TTCCCCTGCT TTGCACTGGC AGCACGGCAT
 GGTTCAGGCT CTGGGGCTTT CTCAATCTGC TCAGTGAAAA TGCCTCACAG CTGAGAAACC

GeneView

GeneView via analysis of contig annotation: USP40 ubiquitin specific peptidase 40

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

Group
Label

Contig->mRNA

Gene Model (contig mRNA transcript) Color Legend

reference

NT_005120->NM_018218

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	mRNA pos	Function	dbSNP allele	Protein residue	Codon pos	Amino acid pos


reference	NT_005120->NM_018218->NP_060688	318888	reverse	3407	missense	C	Thr [T]	2	1136
					contig reference	T	Met [M]	2	1136

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs2971863 maps exactly once on NCBI human chromosome 2

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
2	NW_001838868.1	332368	226186826	plus	A	alt_assembly_8	HuRef	HuRef	view	300
2	NW_921618.1	39021935	228107405	plus	A	alt_assembly_1	Celera	Celera	view	300
2	NT_005120.15	318888	234050873	plus	A	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NC_000002.6 AC019221

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):
NM_018218.2

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss23206493	AFD_EUR_PANEL	European	46	IG	0.478	0.391	0.130	0.655	0.674	0.326

	AFD_AFR_PANEL	African American	40	IG	0.350	0.500	0.150	1.000	0.600	0.400

	AFD_CHN_PANEL	Asian	48	IG	0.833	0.167		0.752	0.917	0.083

ss44191509	HapMap-CEU	European	114	IG	0.614	0.333	0.053		0.781	0.219

	HapMap-HCB	Asian	90	IG	0.889	0.111			0.944	0.056

	HapMap-JPT	Asian	88	IG	0.886	0.114			0.943	0.057

	HapMap-YRI	Sub-Saharan African	118	IG	0.254	0.458	0.288		0.483	0.517

ss48420697	AGI_ASP population	multiple	66	IG	0.455	0.455	0.091	1.000	0.682	0.318

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.374+/-0.217	371	299	9	0

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 .