Reference SNP(refSNP) Cluster Report: rs2362505

Reference SNP(refSNP) Cluster Report: rs2362505

refSNP ID: rs2362505
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	100/129
Map to Genome Build:	36.3

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

HGVS Names
NM_022126.2:c.717-11094T>G
NT_035040.4:g.371267T>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss3319503 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2362505 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
ss3319503	TSC-CSHL\|TSC1508684	fwd/B	G/T	agggaggatctgctgacgtgagcccagatt	cgattcttgtgcgagggagacgaaccaggt	09/20/01	10/25/06	100	Genomic	unknown
ss5685963	SC_JCM\|NT_035040.1_371264	fwd/B	G/T	agggaggatctgctgacgtgagcccagatt	cgattcttgtgcgagggagacgaaccaggt	01/10/03	10/10/03	111	Genomic	unknown
ss19875155	CSHL-HAPMAP\|CSHL-HuFF-200402.chr10.NT_035040.4_371267	fwd/B	G/T	agggaggatctgctgacgtgagcccagatt	cgattcttgtgcgagggagacgaaccaggt	02/21/04	03/04/04	120	Genomic	unknown
ss20637329	SSAHASNP\|WGSA-200403-chr10.chr10.NT_035040.4_371267	fwd/B	G/T	agggaggatctgctgacgtgagcccagatt	cgattcttgtgcgagggagacgaaccaggt	03/18/04	03/18/04	121	Genomic	unknown
ss24581073	PERLEGEN\|afd2314891	fwd/B	G/T	agggaggatctgctgacgtgagcccagatt	cgattcttgtgcgagggagacgaaccaggt	08/10/04	09/13/04	123	Genomic	unknown
ss38654486	ABI\|hCV1662035	fwd/B	G/T	agggaggatctgctgacgtgagcccagatt	cgattcttgtgcgagggagacgaaccaggt	07/15/05	07/15/05	126	Genomic	unknown
ss83635152	HGSV\|Cor18555_SNV_20070510.chr10_126280729	fwd/B	G/T	agggaggatctgctgacgtgagcccagatt	cgattcttgtgcgagggagacgaaccaggt	11/27/07	12/05/07	130	Genomic	unknown
ss88393087	BCMHGSC_JDW\|JWB-0350009	fwd/B	G/T	agggaggatctgctgacgtgagcccagatt	cgattcttgtgcgagggagacgaaccaggt	02/26/08	02/27/08	129	Genomic	unknown

Fasta sequence (Legend)

 CAGCCGTAAA TAAGCCCCGT TTCCTCCCTG TGGACAGAGA CTGGTGGGTG CCAAGGTTCA
 CGGCAAAAAC CTTTCCCCGC CAGGCCCCAC TGCTCTCTGC CTGGCTGGCA CACGCCCTTG
 CCCTCAGGCC TGGCTCCCCG GGTCCTGTTG ACCACCAGGC TGCAGATCCC AAGGAATGCA
 GGCATCTGGG TGGCCCCACG TGGAGCACCA GCCATGGGGA GGCCGTGGGC TACCAGGCCC
 TGCGTGCACT CGCAGCATGC ACCACTCCTT CTCCAGGTCC CGTTGACCTC CATGTGTGCT
 GTGCCCCGTC CTCCGCTGCA CTGCCTCTTC GTAGTGCCCC AGCTCCATCC GGGGGTGGGT
 GGGAGTGGAG ACCCCTGCCT ACAGGCCTCC GGGTCTAGCC AGAGTCAACC AGCCCACCAG
 AGACACCCAG ATGCAGGCTA TGCCCCACGT GCCCAGGGAG GATCTGCTGA CGTGAGCCCA
 GATT
 K
 CGATTCTTGT GCGAGGGaga cgaaccaggt ttaaacccca gctctgccac ttctggctgt
 gactttgagc atggctgttc atctctgggg gtctctctcc tcatctCAGA GAAGCAGATC
 ATGGTGCGCA CCCCATGGCG CGCTGTGCAG AGCACATAGA GACGCCACCC ACAG

GeneView

GeneView via analysis of contig annotation: LHPP phospholysine phosphohistidine inorganic pyrophosphate phosphatase

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_035040->NM_022126

function

HuRef

NW_001838010->NM_022126

function

Celera

NW_924884->NM_022126

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	Function


reference	NT_035040->NM_022126->NP_071409	371267	forward	intron

HuRef	NW_001838010->NM_022126->NP_071409	298381	forward	intron

Celera	NW_924884->NM_022126->NP_071409	37067470	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs2362505 maps exactly once on NCBI human chromosome 10

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
10	NW_001838010.1	298381	119977479	plus	G	alt_assembly_8	HuRef	HuRef	view	484
10	NW_924884.1	37067470	120064653	plus	T	alt_assembly_1	Celera	Celera	view	484
10	NT_035040.4	371267	126280729	plus	T	ref_assembly	reference	reference	view	484

NCBI Resource Links

Submitter-Referenced
GenBank
NT_035040.1

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AL513190.13 NC_000010.9	AC019276.3

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	G/G	G/T	T/T	HWP	G	T
ss24581073	AFD_EUR_PANEL	European	48	IG	0.292	0.417	0.292	0.439	0.500	0.500

	AFD_AFR_PANEL	African American	42	IG	0.524	0.381	0.095	1.000	0.714	0.286

	AFD_CHN_PANEL	Asian	44	IG	0.409	0.409	0.182	0.527	0.614	0.386

ss3319503	CHMJ	Asian	74	IG					0.568	0.432

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.478+/-0.102	71	50	0	0

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: PERLEGEN

DoubleHit found by: BCM_SSAHASNP

UNKNOWN

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Revised: May 25, 2006 1:38 PM .