Reference SNP(refSNP) Cluster Report: rs1060257

Reference SNP(refSNP) Cluster Report: rs1060257

refSNP ID: rs1060257
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	86/129
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_003486.5:c.*1282G>A
NT_010498.15:g.41479493C>T

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss10804230 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1060257 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
ss1543691	LEE\|852422	fwd/T	A/G	gagctgtcgctgcctccatggcagcagcca	ggacccccagaacaagaagaccccgcagga	09/13/00	10/10/03	86	cDNA	unknown
ss4429861	LEE\|e852422	fwd/T	A/G	gagctgtcgctgcctccatggcagcagcca	ggacccccagaacaagaagacccccccgca	04/26/02	10/10/03	106	cDNA	unknown
ss10804230	BCM_SSAHASNP\|chr16.NT_019609.11_2310767	rev/B	C/T	tcctgcggggtcttcttgttctgggggtcc	tggctgctgccatggaggcagcgacagctc	06/30/03	11/07/03	116	Genomic	unknown
ss16230877	CGAP-GAI\|1469894	fwd/T	A/G	gagctgtcgctgcctccatggcagcagcca	ggacccccagaacaagaagacccccccgca	11/18/03	11/22/03	121	cDNA	unknown
ss23778863	PERLEGEN\|afd4524559	rev/B	C/T	tcctgcggggtcttcttgttctgggggtcc	tggctgctgccatggaggcagcgacagctc	08/10/04	09/13/04	123	Genomic	unknown
ss83146132	HGSV\|Cor19240_SNV_20070510.chr16_86422795	rev/B	C/T	tcctgcggggtcttcttgttctgggggtcc	tggctgctgccatggaggcagcgacagctc	11/30/07	12/04/07	130	Genomic	unknown

Fasta sequence (Legend)

 CCAAGCACTG CTCACGTCTC TGCCGCCTGC GTTTGGAGGC CCCTGGGCTC TCACCCAGTC
 CCCACCCGCC TGCAGAGAGG GAACTAGGGC ACCCCTTGTT TCTGTTGTTC CCGTGAATTT
 TTTTCGCTAT GGGAGGCAGC CGAGGCCTGG CCAATGCGGC CCACTTTCCT GAGCTGTCGC
 TGCCTCCATG GCAGCAGCCA
 R
 GGACCCCCAG AACAAGAAGA CCCCGCAGGA TCCCTCCTGA GCTCGGGGGG CTCTGCCTTC
 TCAGGCCCCG GGCTTCCCTT CTCCCCAGCC AGAGGTGGAG CCAAGTGGTC CAGCGTCACT
 CCAGTGCTCA GCTGTGGCTG GAGGAGCTGG CCTGTGGCAC AGCCCTGAGT GTCCCAAGCC
 GGGAGCCAAC GAAGCCGGAC

GeneView

GeneView via analysis of contig annotation: SLC7A5 solute carrier family 7 (cationic amino acid transporter, y+ system), member 5

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_010498->NM_003486

function

HuRef

NW_001838330->NM_003486

function

Celera

NW_926528->NM_003486

function

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


reference	NT_010498->NM_003486->	41479493	reverse	2878	3' UTR

HuRef	NW_001838330->NM_003486->	327692	reverse	2878	3' UTR

Celera	NW_926528->NM_003486->	13402513	reverse	2878	3' UTR

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs1060257 maps exactly once on NCBI human chromosome 16

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
16	NW_926528.1	13402513	72162599	minus	C	alt_assembly_1	Celera	Celera	view	200
16	NW_001838330.1	327692	73605784	minus	C	alt_assembly_8	HuRef	HuRef	view	200
16	NT_010498.15	41479493	86422795	minus	C	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_019609 BE547573 Hs.184601

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank HTGS Finished:	GenBank mRNA:
NM_003486.5	AC126696.1 NC_000016.8	AB018009.1 AF104032.1 BC039692.2 BC042600.1 M80244.1

UniGene Cluster ID
513797

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss23778863	AFD_EUR_PANEL	European	48	IG		0.583	0.417	0.050	0.292	0.708

	AFD_AFR_PANEL	African American	46	IG	0.174	0.565	0.261	0.527	0.457	0.543

	AFD_CHN_PANEL	Asian	44	IG	0.409	0.455	0.136	1.000	0.636	0.364

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.496+/-0.043	71	50	0	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 .