Reference SNP(refSNP) Cluster Report: rs1024561

Reference SNP(refSNP) Cluster Report: rs1024561

refSNP ID: rs1024561
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_006754.2:c.457-925C>T
NM_182715.1:c.403-925C>T
NT_007933.14:g.30918084G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss1489304 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1024561 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
ss1489304	TSC-CSHL\|TSC0247760	fwd/T	A/G	ggtaggaataatataaaatttgtatctttt	gatgctatatatgctaaacatatgcgtaca	09/07/00	04/07/04	86	Genomic	95 %
ss5717711	SC_JCM\|NT_007933.10_30917136	fwd/T	A/G	ggtaggaataatataaaatttgtatctttt	gatgctatatatgctaaacatatgcgtaca	01/10/03	10/10/03	111	Genomic	unknown
ss23991648	PERLEGEN\|afd0547571	fwd/T	A/G	ggtaggaataatataaaatttgtatctttt	gatgctatatatgctaaacatatgcgtaca	08/10/04	09/13/04	123	Genomic	unknown
ss74822130	AFFY\|SNP_M-327349	fwd/T	A/G	ggtaggaataatataaaatttgtatctttt	gatgctatatatgctaaacatatgcgtaca	08/09/07	08/09/07	128	Genomic	unknown

Fasta sequence (Legend)

 tcagccactt actcccagga ccatacctta gaccttgtca tcaccaataa ctgtatcctt
 ccatactctg ttttgatcat cccattttcc cataacacct ctttccagct cactgtctct
 ggcaccccaa tcctaaaact cctttgaccc caccaagacc tacaatctga tcctactgct
 ttcttactgt atcaccactt cactaatgtc ctcacttatt ttaatcaatt tctgttctaa
 gggccttcat tatcatctct tgcacatact ctcaactcac ttatccttct TCTGCAAAAC
 TCTAACTTTA GTTAAACCAA ATTCTCCATG AGATGGATAA TAAAATGGTG AAAAGCACAC
 ACCAGAATGG TATCTCTTTT AAATTTCCTA ACCACAAATT TTAAGAATGC TCACTATATT
 AAGAAAAAGG CAACAACAAA AATCTCCCAA GACACCTTAT CACTATTAAC TCTGTACTAA
 ATCCTTTGCT ATTTATTACA AAGAATGGGA TGGTTTTAAT ATTTTAGAAT AAATGGTTCT
 AATGGGTGGT TTTAATATTT TAGATCATAA GTCTAATCTT GTTTGATCTT CCTTCAAATT
 AATGACCAGG GTAGGAATAA TATAAAATTT GTATCTTTT
 R
 GATGCTATAT ATGCTAAACA TATGCGTACA CTCAAGGATA GGAGCTCTTA CATATCTGCA
 GCAAAAATCT TTCTAACCTC AGAATGGATT TTGGAGCTTA TCACAGAAGC ATTTTGTTTT
 TTAAATAAAC CCAATTAGTT TTTAATTATT TTGCCAGCCA CCTTTTAGTC ATTTAttagg
 ttggtgcaaa agttattatg gtttttgcta tttattttaa tgataaaaac cacaattatt
 tttgtaccaa cctaaTATTT AGGATAAATA CCAGTGATCT CTTAGGAGAT ATAGAAGCTA
 TGCTATATAG CTTGCCCACT TGGTCAAGAC AACACTGAAT GAATACTTAG GATTAGAGAA
 CCAAAAATAA TTACTAATTA CATGAA

GeneView

GeneView via analysis of contig annotation: SYPL1 synaptophysin-like 1

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_007933->NM_006754

function

reference

NT_007933->NM_182715

function

HuRef

NW_001839071->NM_006754

function

HuRef

NW_001839071->NM_182715

function

Celera

NW_923640->NM_006754

function

Celera

NW_923640->NM_182715

function

CRA_TCAGchr7v2

NT_079596->NM_006754

function

CRA_TCAGchr7v2

NT_079596->NM_182715

function

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


reference	NT_007933->NM_006754->NP_006745	30918084	reverse	intron

reference	NT_007933->NM_182715->NP_874384	30918084	reverse	intron

HuRef	NW_001839071->NM_006754->NP_006745	25560551	forward	intron

HuRef	NW_001839071->NM_182715->NP_874384	25560551	forward	intron

Celera	NW_923640->NM_006754->NP_006745	3298791	reverse	intron

Celera	NW_923640->NM_182715->NP_874384	3298791	reverse	intron

CRA_TCAGchr7v2	NT_079596->NM_006754->NP_006745	5131100	reverse	intron

CRA_TCAGchr7v2	NT_079596->NM_182715->NP_874384	5131100	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs1024561 maps exactly once on NCBI human chromosome 7

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
7	NW_001839071.2	25560551	100093963	minus	C	alt_assembly_8	HuRef	HuRef	view	639
7	NW_923640.1	3298791	100540040	plus	G	alt_assembly_1	Celera	Celera	view	639
7	NT_079596.2	5131100	105095532	plus	G	alt_assembly_2	CRA_TCAGchr7v2	CRA_TCAGchr7v2	view	639
7	NT_007933.14	30918084	105521744	plus	G	ref_assembly	reference	reference	view	639

NCBI Resource Links

Submitter-Referenced
GenBank
NT_007933.10

dbSNP Blast Analysis
GenBank HTGS Finished:
AC005095.2 NC_000007.12

UniGene Cluster ID
80919

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss1489304	SC_12_A	Asian	22	IG	0.182	0.636	0.182	0.371	0.500	0.500

	SC_12_AA	African American	16	IG		0.125	0.875	1.000	0.062	0.938

	SC_12_C	European	14	IG			1.000			1.000

	SC_95_C	European	78	IG		0.103	0.897	0.752	0.051	0.949

	HapMap-CEU	European	116	IG	0.017	0.138	0.845	0.752	0.086	0.914

	HapMap-HCB	Asian	88	IG	0.295	0.477	0.227	0.655	0.534	0.466

	HapMap-JPT	Asian	86	IG	0.140	0.442	0.419	0.584	0.360	0.640

	HapMap-YRI	Sub-Saharan African	116	IG			1.000			1.000

ss23991648	AFD_EUR_PANEL	European	48	IG		0.167	0.833	0.752	0.083	0.917

	AFD_AFR_PANEL	African American	42	IG		0.048	0.952	1.000	0.024	0.976

	AFD_CHN_PANEL	Asian	48	IG	0.250	0.417	0.333	0.439	0.458	0.542

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.313+/-0.242	401	295	63	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 .