Reference SNP(refSNP) Cluster Report: rs28417600

Reference SNP(refSNP) Cluster Report: rs28417600

refSNP ID: rs28417600
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	125/129
Map to Genome Build:	36.3

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

HGVS Names
NM_133477.1:c.106-55932A>G
NT_016354.18:g.44436798A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss35138185 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs28417600 during BLAST analysis for the current build.

NCBI Assay ID	Handle\|Submitter ID	Validation Status	ss to rs Orientation /Strand	Alleles	5' Near Seq 30 bp	3' Near Seq 30 bp	Entry Date	Update Date	Build Added	Molecule Type	Freq Warning	Ancestral Allele	Success Rate
ss35138185	SSAHASNP\|TA-079.chr4_120246256		fwd/T	A/G	cagagcctaatccttgctggatggtagcac	tttcatcacacaaaaaccacagctcctctt	03/11/05		125	Genomic			unknown

Fasta sequence (Legend)

 AATATGATTT TCGTCGAGCC ACCTGATAAC TCTACAATTG ACCTTTTAGC TCTGACATTC
 CCTGAGACTG AGTTTTCCAA CAAACAACTT CTCTTTGTTG TTTGGGTTAT GCTTAAGAGC
 CAGCGTTCTG AAAATCCTGG CTTCAGGTTT CCAAACTAGC AGGTTGTGCT CAGAGCCTAA
 TCCTTGCTGG ATGGTAGCAC
 R
 TTTCATCACA CAAAAACCAC AGCTCCTCTT GGTCCTTGGC CTGATGCTCT GCAGCTTCTT
 TGGCCAACTC AACTAAAAGT GCAGTGGGGA AGCCCCATTC ATGGTAATTT CCAGAGAACC
 ATTTGCCTCA CTTGGGGAAA CGGGTATAGC ACAATCCCTG ATAGTTTCTG GACAAAAAGG
 TTCCATGTTT TCCCCTATGC

GeneView

GeneView via analysis of contig annotation: SYNPO2 synaptopodin 2

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_016354->NM_133477

function

HuRef

NW_001838920->NM_133477

function

Celera

NW_922195->NM_133477

function

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


reference	NT_016354->NM_133477->NP_597734	44436798	forward	intron

HuRef	NW_001838920->NM_133477->NP_597734	457456	forward	intron

Celera	NW_922195->NM_133477->NP_597734	418543	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs28417600 maps exactly once on NCBI human chromosome 4

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
4	NW_001838920.1	457456	115610887	plus	A	alt_assembly_8	HuRef	HuRef	view	200
4	NW_922195.1	418543	117249205	plus	A	alt_assembly_1	Celera	Celera	view	200
4	NT_016354.18	44436798	120108101	plus	A	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced

dbSNP Blast Analysis
GenBank HTGS Finished:
AC096745.2 NC_000004.10

Population Diversity

There is no frequency data.

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 .