Reference SNP(refSNP) Cluster Report: rs3935012

Reference SNP(refSNP) Cluster Report: rs3935012

refSNP ID: rs3935012
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	108/129
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_025154.3:c.*1243T>G
NT_007819.16:g.403170T>G

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss5192992 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3935012 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
ss5192992	TSC-CSHL\|TSC0021235	fwd/B	G/T	attgcacaacagtcctcaaatacactgatg	atgaaactattcatacatcaagcagcattt	09/20/02	10/10/03	108	Genomic	unknown
ss6161827	SC_JCM\|NT_007819.10_209885	fwd/B	G/T	attgcacaacagtcctcaaatacactgatg	atgaaactattcatacatcaagcagcattt	01/10/03	10/10/03	111	Genomic	unknown
ss42949385	ABI\|hCV26241542	fwd/B	G/T	attgcacaacagtcctcaaatacactgatg	atgaaactattcatacatcaagcagcattt	07/18/05	07/18/05	126	Genomic	unknown

Fasta sequence (Legend)

 TCACCATTCT CACGTGATTC TTGTGAGACT CTTTTTGGTT ATAATTACTA TTTAATATTT
 AGACTATTTT ACTGAGCAGA CTTTATAAAT GAGATATCTA CAAGGCACTT AAAGTGTTAC
 AGATGTTTTA CCTTAAGAAT TATTTAAGTT GTGTTGGGTT AAGACAGTTT TCAGTGTACC
 GTAAATGTTG TGTTTTCAGA AAAAGACAAA ACGATGGTGC TGACTGGTTT TCTGTATATT
 GCACAACAGT CCTCAAATAC ACTGATG
 K
 ATGAAACTAT TCATACATCA AGCAGCATTT TTTTCACTCT CCTTAGAATT GGAACTATGC
 AGTTAAGGCA GATAAAATGT ACAGATGTTT CATATATTAC AGGTTACATA TATAAATCAA
 AATTTCCTAT ATAAAACTGA TTTGGGATTT GGGGTGGaaa tattttgaat attaatttat
 ttttaaaGAT GCAAGATAGG ACTTTGTGCA ATGTATTTTT GTAAATGCTT TTCAAAATAT
 CTGTCTTTGG TAGTGCTTCT GCTGCTGCCA CCAAATTGAT AAGATGCTAT TAAGAGGGTT
 TAAATAAAGA GTTTTAATTT TTAAAAGGGC ATGGGATATA AACAGCCTAT TTCTTTTCTC
 AGTTTGCTGT TTCTGCCCTG GGATGTGGGA GGGACTGGGT TTGCTGGTTC TTGTTGGAAG
 CTCTGT

GeneView

GeneView via analysis of contig annotation: UNC84A unc-84 homolog A (C. elegans)

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

GeneView via analysis of contig annotation: C7orf20 chromosome 7 open reading frame 20

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_007819->NM_025154

function

HuRef

NW_001838998->NM_025154

function

Celera

NW_923206->NM_025154

function

CRA_TCAGchr7v2

NT_079592->NM_025154

function

reference

NT_007819->NM_015949

function

HuRef

NW_001838998->NM_015949

function

Celera

NW_923206->NM_015949

function

CRA_TCAGchr7v2

NT_079592->NM_015949

function

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


reference	NT_007819->NM_025154->	403170	forward	3484	3' UTR

HuRef	NW_001838998->NM_025154->	635122	forward	3480	3' UTR

Celera	NW_923206->NM_025154->	825994	forward	3427	3' UTR

CRA_TCAGchr7v2	NT_079592->NM_025154->	919160	forward	3484	3' UTR

reference	NT_007819->NM_015949->NP_057033	403170	forward		5' near gene

HuRef	NW_001838998->NM_015949->NP_057033	635122	forward		5' near gene

Celera	NW_923206->NM_015949->NP_057033	825994	forward		5' near gene

CRA_TCAGchr7v2	NT_079592->NM_015949->NP_057033	919160	forward		5' near gene

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs3935012 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_001838998.1	635122	832877	plus	T	alt_assembly_8	HuRef	HuRef	view	267
7	NT_007819.16	403170	880737	plus	T	ref_assembly	reference	reference	view	267
7	NW_923206.1	825994	883597	plus	T	alt_assembly_1	Celera	Celera	view	267
7	NT_079592.2	919160	969160	plus	T	alt_assembly_2	CRA_TCAGchr7v2	CRA_TCAGchr7v2	view	267

NCBI Resource Links

Submitter-Referenced
GenBank
NT_007819.10

dbSNP Blast Analysis
GenBank HTGS Finished:
AC099731.5 NC_000007.12

UniGene Cluster ID
438072

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 .