Reference SNP(refSNP) Cluster Report: rs1617742

Reference SNP(refSNP) Cluster Report: rs1617742

refSNP ID: rs1617742
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	89/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	A/T
Ancestral Allele:	Not available
Clinical Association:	unknown

HGVS Names
NM_001005291.1:c.*526A>T
NM_004176.3:c.*526A>T
NT_010718.15:g.17312759T>A

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss2433125 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1617742 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
ss2433125	SC_JCM\|AL354000.4_87620		fwd/B	A/T	cttagaatgagaagttttggccggagaaat	aaaatggaaattttattaaccggggttttg	11/03/00	10/10/03	89	Genomic			unknown

Fasta sequence (Legend)

 TTTCCCTGTG CTGACGGAAG CCAACTTGGC TTTCCCGGAC TGCAAGCAGG GCTCTGCCCC
 AGAGGCCTTT CTTTCGTCGT GGGAAAGAAA CGTGTACATA GTGTAGGTCA ACCGGGCTTA
 GCCTCTGACC TGAGGCTCCT GTGCTACTTT GCCTTTGGAC AACTTTATTT CTTAGAATGA
 GAAGTTTTGG CCGGAGAAAT
 W
 AAAATGGAAA TTTTATTAAC CGGGGTTTTG TGTCTTCAGC TGATGGATGT GCTGACTAGT
 GAGAGTGCTT GGGCCCTCCC CCAGCACCTA GGGAAAGGCT TCCCCTCCCC CTCCGGCCAC
 AAGGTACACA ACTTTTAACT TAGCTCTTCC CGATGTTTGT TTGTTAGTGG GAGGAGTGGG
 GAGGGCTGGC TGTATGGCCT

GeneView

GeneView via analysis of contig annotation: RAI1 retinoic acid induced 1

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

GeneView via analysis of contig annotation: SREBF1 sterol regulatory element binding transcription factor 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

HuRef

NW_001838410->NM_030665

function

reference

NT_010718->NM_001005291

function

reference

NT_010718->NM_004176

function

HuRef

NW_001838410->NM_001005291

function

HuRef

NW_001838410->NM_004176

function

Celera

NW_926628->NM_001005291

function

Celera

NW_926628->NM_004176

function

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


HuRef	NW_001838410->NM_030665->NP_109590	620575	reverse		3' near gene

reference	NT_010718->NM_001005291->	17312759	reverse	4254	3' UTR

reference	NT_010718->NM_004176->	17312759	reverse	4164	3' UTR

HuRef	NW_001838410->NM_001005291->	620575	forward	4253	3' UTR

HuRef	NW_001838410->NM_004176->	620575	forward	4163	3' UTR

Celera	NW_926628->NM_001005291->	960093	reverse	4254	3' UTR

Celera	NW_926628->NM_004176->	960093	reverse	4164	3' UTR

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs1617742 maps exactly once on NCBI human chromosome 17

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
17	NW_001838410.2	620575	17467656	plus	A	alt_assembly_8	HuRef	HuRef	view	200
17	NT_010718.15	17312759	17656135	minus	T	ref_assembly	reference	reference	view	200
17	NW_926628.1	960093	18654883	minus	T	alt_assembly_1	Celera	Celera	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
AL354000 AL035362

dbSNP Blast Analysis
GenBank HTGS Finished:
AC122129.9 AL354000.7 NC_000017.9

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

Disclaimer Privacy statement

Revised: May 25, 2006 1:38 PM .