Reference SNP(refSNP) Cluster Report: rs239955

Reference SNP(refSNP) Cluster Report: rs239955

refSNP ID: rs239955
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	79/129
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_000941.2:c.-4-6351C>T
NT_007933.14:g.811232C>T

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss10403887 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs239955 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
ss309001	KWOK\|OVLP-000621-364049	fwd/T	A/G	cattatgacacgtgcaacacaaaatgtgca	aaatcaaaaacatttaagcgcaaagattta	06/30/00	10/10/03	79	Genomic	97 %
ss561068	SC_JCM\|AC006330.3_38812	rev/B	C/T	taaatctttgcgcttaaatgtttttgattt	tgcacattttgtgttgcacgtgtcataatg	07/12/00	10/10/03	80	Genomic	unknown
ss1042002	KWOK\|OVLP-000804-561602	fwd/T	A/G	cattatgacacgtgcaacacaaaatgtgca	aaatcaaaaacatttaagcgcaaagattta	09/02/00	10/10/03	87	Genomic	97 %
ss1635191	KWOK\|OVLP-000925-242148	fwd/T	A/G	cattatgacacgtgcaacacaaaatgtgca	aaatcaaaaacatttaagcgcaaagattta	10/04/00	10/10/03	87	Genomic	97 %
ss3091374	TSC-CSHL\|TSC1190683	rev/B	C/T	taaatctttgcgcttaaatgtttttgattt	tgcacattttgtgttgcacgtgtcataatg	06/07/01	10/10/03	98	Genomic	unknown
ss10403887	BCM_SSAHASNP\|chr7.NT_007933.12_811232	rev/B	C/T	taaatctttgcgcttaaatgtttttgattt	tgcacattttgtgttgcacgtgtcataatg	06/29/03	10/10/03	116	Genomic	unknown
ss17919379	CSHL-HAPMAP\|CSHL-HuCC-200402.chr7.NT_007933.13_811232	rev/B	C/T	taaatctttgcgcttaaatgtttttgattt	tgcacattttgtgttgcacgtgtcataatg	02/19/04	03/04/04	120	Genomic	unknown
ss43048100	ABI\|hCV2973045	rev/B	C/T	taaatctttgcacttaaatgtttttgattt	tgcacattttgtgttgcacgtgtcataatg	07/18/05	07/18/05	126	Genomic	unknown
ss84893840	HGSV\|Cor19240_SNV_20070510.chr7_75221607	rev/B	C/T	taaatctttgcgcttaaatgtttttgattt	tgcacattttgtgttgcacgtgtcataatg	11/30/07	12/08/07	130	Genomic	unknown
ss86040891	HGSV\|Cor18956_SNV_20070510.chr7_75221607	rev/B	C/T	taaatctttgcgcttaaatgtttttgattt	tgcacattttgtgttgcacgtgtcataatg	11/30/07	12/11/07	130	Genomic	unknown
ss93708319	BCMHGSC_JDW\|JWB-2328965	rev/B	C/T	taaatctttgcgcttaaatgtttttgattt	tgcacattttgtgttgcacgtgtcataatg	02/26/08	03/05/08	129	Genomic	unknown

Fasta sequence (Legend)

 TCTGCGGTCC TGCCCCAGAG CCTGACAGGT GTCTGAGATG CTCCTCCTCT CGAAGCTTCG
 TACTCATTCT TCAGACCTCA GCTCCACCAT CCCCTCCCCA GCACACACTT CCTTGGCGCA
 GAATCCAGGG CGCAATAACT ACTCAAGGGA ATGAAGGGAA TCGGTGAATG CATTATGACA
 CGTGCAACAC AAAATGTGCA
 R
 AAATCAAAAA CATTTAAGCG CAAAGATTTA AAACACACAT TGGggccggc cgtggtggct
 aacgcctgta atcacagcac tttgggaggc tgaggcaggc atatcacttg aggtcaggag
 tttgaggcca gcctggccaa catggtgaaa ccccgtctct actaaaaata caaaaattag
 ctgggcgtgg tgctgcgagc aggtcatggt ggcagacacc tgtaatccca gctatttggg
 aggctgaggc aggagaatcg cttgaacccg ggaggcggag gttgcagtga gccaagatcg
 tgccacttgc actccagcct gggcaacaga gcaagactgt ctcaaTCAAT CAATCAATTA
 ACAAATAAAA CACACATTGG GCTTCCAGTG TACCTGTCTG GACAGAtccc aaatgtcctt
 cgtttgtgga gtccctggta tctcagcaaa tttttaatgg tatccgtagg ccaaaaaaaa
 atgcctaaca gttccacgta tagttaggtc tgaacaacca ctgcaaaccc agcttcgcaa
 agatgtaaaa tcctaagaag gaatgcagca aggatctcac gttggaaccg tgaactgtcc
 caagctagca cttcgcatgg agttcaacag aCTTGAGCGT CCGCCGCATT GAGAATGATC
 ACTTGTGAGT TTGCTGCAGT GCCCTGGCAC AGTTTGGGAG CCACCTCTGC TATGCCAAAT
 ACTCTGA

GeneView

GeneView via analysis of contig annotation: POR P450 (cytochrome) oxidoreductase

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_000941

function

HuRef

NW_001839047->NM_000941

function

Celera

NW_923484->NM_000941

function

CRA_TCAGchr7v2

NT_079595->NM_000941

function

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


reference	NT_007933->NM_000941->NP_000932	811232	forward	intron

HuRef	NW_001839047->NM_000941->NP_000932	475842	forward	intron

Celera	NW_923484->NM_000941->NP_000932	442251	forward	intron

CRA_TCAGchr7v2	NT_079595->NM_000941->NP_000932	811232	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs239955 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_923484.1	442251	70445497	minus	C	alt_assembly_1	Celera	Celera	view	200
7	NW_001839047.1	475842	70663702	minus	C	alt_assembly_8	HuRef	HuRef	view	200
7	NT_079595.2	811232	74910020	minus	C	alt_assembly_2	CRA_TCAGchr7v2	CRA_TCAGchr7v2	view	200
7	NT_007933.14	811232	75414892	minus	C	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_007933 AC005067 AC006330.3 AC006330.4

dbSNP Blast Analysis
GenBank HTGS Finished:
AC005067.2 NC_000007.12

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

DoubleHit found by: BCM_SSAHASNP, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .