Reference SNP(refSNP) Cluster Report: rs41301394

Reference SNP(refSNP) Cluster Report: rs41301394

refSNP ID: rs41301394
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	127/129
Map to Genome Build:	36.3

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

HGVS Names
NM_000941.2:c.831-35C>T
NT_007933.14:g.847079C>T

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss81655548 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs41301394 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
ss52653284	EGP_SNPS\|POR-030137		fwd/B	C/T	ccttggagacagagactcagatcaaagccc	ggccgctcactgtgcttctctcctccccac	06/02/06	12/16/06	127	Genomic			unknown
ss81655548	HGSV\|Cor18555_SNV_20070510.chr7_75257454		fwd/B	C/T	ccttggagacggagactcagatcaaagccc	ggccgctcactgtgcttctctcctccccac	11/27/07	12/01/07	130	Genomic			unknown

Fasta sequence (Legend)

 TTTCCACATC TGTAAACAGA CACTGATGAC CCAGCTCTGC CCATGTGGTG GGACTATAGA
 GAGAACTGCA TTAGGGCTGG GCGAGGTGGC TCACAGCTCT AATCCCAGCA CTCTGGGAGG
 CCGAGGTGGG TGAATCACCT GAGGTCAGGA GTTCAAGACC AGCCTGGCCA ACATGGTGAA
 ACCCCGTCTC TAGTAAAAAT ATAAAAGTTA ACCAGGCATG GTGGCGAATG CCTGTAATTC
 CAGCTGCTCA GGAGGCTGAG GCAGGAGAAT TGCTTGAACC TGGGAGGCAG AGGTTGCAGT
 GAGCCGAGAT CGCGCCGCTG CACTCCAGCC TGGGTGGCAG AGCGAAACTC TGTCTCAAAA
 AAAAAAAAGA GAACTGCATT GGACCAGGCT GGGAGAGCCC TTGATGTAAC CGGTGAGATT
 TCCTCATGGA GATCTCTGAG ATTCCCTGTG CTTTGTGCAA CCAGAAGCGT CCTTGGAGAC
 GGAGACTCAG ATCAAAGCCC
 Y
 GGCCGCTCAC TGTGCTTCTC TCCTCCCCAC CCAGCCCCTT TGATGCCAAG AATCCGTTCC
 TGGCTGCAGT CACCACCAAC CGGAAGCTGA ACCAGGGAAC CGAGCGCCAC CTCATGCACC
 TGGAATTGGA CATCTCGGAC TCCAAAATCA GGTACCAGCT GCCACTGTCA CCCCCTGAAC
 CCTCACTCTG GGCCTCCTGA

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	847079	forward	intron

HuRef	NW_001839047->NM_000941->NP_000932	511755	forward	intron

Celera	NW_923484->NM_000941->NP_000932	478101	forward	intron

CRA_TCAGchr7v2	NT_079595->NM_000941->NP_000932	847079	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs41301394 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	478101	70481347	plus	C	alt_assembly_1	Celera	Celera	view	255
7	NW_001839047.1	511755	70699615	plus	C	alt_assembly_8	HuRef	HuRef	view	255
7	NT_079595.2	847079	74945867	plus	C	alt_assembly_2	CRA_TCAGchr7v2	CRA_TCAGchr7v2	view	255
7	NT_007933.14	847079	75450739	plus	C	ref_assembly	reference	reference	view	255

NCBI Resource Links

Submitter-Referenced
GenBank
DQ640499

dbSNP Blast Analysis
GenBank HTGS Finished:
AC006330.5 NC_000007.12

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss52653284	EGP_YORUB-PANEL	Sub-Saharan African	24	IG	0.833	0.167		1.000	0.917	0.083

	EGP_HISP-PANEL	Hispanic	44	IG	0.773	0.227		0.584	0.886	0.114

	EGP_CEPH-PANEL	European	44	IG	0.545	0.409	0.045	0.752	0.750	0.250

	EGP_AD-PANEL	African American	30	IG	0.800	0.133	0.067	0.150	0.867	0.133

	EGP_ASIAN-PANEL	Asian	46	IG	0.435	0.391	0.174	0.479	0.630	0.370

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.329+/-0.237	95	95	0	0

Validation Summary:

Validation status	Marker displays Mendelian segregation	PCR results confirmed in multiple reactions	Homozygotes detected in individual genotype data
	UNKNOWN	UNKNOWN	YES

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Revised: May 25, 2006 1:38 PM .