Reference SNP(refSNP) Cluster Report: rs10404335

Reference SNP(refSNP) Cluster Report: rs10404335

refSNP ID: rs10404335
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	119/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	C/T
Ancestral Allele:	C
Clinical Association:	unknown

HGVS Names
NM_030901.1:c.123G>A
NP_112163.1:p.G41G
NT_011295.10:g.6254846C>T

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss69375182 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs10404335 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
ss14695007	BCM_SSAHASNP\|chr19.NT_011295.10_6254847	fwd/B	C/T	tgagattgtggccaggatgatgagcagatt	ccgagcacagtgaccaggtacatggacaga	11/10/03	11/22/03	119	Genomic	unknown
ss48412567	APPLERA_GI\|hCV25653506	fwd/B	C/T	tgagattgtggccaggatgatgagcagatt	ccgagcacagtgaccaggtacatggacaga	09/28/05	11/03/06	126	Genomic	unknown
ss69375182	SI_EXO\|NT_011295.10_6254847	fwd/B	C/T	tgagattgtggccaggatgatgagcagatt	ccgagcacagtgaccaggtacatggacaga	04/12/07	04/12/07	127	Genomic	unknown

Fasta sequence (Legend)

 GGATTTCCAA GTCTGTGCAG AAGGACAGCC ACAATACCAT TAAGCTTTGT GACAAGGAAT
 TCAGGGCAGC AATCATCCAG GATGCCAGAA CCAGGAGTCC ACAGAGCCGA GGGTTCATGA
 TGACTGTGTA GTGCAGAGGA TGACAGATGG CCACAAACCG ATCATAGGCC ATCACAGCCA
 GGAGTAAGCT GTCTAACCCT CCAAAAAGTA CAAAAAAGCA CATCTGGGTG ATGCAGCCTG
 CATAGGTGAT GACTCTGCTC TGTGTCTGGA TGTTAATGAG CATCTTTGGG ATTGTAGTGG
 AGATGAAACA GATGTCTGCA AAGGACAGGT TGGAGAGGAA GAAGTACATG GGGGTGTGGA
 GGTGGGAGTC TGAGATTGTG GCCAGGATGA TGAGCAGATT
 Y
 CCGAGCACAG TGACCAGGTA CATGGACAGA AACAGCCCAA AGAGGAAGGG CTGCAATTCT
 GGTTCCTCAG AAAGTCCCAG AAGAACAAAT TCTGAAATCC CTGTGTCATT CTCTGGTTCC
 ATCTTTTTTT TTCTATTTAT TTATTTATTT ATTTATTTAT TTATTTATTT ATTAACATAG
 ACAGGGTCTC TCACTCTGTT GCCAACGCTG GTCTGAACCT CCTGGACTCA TGCGATCCTC
 CCACTTCAGC CTACAAAAGT GCTGAGATTA TAGGCATAAG CCATTGTGCC CAGGCTTGGT
 TGCATCTTTT CAATGTGACT ACCAAAAAGA GAGAGAATAT GACAATGTAA TTATGCATTA
 CAAACCTATC AGAAATTCTC TCATTTATAC TCCGGAGTCA

GeneView

GeneView via analysis of contig annotation: OR7A17 olfactory receptor, family 7, subfamily A, member 17

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_011295->NM_030901

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	mRNA pos	Function	dbSNP allele	Protein residue	Codon pos	Amino acid pos


reference	NT_011295->NM_030901->NP_112163	6254847	reverse	123	synonymous	A	Gly [G]	3	41
					contig reference	G	Gly [G]	3	41

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs10404335 maps exactly once on NCBI human chromosome 19

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
19	NW_001838484.1	284403	14560023	plus	C	alt_assembly_8	HuRef	HuRef	view	400
19	NT_011295.10	6254847	14853045	plus	C	ref_assembly	reference	reference	view	400
19	NW_927195.1	6104040	14887794	plus	C	alt_assembly_1	Celera	Celera	view	400

NCBI Resource Links

Submitter-Referenced
GenBank
NT_011295.10

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):
NM_030901.1

UniGene Cluster ID
247717

3D structure mapping
NP_112163

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss48412567	AGI_ASP population	multiple	66	IG	0.545	0.273	0.182	0.050	0.682	0.318

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.434+/-0.169	33	33	0	0

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 .