Reference SNP(refSNP) Cluster Report: rs12341025

Reference SNP(refSNP) Cluster Report: rs12341025

refSNP ID: rs12341025
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	120/129
Map to Genome Build:	36.3

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

HGVS Names
NM_001005235.1:c.928T>C
NP_001005235.1:p.Y310H
NT_008470.18:g.32808400T>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss18828635 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs12341025 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
ss18828635	SC_SNP\|SC-CHR9-12_NA17119-200402.chr9.NT_008470.16_27144931	fwd/B	C/T	aggggtttgaagaaattaagacacagaatt	actcatagaaagaacaaaatgttggcatgt	02/20/04	10/26/06	120	Genomic	unknown
ss74821884	AFFY\|SNP_M-326930	fwd/B	C/T	aggggtttgaagaaattaagacacagaatt	actcatagaaagaacaaaatgttggcatgt	08/09/07	08/09/07	128	Genomic	unknown
ss74874808	ILLUMINA\|ILMN_Human_1M_rs12341025	fwd/B	C/T	aggggtttgaagaaattaagacacagaatt	actcatagaaagaacaaaatgttggcatgt	08/28/07	08/29/07	129	Genomic	unknown

Fasta sequence (Legend)

 GCTCCCACCT CACTGTAGTG GTCCTGTTCT ATGGGAGTGT CATCTATGTC TATTTTAGGC
 CTCTGTCCAT GTACTCAGTG ATGAAGGGCC GGGTAGCCAC AGTTATGTAC ACAGTAGTGA
 CACCCATGCT GAACCCTTTC ATCTACAGCC TGAGGAACAA AGATATGAAA AGGGGTTTGA
 AGAAATTAAG ACACAGAATT
 Y
 ACTCATAGAA AGAACAAAAT GTTGGCATGT CAAAATCAGG ACATGACCTA AAAGATTATT
 ATCAGTTTAT CCTCCCTTCC TAACCCTTTT CCACATGGCA TTCAAAGAGG TCATGAAAAG
 TGGTGTTGGA TATCAGTAAG AGAATTAACC TGGGAGCAAA ACACTCAGTT TCTTtatata
 tatatatata tatatgtata cacacacaca catatatata taCACACata ctttaagttc
 tgggatacat gtgcagaacg tgcaggttca ttacataggt atacacgtgc catggtggtt
 tgctgcaccc atcaacctgt catctacatt aggtatttct cctaatgcaa tccttctcct
 agctccccac cccctggcag gccccagtgt gtgatgttcc cctccctttg tccgtgtgtt
 ctcattgttc aactcccact tatgagtgag aacatgtggt gtttggtttt ctgttcttga
 gttagtttgc tgagaatgat

GeneView

GeneView via analysis of contig annotation: OR1L4 olfactory receptor, family 1, subfamily L, member 4

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_008470->NM_001005235

function

HuRef

NW_001839239->NM_001005235

function

Celera

NW_924573->NM_001005235

function

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


reference	NT_008470->NM_001005235->NP_001005235	32808401	forward	928	missense	C	His [H]	1	310
					contig reference	T	Tyr [Y]	1	310

HuRef	NW_001839239->NM_001005235->NP_001005235	829064	forward	928	missense	C	His [H]	1	310
					contig reference	T	Tyr [Y]	1	310

Celera	NW_924573->NM_001005235->NP_001005235	9623344	forward	928	missense	C	His [H]	1	310
					contig reference	T	Tyr [Y]	1	310

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs12341025 maps exactly once on NCBI human chromosome 9

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
9	NW_001839239.1	829064	95101756	plus	T	alt_assembly_8	HuRef	HuRef	view	200
9	NW_924573.1	9623344	96135513	plus	T	alt_assembly_1	Celera	Celera	view	200
9	NT_008470.18	32808401	124527017	plus	T	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_008470

dbSNP Blast Analysis
GenBank HTGS Finished:
AC006313.1 NC_000009.10

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/T	T/T	HWP	C	T
ss18828635	HapMap-CEU	European	120	IG		1.000			1.000

	HapMap-HCB	Asian	90	IG		1.000			1.000

	HapMap-JPT	Asian	90	IG		1.000			1.000

	HapMap-YRI	Sub-Saharan African	120	IG	0.033	0.967	1.000	0.017	0.983

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.009+/-0.068	270	210	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

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Revised: May 25, 2006 1:38 PM .