Reference SNP(refSNP) Cluster Report: rs11230983

Reference SNP(refSNP) Cluster Report: rs11230983

refSNP ID: rs11230983
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:	A/G
Ancestral Allele:	A
Clinical Association:	unknown

HGVS Names
NM_001001967.1:c.371G>A
NP_001001967.1:p.R124H
NT_033903.7:g.847078G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss16145057 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs11230983 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
ss16145057	SC_SNP\|NT_033903.6_714326	fwd/T	A/G	ctttcatgttagcagcgatggcttatgacc	ttttgtggcagtttgtaaacccttgctgta	11/18/03	10/26/06	120	Genomic	unknown
ss18487913	SC_SNP\|SC-CHR9-12_NA11321-200402.chr11.NT_033903.6_714326	fwd/T	A/G	ctttcatgttagcagcgatggcttatgacc	ttttgtggcagtttgtaaacccttgctgta	02/20/04	03/04/04	120	Genomic	unknown
ss24099919	PERLEGEN\|afd1693881	fwd/T	A/G	ctttcatgttagcagcgatggcttatgacc	ttttgtggcagtttgtaaacccttgctgta	08/10/04	09/13/04	123	Genomic	unknown
ss65725239	ILLUMINA\|Human1-rs11230983	fwd/T	A/G	ctttcatgttagcagcgatggcttatgacc	ttttgtggcagtttgtaaacccttgctgta	10/10/06	10/10/06	127	Genomic	unknown
ss66795455	ILLUMINA\|HumanHap300v1.1_rs11230983	fwd/B	A/G	ctttcatgttagcagcgatggcttatgacc	ttttgtggcagtttgtaaacccttgctgta	11/09/06	11/09/06	127	Genomic	unknown
ss66928113	ILLUMINA\|HumanHap550v1.1_rs11230983	fwd/T	A/G	ctttcatgttagcagcgatggcttatgacc	ttttgtggcagtttgtaaacccttgctgta	11/14/06	11/14/06	127	Genomic	unknown
ss67083044	ILLUMINA\|HumanHap650Yv1.0_rs11230983	fwd/T	A/G	ctttcatgttagcagcgatggcttatgacc	ttttgtggcagtttgtaaacccttgctgta	11/14/06	11/14/06	127	Genomic	unknown
ss69317876	PERLEGEN\|PGP01693881	fwd/T	A/G	ctttcatgttagcagcgatggcttatgacc	ttttgtggcagtttgtaaacccttgctgta	01/30/07	03/31/08	127	Genomic	unknown
ss70392555	ILLUMINA\|HumanHap300v2.0_rs11230983	fwd/T	A/G	ctttcatgttagcagcgatggcttatgacc	ttttgtggcagtttgtaaacccttgctgta	04/18/07	11/18/07	127	Genomic	unknown
ss70526067	ILLUMINA\|HumanHap550v3.0__rs11230983	rev/B	C/T	tacagcaagggtttacaaactgccacaaaa	ggtcataagccatcgctgctaacatgaaag	04/20/07	03/30/08	130	Genomic	unknown
ss71056028	ILLUMINA\|HumanHap650Yv3.0_rs11230983	fwd/T	A/G	ctttcatgttagcagcgatggcttatgacc	ttttgtggcagtttgtaaacccttgctgta	04/23/07	04/23/07	127	Genomic	unknown
ss74808897	AFFY\|SNP_M-181268	fwd/T	A/G	ctttcatgttagcagcgatggcttatgacc	ttttgtggcagtttgtaaacccttgctgta	08/09/07	08/09/07	128	Genomic	unknown
ss75816723	ILLUMINA\|ILMN_Human_1M_rs11230983	fwd/T	A/G	ctttcatgttagcagcgatggcttatgacc	ttttgtggcagtttgtaaacccttgctgta	08/28/07	08/29/07	129	Genomic	unknown
ss76521325	AFFY\|AFFY_6_1M_SNP_A-8382435	rev/B	C/T	acaaactgccacaaaa	ggtcataagccatcgc	08/28/07	08/30/07	129	Genomic	unknown
ss85091836	KRIBB_YJKIM\|KHS896444	fwd/T	A/G	ctttcatgttagcagcgatggcttatgacc	ttttgtggcagtttgtaaacccttgctgta	12/04/07	12/08/07	130	Genomic	unknown

Fasta sequence (Legend)

 CCATACAATC ATGTGCTTTT TCCTTAGTCA CTTGTCCTTG ACAGACTTCT GTTTTTCCAC
 TGTAGTTACA CCTAAACTGT TGGAGAACTT GGTTGTGGAA TACAGAACCA TCTCTTTCTC
 TGGTTGCATC ATGCAATTTT GTTTTGCTTG CATTTTTGGA GTGACAGAAA CTTTCATGTT
 AGCAGCGATG GCTTATGACC
 R
 TTTTGTGGCA GTTTGTAAAC CCTTGCTGTA TACCACTATT ATGTCTCAGA AGCTCTGTGC
 TCTTCTGGTG GCTGGGTCCT ATACATGGGG GATAGTGTGC TCCCTGATAC TCACATATTT
 TCTTCTTGAC TTATCGTTTT GTGAATCTAC CTTCATAAAT AATTTTATCT GTGACCACTC
 TGTAATTGTT TCTGCCTCCT

GeneView

GeneView via analysis of contig annotation: OR5D13 olfactory receptor, family 5, subfamily D, member 13

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_033903->NM_001001967

function

HuRef

NW_001838023->NM_001001967

function

Celera

NW_925106->NM_001001967

function

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


reference	NT_033903->NM_001001967->NP_001001967	847079	forward	371	missense	A	His [H]	2	124
					contig reference	G	Arg [R]	2	124

HuRef	NW_001838023->NM_001001967->NP_001001967	1254067	forward	371	missense	A	His [H]	2	124
					contig reference	G	Arg [R]	2	124

Celera	NW_925106->NM_001001967->NP_001001967	1229502	forward	371	missense	A	His [H]	2	124
					contig reference	G	Arg [R]	2	124

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs11230983 maps exactly once on NCBI human chromosome 11

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
11	NW_001838023.1	1254067	51870208	plus	G	alt_assembly_8	HuRef	HuRef	view	200
11	NW_925106.1	1229502	52881426	plus	G	alt_assembly_1	Celera	Celera	view	200
11	NT_033903.7	847079	55297860	plus	G	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_033903

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank HTGS Finished:	GenBank HTGS Draft:
NM_001001967.1	AC036111.7 NC_000011.8	AC021530.7 AC022289.2

UniGene Cluster ID
553743

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G	N
ss16145057	HapMap-CEU	European	120	IG		0.200	0.800	0.403	0.100	0.900

	HapMap-HCB	Asian	88	IG		0.227	0.773	0.403	0.114	0.886

	HapMap-JPT	Asian	88	IG		0.250	0.750	0.371	0.125	0.875

	HapMap-YRI	Sub-Saharan African	120	IG		0.117	0.883	0.655	0.058	0.942

	CHMJ	Asian	74	IG					0.203	0.784	0.014

ss24099919	AFD_EUR_PANEL	European	48	IG		0.292	0.708	0.439	0.146	0.854

	AFD_AFR_PANEL	African American	46	IG			1.000			1.000

	AFD_CHN_PANEL	Asian	48	IG		0.417	0.583	0.200	0.208	0.792

ss69317876	HapMap-CEU	European	120	GF		0.200	0.800		0.100	0.900

	HapMap-HCB	Asian	90	GF	0.022	0.222	0.756		0.133	0.867

	HapMap-JPT	Asian	90	GF		0.244	0.756		0.122	0.878

	HapMap-YRI	Sub-Saharan African	120	GF		0.117	0.883		0.058	0.942

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.182+/-0.241	332	260	270	0

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

UNKNOWN

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Revised: May 25, 2006 1:38 PM .