Reference SNP(refSNP) Cluster Report: rs6603923

Reference SNP(refSNP) Cluster Report: rs6603923

refSNP ID: rs6603923
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	116/129
Map to Genome Build:	36.3

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

HGVS Names
NM_152232.2:c.1258-623T>G
NT_004610.18:g.2001009A>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss41173442 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs6603923 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
ss9862802	BCM_SSAHASNP\|chr1.NT_077921.1_794130	fwd/T	A/C	gtaggcagcagctgggacaaactagagcac	ctttgaactgggcatcctccgacctaaagt	06/27/03	10/10/03	116	Genomic	unknown
ss11203311	SC_JCM\|chr1.NT_077921.1_794130	fwd/T	A/C	gtaggcagcagctgggacaaactagagcac	ctttgaactgggcatcctccgacctaaagt	07/03/03	10/10/03	116	Genomic	unknown
ss41173442	ABI\|hCV55641	fwd/T	A/C	gtaggcagcagctgggacaaactagagcac	ctttgaactgggcatcctccgacctaaagt	07/16/05	03/31/08	126	Genomic	unknown
ss66274133	AFFY\|SNP_A-4304542	fwd/T	A/C	ggacaaactagagcac	ctttgaactgggcatc	10/27/06	03/31/08	127	Genomic	unknown
ss68760345	PERLEGEN\|PGP03978435	fwd/T	A/C	gtaggcagcagctgggacaaactagagcac	ctttgaactgggcatcctccgacctaaagt	01/30/07	03/31/08	127	Genomic	unknown
ss76418768	AFFY\|AFFY_6_1M_SNP_A-4304542	fwd/T	A/C	ggacaaactagagcac	ctttgaactgggcatc	08/28/07	08/30/07	129	Genomic	unknown

Fasta sequence (Legend)

 ATAAGTTCAT CTATGTTAGA GACTTAGAGC AGAGCCTGAG ACAGGAAGCA CTCCTACCAA
 GGTGCTGATA GATTTCCTTT TCCCTGGAAG TCACCTCAGT CATCCCTCTT GAACCCAATA
 CATGAGATGA GGTACAGAGT CCACTGTCTC TGTCACCTGC AAAGATCAAT TGGGGTCTCC
 CCTGATCCCT GGGTCCTTCC TACCTCCCCA GACCTTAGGG TCAGCTCTCA TTCCAGTCTC
 TCCCCACCTC CCAACCCCCC ATCACTCTCA GTAGGCAGCA GCTGGGACAA ACTAGAGCAC
 M
 CTTTGAACTG GGCATCCTCC GACCTAAAGT CCAGTCCCAG TTCTGTTCGC AATTTGCTGT
 GTGACTCTGA ACAAGTTTCT GAACCTTGCT GGGCTAACGC TGAAAGGACT TCCAGCTCAA
 ATATCCCATG GACCTGGCTC CTAGATTTTC CCTCCATAAA TGGTAGTGTC CATTTGGCTA
 TATCTTTAGG GCTCACCTGG CCTCAGGGAC TGATACACAC AGACAGGTAG CCAAGGGAGT
 CGGGCCCTGG CCTTCTCCCT TCCCTGCCTA GCAGGTGAGG TCCTGACTCA GAAAGACTCT

GeneView

GeneView via analysis of contig annotation: TAS1R2 taste receptor, type 1, member 2

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_004610->NM_152232

function

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


reference	NT_004610->NM_152232->NP_689418	2001009	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs6603923 maps exactly once on NCBI human chromosome 1

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
1	NW_001838573.1	798721	17422990	plus	C	alt_assembly_8	HuRef	HuRef	view	300
1	NW_927841.1	1980593	17504150	plus	C	alt_assembly_1	Celera	Celera	view	300
1	NT_004610.18	2001009	19049254	plus	A	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_077921

dbSNP Blast Analysis
GenBank HTGS Finished:
AL831755.9

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/C	C/C	HWP	A	C
ss41173442	HapMap-CEU	European	120	IG	0.717	0.283			0.858	0.142

	HapMap-HCB	Asian	88	IG	0.273	0.432	0.295		0.489	0.511

	HapMap-JPT	Asian	90	IG	0.311	0.422	0.267		0.522	0.478

ss66274133	HapMap-CEU	European	118	GF	0.712	0.288			0.856	0.144

	HapMap-HCB	Asian	90	GF	0.267	0.422	0.311		0.478	0.522

	HapMap-JPT	Asian	90	GF	0.311	0.422	0.267		0.522	0.478

	HapMap-YRI	Sub-Saharan African	120	GF	0.500	0.317	0.183		0.658	0.342

ss68760345	HapMap-CEU	European	120	GF	0.700	0.300			0.850	0.150

	HapMap-HCB	Asian	90	GF	0.267	0.444	0.289		0.489	0.511

	HapMap-JPT	Asian	88	GF	0.295	0.432	0.273		0.511	0.489

	HapMap-YRI	Sub-Saharan African	120	GF	0.517	0.350	0.133		0.692	0.308

Concordant Genotype	Total Sample	A/A	A/C	C/C
ss41173442	177	93	59	24
ss66274133	257	138	82	37
ss68760345	258	138	82	37

RefSNP Genotype Summary	Total Individual	A/A	A/C	C/C
rs6603923	270	139	82	37

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
175	ss41173442	A/A	CSHL-HAPMAP	HapMap-CEU	NA06991	CEPH1341.02	r23_ch1_CEU_affymetrix:genotype_protocol_1
175	ss66274133	A/C	CSHL-HAPMAP	HapMap-CEU	NA06991	CEPH1341.02	chr1-HapMap-CEU
175	ss68760345	A/A	CSHL-HAPMAP	HapMap-CEU	NA06991	CEPH1341.02	chr1-HapMap-CEU
186	ss41173442	A/A	CSHL-HAPMAP	HapMap-CEU	NA06993	CEPH1341.13	r23_ch1_CEU_affymetrix:genotype_protocol_1
186	ss66274133	A/A	CSHL-HAPMAP	HapMap-CEU	NA06993	CEPH1341.13	chr1-HapMap-CEU
186	ss68760345	A/C	CSHL-HAPMAP	HapMap-CEU	NA06993	CEPH1341.13	chr1-HapMap-CEU
5141	ss66274133	A/A	CSHL-HAPMAP	HapMap-YRI	NA19098	YOR105.03	chr1-HapMap-YRI
5141	ss68760345	A/C	CSHL-HAPMAP	HapMap-YRI	NA19098	YOR105.03	chr1-HapMap-YRI
5162	ss41173442	C/C	CSHL-HAPMAP	HapMap-HCB	NA18547	CH18547	r23_ch1_HCB_affymetrix:genotype_protocol_1
5162	ss66274133	C/C	CSHL-HAPMAP	HapMap-HCB	NA18547	CH18547	chr1-HapMap-HCB
5162	ss68760345	A/C	CSHL-HAPMAP	HapMap-HCB	NA18547	CH18547	chr1-HapMap-HCB
5243	ss66274133	A/C	CSHL-HAPMAP	HapMap-YRI	NA18507	YOR009.03	chr1-HapMap-YRI
5243	ss68760345	A/A	CSHL-HAPMAP	HapMap-YRI	NA18507	YOR009.03	chr1-HapMap-YRI
5260	ss66274133	C/C	CSHL-HAPMAP	HapMap-YRI	NA18855	YOR023.02	chr1-HapMap-YRI
5260	ss68760345	A/C	CSHL-HAPMAP	HapMap-YRI	NA18855	YOR023.02	chr1-HapMap-YRI
5264	ss66274133	C/C	CSHL-HAPMAP	HapMap-YRI	NA18862	YOR024.03	chr1-HapMap-YRI
5264	ss68760345	A/A	CSHL-HAPMAP	HapMap-YRI	NA18862	YOR024.03	chr1-HapMap-YRI
5276	ss66274133	A/C	CSHL-HAPMAP	HapMap-YRI	NA19138	YOR043.03	chr1-HapMap-YRI
5276	ss68760345	A/A	CSHL-HAPMAP	HapMap-YRI	NA19138	YOR043.03	chr1-HapMap-YRI
5286	ss66274133	C/C	CSHL-HAPMAP	HapMap-YRI	NA19211	YOR050.01	chr1-HapMap-YRI
5286	ss68760345	A/C	CSHL-HAPMAP	HapMap-YRI	NA19211	YOR050.01	chr1-HapMap-YRI
5288	ss66274133	C/C	CSHL-HAPMAP	HapMap-YRI	NA19210	YOR050.03	chr1-HapMap-YRI
5288	ss68760345	A/C	CSHL-HAPMAP	HapMap-YRI	NA19210	YOR050.03	chr1-HapMap-YRI
5301	ss66274133	C/C	CSHL-HAPMAP	HapMap-YRI	NA19142	YOR071.01	chr1-HapMap-YRI
5301	ss68760345	A/C	CSHL-HAPMAP	HapMap-YRI	NA19142	YOR071.01	chr1-HapMap-YRI
5303	ss66274133	A/A	CSHL-HAPMAP	HapMap-YRI	NA19141	YOR071.03	chr1-HapMap-YRI
5303	ss68760345	A/C	CSHL-HAPMAP	HapMap-YRI	NA19141	YOR071.03	chr1-HapMap-YRI

Genotype data submitted for	270	samples from	270	individuals	Individual with multiple genotypes submission:	270

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 .