Reference SNP(refSNP) Cluster Report: rs221789

Reference SNP(refSNP) Cluster Report: rs221789

refSNP ID: rs221789
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	79/129
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_005273.2:c.-115T>C
NT_007933.14:g.25505797T>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44823104 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs221789 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
ss288210	KWOK\|OVLP-000621-255681	fwd/B	C/T	gacagcgccgcccgcgcaccgccagcgacc	ccgccgcagagtcccaccgccacaggtacc	06/30/00	10/10/03	79	Genomic	97 %
ss700492	SC_JCM\|AF053356.1_101782	rev/T	A/G	ggtacctgtggcggtgggactctgcggcgg	ggtcgctggcggtgcgcgggcggcgctgtc	07/27/00	04/07/04	87	Genomic	unknown
ss1841644	KWOK\|OVLP-000925-654994	fwd/B	C/T	gacagcgccgcccgcgcaccgccagcgacc	ccgccgcagagtcccaccgccacaggtacc	10/05/00	10/10/03	87	Genomic	97 %
ss11896748	WI_SSAHASNP\|chr7.NT_007933.12_25505105	fwd/B	C/T	gacagcgccgcccgcgcaccgccagcgacc	ccgccgcagagtcccaccgccacaggtacc	07/04/03	10/10/03	116	Genomic	unknown
ss16266060	CGAP-GAI\|1532519	fwd/B	C/T	gacagcgccgcccgcgcaccgccagcgacc	ccgccgcagagtcccaccgccacaggcctc	11/18/03	11/22/03	121	cDNA	unknown
ss19700476	CSHL-HAPMAP\|CSHL-HuDD-200402.chr7.NT_007933.13_25505105	fwd/B	C/T	gacagcgccgcccgcgcaccgccagcgacc	ccgccgcagagtcccaccgccacaggtacc	02/20/04	03/04/04	120	Genomic	unknown
ss22548825	SSAHASNP\|WGSA-200403-chr7.chr7.NT_007933.13_25505105	fwd/B	C/T	gacagcgccgcccgcgcaccgccagcgacc	ccgccgcagagtcccaccgccacaggtacc	03/21/04	03/21/04	121	Genomic	unknown
ss22926249	SSAHASNP\|AACC-200403.chr7.NT_007933.13_25505105	fwd/B	C/T	gacagcgccgcccgcgcaccgccagcgacc	ccgccgcagagtcccaccgccacaggtacc	03/22/04	03/22/04	121	Genomic	unknown
ss44823104	ABI\|hCV2868110	fwd/B	C/T	gacagcgccgcccgcgcaccgccagcgacc	ccgccgcagagtcccaccgccacaggtacc	07/19/05	07/19/05	126	Genomic	unknown
ss74984271	ILLUMINA\|ILMN_Human_1M_rs221789	fwd/B	C/T	gacagcgccgcccgcgcaccgccagcgacc	ccgccgcagagtcccaccgccacaggtacc	08/28/07	08/29/07	129	Genomic	unknown
ss78202258	HGSV\|Cor12878_SNV_20070510.chr7_99916172	fwd/B	C/T	gacagcgccgcccgcgcaccgccagcgacc	ccgccgcagagtcccaccgccacaggtacc	10/17/07	10/18/07	129	Genomic	unknown
ss114165711	1000GENOMES\|NA19240_2008_12_16_1637925_chr7_100109457	fwd/B	C/T	gacagcgccgcccgcgcaccgccagcgacc	ccgccgcagagtcccaccgccacaggtacc	12/18/08	12/18/08	130	Genomic	unknown

Fasta sequence (Legend)

 GTCCACAAAG CGTAGGGTGA GAACCTTGGG AGCGACTGGG CCCGTCTTTG CTCCCTCGGT
 GGGGTTTTGT CTCCTGGCTT CCCCCAAGTG CGAGGCAGTT GGTCTCGCCC AGCCGGGTCC
 TGGGCGCGGC GGCGGCAGCC GCGTCACTGG CGGGCGGGAT CCCTCCGCTC TGGGGAGGCA
 GCGCTGGCGG CGGGGCTGGG GCCACTGAGG AAATCCATCC GCGCCGCCGC CGCCGCCGCC
 GCCGCCGCCG CCGCCTCCGC CGCGGAGGAA GACAGCGCCG CCCGCGCACC GCCAGCGACC
 Y
 CCGCCGCAGA GTCCCACCGC CACAGGTACC TTCGCTGGCA AAAGGAGTCC TCTCGCCCCC
 CAGCCCCAAT TTCCCCCAGG GGAACCTCTC TTCCTTCGGT CTCCCGGGGC TGGCCTCCTG
 GGAGCGGACG TAACTCCCCA GACCTCCGCT CCCTTCCCCT CTTGCCCGGT CGCTCCCAAA
 CCCGGAAGGG GAACTGGGGA ACCCTCGCCC CCCACCGTGC GTGCGCTTCC CCGCACCATC
 AGCGAAGTTT TTGCCCGACC CCAGACCCCA GCCCAGCCCC GACTGCCTCT TGCTCCCTCG

GeneView

GeneView via analysis of contig annotation: GNB2 guanine nucleotide binding protein (G protein), beta polypeptide 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_007933->NM_005273

function

HuRef

NW_001839065->NM_005273

function

Celera

NW_923574->NM_005273

function

CRA_TCAGchr7v2

NT_079595->NM_005273

function

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


reference	NT_007933->NM_005273->	25505797	forward	147	5' UTR

HuRef	NW_001839065->NM_005273->	253019	reverse	144	5' UTR

Celera	NW_923574->NM_005273->	23541119	forward	144	5' UTR

CRA_TCAGchr7v2	NT_079595->NM_005273->	25532338	forward	147	5' UTR

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs221789 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_001839065.2	253019	94902225	minus	G	alt_assembly_8	HuRef	HuRef	view	300
7	NW_923574.1	23541119	95002082	plus	C	alt_assembly_1	Celera	Celera	view	300
7	NT_079595.2	25532338	99631126	plus	T	alt_assembly_2	CRA_TCAGchr7v2	CRA_TCAGchr7v2	view	300
7	NT_007933.14	25505797	100109457	plus	T	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_007933 AC009488 AF053356.1 BM802781

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank HTGS Finished:
NM_005273.2	AF053356.1

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss700492	SC_12_AA	African American	16	IG	0.875	0.125		1.000	0.938	0.062

	SC_12_C	European	14	IG	0.857	0.143		1.000	0.929	0.071

	SC_95_C	European	90	IG	0.733	0.244	0.022	1.000	0.856	0.144

Concordant Genotype	Total Sample	C/C	C/T	T/T
ss700492	111

RefSNP Genotype Summary	Total Individual	C/C	C/T	T/T
rs221789	113

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
429	ss700492	A/G	TSC-CSHL	SC_95_C	CEPH1416.01		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE
429	ss700492	G/G	TSC-CSHL	SC_12_C	CEPH1416.01		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE
430	ss700492	A/G	TSC-CSHL	SC_12_C	CEPH1416.02		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE
430	ss700492	G/G	TSC-CSHL	SC_95_C	CEPH1416.02		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE

Genotype data submitted for	119	samples from	113	individuals	Individual with multiple genotypes submission:	6

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 .