Reference SNP(refSNP) Cluster Report: rs267305

Reference SNP(refSNP) Cluster Report: rs267305

refSNP ID: rs267305
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:	A/C
Ancestral Allele:	C
Clinical Association:	unknown

HGVS Names
NM_005023.2:c.141-1939C>A
NT_034772.5:g.17005904G>T

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss2273237 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs267305 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
ss347920	KWOK\|OVLP-000621-106775	rev/B	G/T	gccatgatttggagggacaagagtaacaac	actttaggatctaatcacagtctataacac	06/30/00	10/10/03	79	Genomic	99 %
ss349052	KWOK\|OVLP-000621-109553	rev/B	G/T	gccatgatttggagggacaagagtaacaac	actttaggatctaatcacagtctataacac	06/30/00	10/10/03	85	Genomic	99 %
ss961242	KWOK\|OVLP-000804-461373	rev/B	G/T	gccatgatttggagggacaagagtaacaac	actttaggatctaatcacagtctataacac	09/01/00	10/10/03	86	Genomic	99 %
ss1034743	KWOK\|OVLP-000804-462928	rev/B	G/T	gccatgatttggagggacaagagtaacaac	actttaggatctaatcacagtctataacac	09/02/00	10/10/03	86	Genomic	97 %
ss2273237	TSC-CSHL\|TSC0687340	fwd/T	A/C	gtgttatagactgtgattagatcctaaagt	gttgttactcttgtccctccaaatcatggc	10/20/00	04/07/04	88	Genomic	95 %
ss3569776	SC_JCM\|AC008494.7_124460	rev/B	G/T	gccatgatttggagggacaagagtaacaac	actttaggatctaatcacagtctataacac	09/24/01	10/10/03	100	Genomic	unknown
ss4991974	YUSUKE\|IMS-JST164738	fwd/T	A/C	gtgttatagactgtgattagatcctaaagt	gttgttactcttgtccctccaaatcatggc	08/12/02	10/10/03	108	Genomic	unknown
ss65791534	ILLUMINA\|Human1-rs267305	fwd/T	A/C	gtgttatagactgtgattagatcctaaagt	gttgttactcttgtccctccaaatcatggc	10/10/06	10/10/06	127	Genomic	unknown
ss66274141	AFFY\|SNP_A-4304550	rev/B	G/T	ggacaagagtaacaac	actttaggatctaatc	10/27/06	08/14/07	127	Genomic	unknown
ss74866930	ILLUMINA\|ILMN_Human_1M_rs267305	fwd/T	A/C	gtgttatagactgtgattagatcctaaagt	gttgttactcttgtccctccaaatcatggc	08/28/07	08/29/07	129	Genomic	unknown
ss76418760	AFFY\|AFFY_6_1M_SNP_A-4304550	rev/B	G/T	ggacaagagtaacaac	actttaggatctaatc	08/28/07	08/30/07	129	Genomic	unknown

Fasta sequence (Legend)

 TTTTGTCTCT GTCTTCTTTT TGCCCTTTTC CTTAATAACG CTTTAATAAA CTGTATTAGT
 AGATGCTTAA TTGTACCTGA CTATAAATAT AATCATTTAC TTTATGTATT ATATCAAAAC
 CAAAAAACCC TGTTAGAGCT CTCCGGGAGG GTTAGATGTA GTATTGCAGG TCCTTTATTA
 GTTCAGTAAA TATTTGAGTG CATACAAACA AAGTGGACCT TCTCTCATGA GACATAATTA
 CCACCAAGGG CAGTGATTTT CACACTTTGT TGCTATTATG TAGAGGTTTT TCCCATGTCT
 AAAGGTTTAT TGTGTTTGGA GAAGCACATT CCTCTGGGGA AAATGGTTAC AACCAAGAGT
 CTATAGAAAA GGCCTGTAGT GTTATAGACT GTGATTAGAT CCTAAAGT
 M
 GTTGTTACTC TTGTCCCTCC AAATCATGGC AAAGACCAAG GATAATGGCT TCCATTTATT
 GCGTGCTTAT TGTGAGTAGG TAAGCACAAT TA

GeneView

GeneView via analysis of contig annotation: PGGT1B protein geranylgeranyltransferase type I, beta subunit

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_034772->NM_005023

function

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


reference	NT_034772->NM_005023->NP_005014	17005904	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs267305 maps exactly once on NCBI human chromosome 5

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
5	NW_001838952.2	24203444	109773264	plus	C	alt_assembly_8	HuRef	HuRef	view	408
5	NW_922751.1	15159581	110538410	minus	G	alt_assembly_1	Celera	Celera	view	408
5	NT_034772.5	17005904	114618790	minus	G	ref_assembly	reference	reference	view	408

NCBI Resource Links

Submitter-Referenced
GenBank
NT_023200.1 AC008585 AC020577 AC020577.2

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/C	C/C	HWP	A	C
ss2273237	AfAm	African American	40	IG	0.050	0.300	0.650	1.000	0.200	0.800

	Caucasian	European	38	IG		0.105	0.895	1.000	0.053	0.947

	Asian	Asian	40	IG	0.250	0.500	0.250	1.000	0.500	0.500

	CEPH	European	42	IG		0.048	0.952	1.000	0.024	0.976

	PDpanel	Global	40	IG		0.350	0.650	0.371	0.175	0.825

	HapMap-CEU	European	116	IG		0.069	0.931	1.000	0.034	0.966

	HapMap-HCB	Asian	90	IG	0.111	0.378	0.511		0.300	0.700

	HapMap-JPT	Asian	88	IG	0.091	0.455	0.455		0.318	0.682

	HapMap-YRI	Sub-Saharan African	118	IG	0.102	0.322	0.576	0.100	0.263	0.737

ss66274141	HapMap-CEU	European	118	GF		0.068	0.932		0.034	0.966

	HapMap-HCB	Asian	90	GF	0.111	0.378	0.511		0.300	0.700

	HapMap-JPT	Asian	90	GF	0.089	0.444	0.467		0.311	0.689

	HapMap-YRI	Sub-Saharan African	120	GF	0.100	0.333	0.567		0.267	0.733

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.335+/-0.235	369	308	269	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 .