Reference SNP(refSNP) Cluster Report: rs836484

Reference SNP(refSNP) Cluster Report: rs836484

refSNP ID: rs836484
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	86/129
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_006908.4:c.36-657G>T
NM_018890.3:c.36-657G>T
NM_198829.1:c.-97-657G>T
NT_007819.16:g.5915144G>T

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss1164216 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs836484 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
ss1164216	KWOK\|OVLP-000804-515942	fwd/T	A/C	ggtctcgaactcctgacctcaagtgatccg	ccacctggacctcccaaagtgctgggatta	09/02/00	10/10/03	86	Genomic	99 %
ss2468179	SC_JCM\|AC009412.4_24713	rev/B	G/T	taatcccagcactttgggaggtccaggtgg	cggatcacttgaggtcaggagttcgagacc	11/03/00	10/10/03	92	Genomic	unknown
ss48292149	EGP_SNPS\|RAC1-013461	rev/B	G/T	taatcccagcactttgggaggtccaggtgg	cggatcacttgaggtcaggagttcgagacc	08/12/05	11/03/06	126	Genomic	unknown

Fasta sequence (Legend)

 ACTCAAGAGA AACAAGATTT TAAAACTTCA CGTCTCTTCT GTGAACATCT GTAGAGCCTC
 TCATCAAGAA TCTTAAGTTT GATCCTGAAG ATATTTTCTT tttttctttt ttttcttttt
 tttttttttt gagaccgagt ctcgtgctgt cgccccagct ggagtgcagt gcagaggcac
 catcttggct cactgcaacc tctgcctccc aggttcaagc gattctcctg cctcagcctc
 ccaagtagct gggattacag ctgtccacca ccacgcctgg ataatttttt tgtattttta
 gtagagatgg gttttcgcca tgttggccag gctggtctcg aactcctgac ctcaagtgat
 ccg
 M
 ccacctggac ctcccaaagt gctgggatta caggctggag ccaccacacc cagccTAAAG
 GTATTTTAAT TAACACTAAT ATACAAACAC AGCCTTCCTC TTTAAGTAAC TTATTCTGCT
 GCCTTAAGTG GGACAGCTCA AAATCCCACC ACAT

GeneView

GeneView via analysis of contig annotation: RAC1 ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1)

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_007819->NM_006908

function

reference

NT_007819->NM_018890

function

reference

NT_007819->NM_198829

function

HuRef

NW_001839003->NM_006908

function

HuRef

NW_001839003->NM_018890

function

HuRef

NW_001839003->NM_198829

function

Celera

NW_923217->NM_006908

function

Celera

NW_923217->NM_018890

function

Celera

NW_923217->NM_198829

function

CRA_TCAGchr7v2

NT_079592->NM_006908

function

CRA_TCAGchr7v2

NT_079592->NM_018890

function

CRA_TCAGchr7v2

NT_079592->NM_198829

function

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


reference	NT_007819->NM_006908->NP_008839	5915144	forward	intron

reference	NT_007819->NM_018890->NP_061485	5915144	forward	intron

reference	NT_007819->NM_198829->NP_942126	5915144	forward	intron

HuRef	NW_001839003->NM_006908->NP_008839	142519	forward	intron

HuRef	NW_001839003->NM_018890->NP_061485	142519	forward	intron

HuRef	NW_001839003->NM_198829->NP_942126	142519	forward	intron

Celera	NW_923217->NM_006908->NP_008839	351936	reverse	intron

Celera	NW_923217->NM_018890->NP_061485	351936	reverse	intron

Celera	NW_923217->NM_198829->NP_942126	351936	reverse	intron

CRA_TCAGchr7v2	NT_079592->NM_006908->NP_008839	6422544	forward	intron

CRA_TCAGchr7v2	NT_079592->NM_018890->NP_061485	6422544	forward	intron

CRA_TCAGchr7v2	NT_079592->NM_198829->NP_942126	6422544	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs836484 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_001839003.1	142519	6299294	minus	G	alt_assembly_8	HuRef	HuRef	view	363
7	NW_923217.1	351936	6308945	plus	C	alt_assembly_1	Celera	Celera	view	363
7	NT_007819.16	5915144	6392711	minus	G	ref_assembly	reference	reference	view	363
7	NT_079592.2	6422544	6472544	minus	G	alt_assembly_2	CRA_TCAGchr7v2	CRA_TCAGchr7v2	view	363

NCBI Resource Links

Submitter-Referenced
GenBank
DQ165078 AC072052 AC072052.1

dbSNP Blast Analysis
GenBank HTGS Finished:
AC009412.6 NC_000007.12

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/C	C/C	HWP	A	C
ss48292149	EGP_YORUB-PANEL	Sub-Saharan African	22	AF	0.091	0.909	1.000	0.045	0.955

	EGP_HISP-PANEL	Hispanic	32	AF	0.125	0.875	1.000	0.062	0.938

	EGP_CEPH-PANEL	European	34	AF	0.059	0.941	1.000	0.029	0.971

	EGP_AD-PANEL	African American	22	AF	0.182	0.818	0.752	0.091	0.909

	EGP_ASIAN-PANEL	Asian	36	AF		1.000			1.000

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.079+/-0.182	95	95	0	0

Validation Summary:

Validation status	Marker displays Mendelian segregation	PCR results confirmed in multiple reactions	Homozygotes detected in individual genotype data
	UNKNOWN	UNKNOWN	YES

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Revised: May 25, 2006 1:38 PM .