Reference SNP(refSNP) Cluster Report: rs6659237

Reference SNP(refSNP) Cluster Report: rs6659237

refSNP ID: rs6659237
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:	C/G
Ancestral Allele:	C
Clinical Association:	unknown

HGVS Names
NM_004326.2:c.-478+12681G>C
NT_034400.4:g.566742G>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44000455 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs6659237 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
ss9814007	BCM_SSAHASNP\|chr1.NT_034400.2_589360	fwd/B	C/G	ggatttatctgtaatgagaaactgaaaaga	aaggacattttaattttgggtaaagggaaa	06/27/03	10/10/03	116	Genomic	unknown
ss20454379	SSAHASNP\|WGSA-200403-chr1.chr1.NT_034400.2_589360	fwd/B	C/G	ggatttatctgtaatgagaaactgaaaaga	aaggacattttaattttgggtaaagggaaa	03/18/04	03/18/04	121	Genomic	unknown
ss23147741	PERLEGEN\|afd1102813	fwd/B	C/G	ggatttatctgtaatgagaaactgaaaaga	aaggacattttaattttgggtaaagggaaa	08/10/04	10/26/06	123	Genomic	unknown
ss44000455	ABI\|hCV29195834	rev/	C/G	tttccctttacccaaaattaaaatgtcctt	tcttttcagtttctcattacagataaatcc	07/18/05	11/03/06	126	Genomic	unknown
ss65782928	ILLUMINA\|Human1-rs6659237	fwd/B	C/G	ggatttatctgtaatgagaaactgaaaaga	aaggacattttaattttgggtaaagggaaa	10/10/06	10/10/06	127	Genomic	unknown
ss77387476	HGSV\|Cor12156_SNV_20070510.chr1_144250941	fwd/	C/G	ggatttatctgtaatgagaaactgaaaaga	aaggacattttaattttgggtaaagggaaa	10/09/07	10/12/07	129	Genomic	unknown
ss87805929	BCMHGSC_JDW\|JWB-0122002	fwd/	C/G	ggatttatctgtaatgagaaactgaaaaga	aaggacattttaattttgggtaaagggaaa	02/26/08	02/26/08	129	Genomic	unknown

Fasta sequence (Legend)

 TGTGCACCAG CAGTCAGAAG AATGAATGAG ATATAATAGG CTGTATTAAC TTTGAGAATG
 GGATAAAGAA TAATGCAGAA AATAATATAG TGTGCATAAT TTGCCATTGA CTATTTCTGT
 AATTACAATA AAACATTTTA ATGATATACA CTGATGTTAC GATTCACCTT AAAATCAGAA
 ATCAGCATTG GGTCCTTTCA TTTCAAAGAA AACAAAGCAG AAATACAAAG GTTCCAGGGA
 AGAACAACAG ACAGTCTCAA AGACATACAG GGATTTATCT GTAATGAGAA ACTGAAAAGA
 S
 AAGGACATTT TAATTTTGGG TAAAGGGAAA GATGACATTG TATAAATTTA TTTAAAATTA
 ACGAAAATTT CAGAAAATTG CTGGAGCTGG CTTCTGTTTA TCCTTAGTAA TGGAGGTCAG
 AGATAGGCAG GATAATTGGA ATCCTTGATA ATCTCCAATC CTCATTTTAG CTATTAGTTG
 CAGCATCCTG TCCTACCAGT AGTTCTAACA AATGAAAAAA TATAATACCA GACATGACAG
 CTCAGGGTTT GTGAAGTGAA CAGCTCATGA GAAAGGCAGT CTGGGCTATT GAGAAGTCCA

GeneView

GeneView via analysis of contig annotation: BCL9 B-cell CLL/lymphoma 9

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_034400->NM_004326

function

HuRef

NW_001838511->NM_004326

function

Celera

NW_924906->NM_004326

function

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


reference	NT_034400->NM_004326->NP_004317	566742	forward	intron

HuRef	NW_001838511->NM_004326->NP_004317	555543	forward	intron

Celera	NW_924906->NM_004326->NP_004317	374286	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs6659237 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_001838511.1	555543	120439705	plus	C	alt_assembly_8	HuRef	HuRef	view	300
1	NW_924906.1	374286	121957893	minus	G	alt_assembly_1	Celera	Celera	view	300
1	NT_034400.4	566742	145492749	plus	G	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_034400

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AL590667.7 NC_000001.9	AC025709.3

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/G	G/G	HWP	C	G
ss23147741	AFD_EUR_PANEL	European	46	IG	0.913	0.087		1.000	0.957	0.043

	AFD_AFR_PANEL	African American	42	IG	0.095	0.286	0.619	0.343	0.238	0.762

	AFD_CHN_PANEL	Asian	48	IG	1.000				1.000

ss44000455	HapMap-CEU	European	118	IG	1.000				1.000

	HapMap-HCB	Asian	90	IG	1.000				1.000

	HapMap-JPT	Asian	88	IG	1.000				1.000

	HapMap-YRI	Sub-Saharan African	120	IG	0.083	0.417	0.500	1.000	0.292	0.708

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.338+/-0.234	332	260	9	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 .