Reference SNP(refSNP) Cluster Report: rs672607

Reference SNP(refSNP) Cluster Report: rs672607

refSNP ID: rs672607
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	83/129
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_004326.2:c.-477-23230A>G
NT_034400.4:g.593957A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss87806003 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs672607 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
ss846021	SC_JCM\|AL359207.2_5208	fwd/B	C/T	ccttcccccaaacaaaagaccaaaaaacaa	cttcggttcacactttagaaggatgaaatt	07/27/00	04/07/04	83	Genomic	unknown
ss964557	KWOK\|OVLP-000804-478803	fwd/B	C/T	ccttcccccaaacaaaagaccaaaaaacaa	cttcggttcacactttagaaggatgaaatt	09/01/00	10/25/06	86	Genomic	99 %
ss2025881	KWOK\|OVLP-000925-639784	fwd/B	C/T	ccttcccccaaacaaaagaccaaaaaacaa	cttcggttcacactttagaaggatgaaatt	10/06/00	10/10/03	87	Genomic	99 %
ss9887449	BCM_SSAHASNP\|chr1.NT_034400.2_616575	rev/T	A/G	aatttcatccttctaaagtgtgaaccgaag	ttgttttttggtcttttgtttgggggaagg	06/27/03	10/10/03	116	Genomic	unknown
ss11414315	WI_SSAHASNP\|chr1.NT_034400.2_616575	rev/T	A/G	aatttcatccttctaaagtgtgaaccgaag	ttgttttttggtcttttgtttgggggaagg	07/03/03	10/10/03	116	Genomic	unknown
ss20541658	SSAHASNP\|WGSA-200403-chr1.chr1.NT_034400.2_616575	rev/T	A/G	aatttcatccttctaaagtgtgaaccgaag	ttgttttttggtcttttgtttgggggaagg	03/18/04	03/18/04	121	Genomic	unknown
ss23836800	PERLEGEN\|afd1102762	rev/T	A/G	aatttcatccttctaaagtgtgaaccgaag	ttgttttttggtcttttgtttgggggaagg	08/10/04	09/13/04	123	Genomic	unknown
ss78219219	HGSV\|Cor12878_SNV_20070510.chr1_144278156	rev/T	A/G	aatttcatccttctaaagtgtgaaccgaag	ttgttttttggtcttttgtttgggggaagg	10/17/07	10/18/07	129	Genomic	unknown
ss85082561	HGSV\|Cor18517_SNV_20070510.chr1_144278156	rev/T	A/G	aatttcatccttctaaagtgtgaaccgaag	ttgttttttggtcttttgtttgggggaagg	12/06/07	12/08/07	130	Genomic	unknown
ss87806003	BCMHGSC_JDW\|JWB-0122020	rev/T	A/G	aatttcatccttctaaagtgtgaaccgaag	ttgttttttggtcttttgtttgggggaagg	02/26/08	02/26/08	129	Genomic	unknown

Fasta sequence (Legend)

 AGGCAATAGA AAGTCGCCAG CGTCTAAAAT TCATGCAAGA TCACCACAGG AAGAAAAAAA
 AGTTCTGATC AAAAGCAGCT GAGACCTGGA ATCTACAACT GGCCCTACAC TGAATGTATC
 CAGAAAAAGA AGCATGAGAT TAAAGAGCTG CCGTAGGTCC TGTGCACAGT GTGGCTTGGG
 GACTCACAGG GTTTCCTTTT TCCTACCCTA CAGCAACCCA CCTTCCCCCA AACAAAAGAC
 CAAAAAACAA
 Y
 CTTCGGTTCA CACTTTAGAA GGATGAAATT CTACAGCTAG CACTTGCTTC TTTTGTTTTA
 TTATCGAAGA AGTATGACTT CTCTCTTCCA AGTGTTCATA GCCACTTACA CCTTGATGCA
 TTTTTCTAGA AGCTGAGAGT GACAGGAATG AGGATGAGGA ATTTAAGAAA ACAGAGGGTT
 CCCTTAAGCG GAGTTCAGCT ATTTCACAGT TTGGTCTAGA AACTGACCTA CACACAATTA
 GCGTATAGCT

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	593957	forward	intron

HuRef	NW_001838511->NM_004326->NP_004317	582752	forward	intron

Celera	NW_924906->NM_004326->NP_004317	347077	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs672607 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	582752	120466914	minus	G	alt_assembly_8	HuRef	HuRef	view	200
1	NW_924906.1	347077	121930684	plus	C	alt_assembly_1	Celera	Celera	view	200
1	NT_034400.4	593957	145519964	minus	A	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_034400 AC025709 AL359207.2

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AL359207.7 NC_000001.9	AC025709.3

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss23836800	AFD_EUR_PANEL	European	48	IG	0.958	0.042		1.000	0.979	0.021

	AFD_AFR_PANEL	African American	44	IG	0.682	0.227	0.091	0.200	0.795	0.205

	AFD_CHN_PANEL	Asian	48	IG	0.500	0.417	0.083	1.000	0.708	0.292

ss846021	CEPH		184	AF					0.980	0.020

	HapMap-CEU	European	120	IG	0.967	0.033		1.000	0.983	0.017

	HapMap-HCB	Asian	90	IG	0.511	0.422	0.067	0.752	0.722	0.278

	HapMap-JPT	Asian	88	IG	0.227	0.545	0.227	0.584	0.500	0.500

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

ss964557	TSC_42_AA		84	AF					0.750	0.250

	TSC_42_C		84	AF					1.000

	TSC_42_A		84	AF					0.500	0.500

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.357+/-0.226	332	260	9	0

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: PERLEGEN

DoubleHit found by: BCM_SSAHASNP

UNKNOWN

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Revised: May 25, 2006 1:38 PM .