Reference SNP(refSNP) Cluster Report: rs3892269

Reference SNP(refSNP) Cluster Report: rs3892269

refSNP ID: rs3892269
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	108/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	A/C
Ancestral Allele:	Not available
Clinical Association:	unknown

HGVS Names

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss1293689 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3892269 during BLAST analysis for the current build.

NCBI Assay ID	Handle\|Submitter ID	Validation Status	ss to rs Orientation /Strand	Alleles	5' Near Seq 30 bp	3' Near Seq 30 bp	Entry Date	Update Date	Build Added	Molecule Type	Freq Warning	Ancestral Allele	Success Rate
ss1293689	TSC-CSHL\|TSC0138363		fwd/T	A/C	gaaaggtggcttggagaagccagcagtctg	gaggctggggaggatggagagtggtttggg	06/14/01	04/07/04	108	Genomic			unknown

Fasta sequence (Legend)

 AGTATgcacc actacactcc agcctgggtg acaaagcaag attctgtctc gaaacaaaaa
 aaaaaagaGG GCCTCAGAGA GCCAGGGACC AGGGAACGAT ATGACGCAGT GTTCTGAGGA
 CAGAGAGAGG GAAGAATGGG GAGGGGAAGG AGTGGCACAT GGGGTTGAGC AGAGGAGAAA
 GTCAGAAAGG TGGCTTGGAG AAGCCAGCAG TCTG
 M
 GAGGCTGGGG AGGATGGAGA GTGGTTTGGG GTTTGGGGTC GGGGTCTAAC GTGATCAGTT
 GCAGAAGCAT TACACGGTGG CCTGGTTTCT TTACTCAGCC CCTGGGGTAG ATCCCAGCCC
 CCCGCGTAGG TCCCTTGGCT GCAAAAGGAA GAGGGAGTGT TTGGATGAAT CTGATGATGA
 GCCAGAGAAG GAGCTCGCCC CTGAGCCTGA GGAGACCTGG GTGGCGGAGA CGCTGTGTGG
 CCTCAAGATG AAGGCGAAGC GACGGCGAGT GTCGCTCGTG CTCCCTGAGT ACTACGAGGC
 CTTCAACAGG CTGCTTGGTA GGAGGACACC CCAGAGAGCA CCTCCAATCC TGTTCTTTCT
 AAAAAGAGGA AACTTCCAAT AACCACACTT TTCCAATGGG AATAATATGC CCCAGTGGGT
 GAGCTCTCCA TGCGGGAGGA CTCTGAAGTG ATCACTCATG AGGGACACTT AGGAGTCAAC
 AGAGGATTAG GTAGACTTGA TAAAGGTCGG TGCTTGGGAT AAGAAAGCTT GGTTTTGGgc
 caggcgctgt ggctcccgcc tgagatccca cacgttggga ggctgaggca agaaattgct
 tgaacttagg actttgaagc tgcagtgagc tatgactgca cc

GeneView

GeneView via analysis of contig annotation: tcag7.1017 similar to Williams Beuren syndrome chromosome region 19

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

HuRef

NW_001839065->NM_001004351

function

Celera

NW_923574->NM_001004351

function

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


HuRef	NW_001839065->NM_001004351->NP_001004351	609903	reverse	5' near gene

Celera	NW_923574->NM_001004351->NP_001004351	23180866	forward	5' near gene

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs3892269 was not linked to the human genome 36.3 because it aligned to more than 2 locations on the genome.

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
7	NT_079593.2	10525552	71830304	minus	G	alt_assembly_2	CRA_TCAGchr7v2	CRA_TCAGchr7v2	view	214
7	NT_079593.2	10553864	71858616	minus	G	alt_assembly_2	CRA_TCAGchr7v2	CRA_TCAGchr7v2	view	214
7	NT_007758.11	10530826	72135418	minus	G	ref_assembly	reference	reference	view	214
7	NT_007758.11	10558888	72163480	minus	G	ref_assembly	reference	reference	view	214
7	NT_079593.2	12356658	73661410	minus	G	alt_assembly_2	CRA_TCAGchr7v2	CRA_TCAGchr7v2	view	214
7	NT_007758.11	12361690	73966282	minus	G	ref_assembly	reference	reference	view	214
7	NT_079593.2	12725391	74030143	plus	C	alt_assembly_2	CRA_TCAGchr7v2	CRA_TCAGchr7v2	view	214
7	NT_079595.2	145619	74244407	plus	C	alt_assembly_2	CRA_TCAGchr7v2	CRA_TCAGchr7v2	view	214
7	NT_079595.2	173639	74272427	plus	C	alt_assembly_2	CRA_TCAGchr7v2	CRA_TCAGchr7v2	view	214
7	NT_079595.2	201662	74300450	plus	C	alt_assembly_2	CRA_TCAGchr7v2	CRA_TCAGchr7v2	view	214
7	NT_007758.11	12730423	74335015	plus	C	ref_assembly	reference	reference	view	214
7	NT_007933.14	145619	74749279	plus	C	ref_assembly	reference	reference	view	214
7	NT_007933.14	173639	74777299	plus	C	ref_assembly	reference	reference	view	214
7	NT_007933.14	201662	74805322	plus	C	ref_assembly	reference	reference	view	214
7	NT_079595.2	1893142	75991930	minus	G	alt_assembly_2	CRA_TCAGchr7v2	CRA_TCAGchr7v2	view	214
7	NT_007933.14	1893143	76496803	minus	G	ref_assembly	reference	reference	view	214
7	NW_001839065.2	609903	94545341	minus	T	alt_assembly_8	HuRef	HuRef	view	214
7	NW_923574.1	23180866	94641829	plus	A	alt_assembly_1	Celera	Celera	view	214
7	NT_079595.2	25173354	99272142	plus	A	alt_assembly_2	CRA_TCAGchr7v2	CRA_TCAGchr7v2	view	214
7	NT_007933.14	25146332	99749992	plus	A	ref_assembly	reference	reference	view	214

NCBI Resource Links

Submitter-Referenced

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail		Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/C	HWP	A	C
ss1293689	SC_12_A	Asian	24	IG	1.000	0.001	0.500	0.500

	SC_12_AA	African American	24	IG	1.000	0.001	0.500	0.500

	SC_12_C	European	14	IG	1.000	0.010	0.500	0.500

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.500+/-0	0	0	0	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 .