Reference SNP(refSNP) Cluster Report: rs17093552

Reference SNP(refSNP) Cluster Report: rs17093552

refSNP ID: rs17093552
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	123/129
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_001191.2:c.375+14839G>T
NM_138578.1:c.564+14650G>T
NT_028392.5:g.490900C>A

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss23550826 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs17093552 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
ss23550826	PERLEGEN\|afd0395318		fwd/T	A/C	ttcccacaatgccatgtttaatcattcaaa	ccatgtcaagcacctactgtgtgccaggca	08/10/04	09/13/04	123	Genomic			unknown

Fasta sequence (Legend)

 CTTGGGCAAG AGGCTTGAGG CCACAGAGCA AACAAGGAGT GAGTGGGGCC ATCCTGGAAA
 AACTCCAGAG TTCCCACAAT GCCATGTT
 TAATCATTCA AA
 M
 CCATGTCAAG CA
 CCTACTGTGT GCCAGGCATG CTCCTACCCA CTTTAAATAC TTAACTCATT AAGTCTTCCA
 CTCAGTCAAC AAACAAGGAG GACCCTGG

GeneView

GeneView via analysis of contig annotation: BCL2L1 BCL2-like 1

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_028392->NM_001191

function

reference

NT_028392->NM_138578

function

HuRef

NW_001838664->NM_001191

function

HuRef

NW_001838664->NM_138578

function

Celera

NW_927339->NM_001191

function

Celera

NW_927339->NM_138578

function

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


reference	NT_028392->NM_001191->NP_001182	490900	reverse	intron

reference	NT_028392->NM_138578->NP_612815	490900	reverse	intron

HuRef	NW_001838664->NM_001191->NP_001182	4596050	forward	intron

HuRef	NW_001838664->NM_138578->NP_612815	4596050	forward	intron

Celera	NW_927339->NM_001191->NP_001182	554268	reverse	intron

Celera	NW_927339->NM_138578->NP_612815	554268	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs17093552 maps exactly once on NCBI human chromosome 20

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
20	NW_927339.1	554268	27051159	plus	C	alt_assembly_1	Celera	Celera	view	100
20	NW_001838664.2	4596050	27083940	minus	G	alt_assembly_8	HuRef	HuRef	view	100
20	NT_028392.5	490900	29758469	plus	C	ref_assembly	reference	reference	view	100

NCBI Resource Links

Submitter-Referenced
GenBank
NC_000020.6

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AL160175.5 NC_000020.9	AC023459.2

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/C	C/C	HWP	A	C
ss23550826	AFD_EUR_PANEL	European	48	IG		1.000			1.000

	AFD_AFR_PANEL	African American	46	IG	0.087	0.913	1.000	0.043	0.957

	AFD_CHN_PANEL	Asian	48	IG		1.000			1.000

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.028+/-0.115	71	50	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 .