Reference SNP(refSNP) Cluster Report: rs6545

Reference SNP(refSNP) Cluster Report: rs6545

refSNP ID: rs6545
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	52/129
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_015554.1:c.*2760C>T
NT_010194.16:g.40354662C>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss2957924 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs6545 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
ss8208	CGAP-GAI\|47651	rev/T	A/G	cagctttacaaaggactacccttcagaagg	catcctgtaaacactttattgcatatttaa	08/23/99	04/07/04	52	cDNA	99 %
ss1543005	LEE\|839353	fwd/B	C/T	ttaaatatgcaataaagtgtttacaggatg	ccttctgaagggtagtcctttgtaaagctg	09/13/00	10/10/03	86	cDNA	unknown
ss2957924	TSC-CSHL\|TSC1067462	rev/T	A/G	cagctttacaaaggactacccttcagaagg	catcctgtaaacactttattgcatatttaa	01/29/01	04/07/04	94	Genomic	unknown
ss4429420	LEE\|e839353	fwd/B	C/T	ttaaatatgcaataaagtgtttacaggatg	ccttctgaagggtagtcctttgtaaagctg	04/26/02	10/10/03	106	cDNA	unknown
ss5656461	SC_JCM\|NT_010222.12_1110369	fwd/B	C/T	ttaaatatgcaataaagtgtttacaggatg	ccttctgaagggtagtcctttgtaaagctg	01/10/03	10/10/03	111	Genomic	unknown
ss15995621	SC_SNP\|NT_010194.16_40354662	fwd/B	C/T	ttaaatatgcaataaagtgtttacaggatg	ccttctgaagggtagtcctttgtaaagctg	11/18/03	11/22/03	120	Genomic	unknown
ss16259673	CGAP-GAI\|1519492	fwd/B	C/T	ttaaatatgcaataaagtgtttacaggatg	ccttctgaagggtagtcctttgtaaagctg	11/18/03	11/22/03	120	cDNA	unknown
ss16670648	CSHL-HAPMAP\|CSHL-HuAA-200402.chr15.NT_010194.16_40354662	fwd/B	C/T	ttaaatatgcaataaagtgtttacaggatg	ccttctgaagggtagtcctttgtaaagctg	02/17/04	03/04/04	120	Genomic	unknown
ss23991301	PERLEGEN\|afd2927848	fwd/B	C/T	ttaaatatgcaataaagtgtttacaggatg	ccttctgaagggtagtcctttgtaaagctg	08/10/04	09/13/04	123	Genomic	unknown
ss43797567	ABI\|hCV9708954	fwd/B	C/T	ttaaatatgcaataaagtgtttacaggatg	ccttctgaagggtagtcctttgtaaagctg	07/18/05	07/18/05	126	Genomic	unknown
ss90201779	BCMHGSC_JDW\|JWB-0874178	fwd/B	C/T	ttaaatatgcaataaagtgtttacaggatg	ccttctgaagggtagtcctttgtaaagctg	02/26/08	02/29/08	129	Genomic	unknown

Fasta sequence (Legend)

 TTTTTAAATT TTATTGTTTT ATTTCTTTAA GTTTTTCTTT GCTTTAAGAT TATAGGTATT
 AGGTTTGTTT TTGTTTTTCC ACTTATCTTG AGTTCACTTT GATGTTAAAT CTATTGCTAC
 TTCAGTTGTA AAACCAGCCA AAAGTTTCTG GATGAAGGTC AAGTTTGACC TTTTAGGAGT
 TATTGTACAT AAAGGCTTCA TCCACGAACC ATCCAGCGCA CAGAAGCAAG TGCAAAAATG
 ACACAAGCAC AACTCTCCAG ACGTGGCTCC TTCTCCTTTC TCAGTGCAGA CTCTCACTGA
 AAGCTGCTAT TTTCATCCTC CTTGTGGTTG CTTTTCTTGT TTCTCTTCCA TTGTACATGT
 GGGTTATATA CCATATGTTA AATATGCAAT AAAGTGTTTA CAGGATG
 Y
 CCTTCTGAAG GGTAGTCCTT TGTAAAGCTG TACAGACTTT GCAGTTTAAG CACAATGTGC
 ACATGTTAGT TTTATATACA GCAAAACTTG ATTTTTTGCA GATGGAAAGG TATTTTGTTT
 CTATACAAAG TAAATGGATT GTTTGTGCTT AATGTAAAGC CGCTTTATAA AACTGTAAAA
 TAAAGTTTTT TTCTTAAAAA

GeneView

GeneView via analysis of contig annotation: GLCE glucuronic acid epimerase

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_010194->NM_015554

function

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


reference	NT_010194->NM_015554->	40354662	forward	4842	3' UTR

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs6545 maps exactly once on NCBI human chromosome 15

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
15	NW_001838218.2	4793785	46397225	minus	G	alt_assembly_8	HuRef	HuRef	view	407
15	NW_925884.1	25551410	46453593	plus	T	alt_assembly_1	Celera	Celera	view	407
15	NT_010194.16	40354662	67351397	plus	C	ref_assembly	reference	reference	view	407

NCBI Resource Links

Submitter-Referenced
GenBank
W87398 AB020643 AI332411 Hs.183006

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank mRNA:
NM_015554.1	AB020643.1

UniGene Cluster ID
183006

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	A	C	G	T
ss23991301	AFD_EUR_PANEL	European	48	IG	0.167	0.375	0.458	0.403		0.354		0.646

	AFD_AFR_PANEL	African American	46	IG	0.652	0.304	0.043	1.000		0.804		0.196

	AFD_CHN_PANEL	Asian	48	IG	0.125	0.500	0.375	0.752		0.375		0.625

ss2957924	CEPH		184	AF						0.490		0.510

	HapMap-CEU	European	120	IG	0.050	0.450	0.500	0.343		0.275		0.725

	HapMap-HCB	Asian	88	IG	0.182	0.636	0.182	0.100		0.500		0.500

	HapMap-JPT	Asian	88	IG	0.227	0.523	0.250	1.000		0.489		0.511

	HapMap-YRI	Sub-Saharan African	120	IG	0.900	0.100		0.752		0.950		0.050

	CHMJ	Asian	74	IG					0.514		0.486

ss8208	POOLED_CEPH		188	AF						0.513		0.487

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.495+/-0.048	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: ILLUMINA

DoubleHit found by: BCM_SSAHASNP, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .