Reference SNP(refSNP) Cluster Report: rs681063

Reference SNP(refSNP) Cluster Report: rs681063

refSNP ID: rs681063
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:	A/G
Ancestral Allele:	Not available
Clinical Association:	unknown

HGVS Names
NM_005554.3:c.332G>A
NP_005545.1:p.G111D
NT_029419.11:g.15029946C>T
NT_029419.11:g.15029947C>T
XM_001718439.1:c.1261-87C>T

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss854642 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs681063 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
ss854642	SC_JCM\|AC055736.9_1438		fwd/T	A/G	ggtttcggtggtggagcggcattggctttg	tctgggtggtggagccggccttgctggtgg	07/27/00	10/10/03	83	Genomic			unknown
ss24811400	SEQUENOM\|sqnm198436		rev/B	C/T	ccaccagcaaggccggctccaccacccaga	caaagccaatgccggctccaccaccgaaac	06/18/04	08/05/04	123	cDNA			unknown

Fasta sequence (Legend)

 GTGGTGGCCT GGGTGGTGCA TGTGGAGGAG CTGGCTTTGG CAGCCGCAGT CTGTATGGCC
 TGGGGGGCTC CAAGAGGATC TCCATTGGAG GGGGCAGCTG TGCCATCAGT GGCGGCTATG
 GCAGCAGAGC CGGAGGCAGC TATGGCTTTG GTGGCGCCGG GAGTGGATTT GGTTTCGGTG
 GTGGAGCGGC ATTGGCTTTG
 R
 TCTGGGTGGT GGAGCCGGCC TTGCTGGTGG CTTTGGGGGC CCTGGCTTCC CTGTGTGCCC
 CCCTGGAGGC ATCCAAGAGG TCACGTCACC AGAGTCTCCT GACTCCCCTC AACCTGCAAA
 TCGATCCCAC CATCCAGCGG GTGCGGGCTG AGGAGCGTGA ACAGATCAAG ACCCTCAACA
 ACAAGTTTGC CTCCTTCATC

GeneView

GeneView via analysis of contig annotation: LOC100129218 hypothetical protein LOC100129218

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

GeneView via analysis of contig annotation: KRT6A keratin 6A

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_029419->XM_001718439

function

HuRef

NW_001838059->XM_001715563

function

Celera

NW_925395->XM_001717349

function

reference

NT_029419->NM_005554

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	mRNA pos	Function	dbSNP allele	Protein residue	Codon pos	Amino acid pos


reference	NT_029419->XM_001718439->XP_001718491	15029947	forward		intron

HuRef	NW_001838059->XM_001715563->XP_001715615	156712	forward		intron

Celera	NW_925395->XM_001717349->XP_001717401	156714	forward		intron

reference	NT_029419->NM_005554->NP_005545	15029947	reverse	541	missense	A	Asp [D]	2	111
					contig reference	G	Gly [G]	2	111

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs681063 maps exactly once on NCBI human chromosome 12

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
12	NW_001838059.1	156712	49930552	minus	C	alt_assembly_8	HuRef	HuRef	view	200
12	NT_029419.11	15029947	51172908	minus	C	ref_assembly	reference	reference	view	200
12	NW_925395.1	156714	52532885	minus	C	alt_assembly_1	Celera	Celera	view	200

NCBI Resource Links

Submitter-Referenced
dbSTS	GenBank
sqnm198436	AC055736 AC027562 AC055715

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank mRNA:
NM_005554.3	AK290245.1 BC008807.2 BC014152.2 BC069269.1 BC125058.1 BC139753.1 BT006899.1

UniGene Cluster ID
367762

Population Diversity

	Sample Ascertainment				Genotypes	Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	HWP	A	G
ss24811400	CEPH		184	AF		0.160	0.840

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.269+/-0.249	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 .