Reference SNP(refSNP) Cluster Report: rs11657874

Reference SNP(refSNP) Cluster Report: rs11657874

refSNP ID: rs11657874
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	120/129
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
NM_006311.2:c.6392+1112G>T
NT_010718.15:g.15557065C>A

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss16757199 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs11657874 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
ss16757199	CSHL-HAPMAP\|CSHL-HuAA-200402.chr17.NT_010718.14_14800722		fwd/T	A/C	gcatgatctcgggttcaagtgattcttccg	ccaggttcaagcgattcttctgcctcagtg	02/17/04	03/04/04	120	Genomic			unknown
ss40846588	ABI\|hCV2546643		fwd/T	A/C	gcatgatctcgggttcaagtgattcttccg	ccaggttcaagcgattcttctgcctcagtg	07/17/05	07/17/05	126	Genomic			unknown

Fasta sequence (Legend)

 GCTTCTTATT TATATTCTTC TATCTGCTCT TTGCTCACTT TGATGGGTTG GTAGGTAGGC
 TGGAGAATCA CTTCTGCTAC AAATTTCTCT TTTTCAGGCT CTGAGCCATG GCTTCCATTA
 CTCTGGCTCA TGTGTCCTCT ATGTCTTCAG GTATTTGCCA GAATCTTTGA TCTGCCCATA
 TCTCAGTCTT GTTCTCAGCA TTCtttttat cttttttttt tttttttttt tttgagacgg
 agtctcgctc tgtcgcccag gctgcagtgc aatggcatga tctcgggttc aagtgattct
 tccg
 M
 ccaggttcaa gcgattcttc tgcctcagtg tcctgagtag ctgggattac aggcacctgc
 catcatgcct ggctaatttt ttttttgtat ttttgtagag acggggtttc accatgttgg
 ccaggttggt cttgagctcc tgacttcaga tgatgcaccc agcttggcct cccaaagtgc
 tgggattaca ggcgtgagcc accacgcccg gccTTCTCAG CATTCTTAAA TTTATTTCCC
 TTTGTGCTTG TTAACTATAA TTTAACATTT GCTAATATTT AGTCTACCAC TTTGAAGCAA
 GAATCCTGTG TCCACTTTAT TTTAACCAAA CACAGAATAT CAGGTAAGAA GATATGCTCT
 TTATCAGAGA GCCCTGGCAT ATAACATGTT TCCACTCATG ATGCCACTAT TGG

GeneView

GeneView via analysis of contig annotation: NCOR1 nuclear receptor co-repressor 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_010718->NM_006311

function

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


reference	NT_010718->NM_006311->NP_006302	15557065	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs11657874 maps exactly once on NCBI human chromosome 17

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
17	NW_001838406.2	649081	15826891	minus	G	alt_assembly_8	HuRef	HuRef	view	304
17	NW_926606.1	275015	15862734	plus	C	alt_assembly_1	Celera	Celera	view	304
17	NT_010718.15	15557065	15900441	plus	C	ref_assembly	reference	reference	view	304

NCBI Resource Links

Submitter-Referenced
GenBank
NT_010718

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail		Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	HWP	C
ss16757199	HapMap-CEU	European	108	IG	1.000		1.000

	HapMap-HCB	Asian	90	IG	1.000		1.000

	HapMap-JPT	Asian	90	IG	1.000		1.000

	HapMap-YRI	Sub-Saharan African	118	IG	1.000		1.000

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
		270	210	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 .