Reference SNP(refSNP) Cluster Report: rs785395

Reference SNP(refSNP) Cluster Report: rs785395

refSNP ID: rs785395
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	86/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	C/T
Ancestral Allele:	T
Clinical Association:	unknown

HGVS Names
NM_152730.4:c.2900-1189G>A
NT_025741.14:g.25553231C>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss1983115 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs785395 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
ss941157	KWOK\|OVLP-000804-349017	fwd/B	C/T	tcaggtgagagcatttcaattctatgtgta	aaacttctttctttataaatcacttaatac	09/01/00	10/10/03	86	Genomic	99 %
ss1983115	KWOK\|OVLP-000925-23593	fwd/B	C/T	tcaggtgagagcatttcaattctatgtgta	aaacttctttctttataaatcacttaatac	10/06/00	10/10/03	87	Genomic	99 %
ss2529726	SC_JCM\|AC026593.2_122644	fwd/B	C/T	tcaggtgagagcatttcaattctatgtgta	aaacttctttctttataaatcacttaatac	11/03/00	10/10/03	89	Genomic	unknown
ss10346176	BCM_SSAHASNP\|chr6.NT_025741.12_25553231	fwd/B	C/T	tcaggtgagagcatttcaattctatgtgta	aaacttctttctttataaatcacttaatac	06/29/03	10/10/03	116	Genomic	unknown
ss23511072	PERLEGEN\|afd0339877	fwd/B	C/T	tcaggtgagagcatttcaattctatgtgta	aaacttctttctttataaatcacttaatac	08/10/04	09/13/04	123	Genomic	unknown

Fasta sequence (Legend)

 AAAAGTATAA GAATCCAATT GTCAAGGGTC AGAAAGGACA TCAGTATTGT AAGCTATTTA
 TGTTTATAGT TGCTTAGACT GGTTCTATCT TCATGTGTAG ACACAAATTT TGCCATATTT
 ATAAAAATGT TTCAAGTCTC TCTTCTATGA ATTAACAAAT TAAATAGCCC TCAGGTGAGA
 GCATTTCAAT TCTATGTGTA
 Y
 AAACTTCTTT CTTTATAAAT CACTTAATAC TGTCTCGAGA TTATAAATTT TACAGAAAGA
 ACAATGTCTT GATGAAGTTC AGATATAATC ATTCTTAGTT TAATGATAAT AATTTAAGAT
 GCAAGATATA CATTAGTAAC AAAGGTTATA CAGAAAGACA CTTTTATAAC TCCAAACATA
 ATGTAATTAT TTTTACTTTG

GeneView

GeneView via analysis of contig annotation: C6orf170 chromosome 6 open reading frame 170

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_025741->NM_152730

function

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


reference	NT_025741->NM_152730->NP_689943	25553231	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs785395 maps exactly once on NCBI human chromosome 6

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
6	NW_001838990.2	36091661	119031237	minus	G	alt_assembly_8	HuRef	HuRef	view	200
6	NT_025741.14	25553231	121490495	plus	C	ref_assembly	reference	reference	view	200
6	NW_923184.1	54261802	122193198	plus	C	alt_assembly_1	Celera	Celera	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_025741 AL365508 AL365508.12 AL365508.3

dbSNP Blast Analysis
GenBank HTGS Finished:
AL365508.19

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss23511072	AFD_EUR_PANEL	European	48	IG	0.792	0.208		0.584	0.896	0.104

	AFD_AFR_PANEL	African American	40	IG	0.200	0.300	0.500	0.150	0.350	0.650

	AFD_CHN_PANEL	Asian	48	IG	0.625	0.292	0.083	0.403	0.771	0.229

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.427+/-0.177	71	50	0	0

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: PERLEGEN

DoubleHit found by: BCM_SSAHASNP

UNKNOWN

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Revised: May 25, 2006 1:38 PM .