Reference SNP(refSNP) Cluster Report: rs180039

Reference SNP(refSNP) Cluster Report: rs180039

refSNP ID: rs180039
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	79/129
Map to Genome Build:	36.3

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

HGVS Names
NM_173551.3:c.2394+247C>G
NT_008470.18:g.8834269G>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss17257093 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs180039 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
ss239291	KWOK\|OVLP-000621-326295	fwd/T	C/G	gcactgctctctctagaaaagtttcttcct	tcctgaaaacattttttttgttgtgtgtga	06/30/00	10/10/03	79	Genomic	94 %
ss608368	SC_JCM\|AL353782.3_136882	fwd/T	C/G	gcactgctctctctagaaaagtttcttcct	tcctgaaaacattttttttgttgtgtgtga	07/12/00	10/10/03	80	Genomic	unknown
ss676544	SC_JCM\|AC007800.3_102162	fwd/T	C/G	gcactgctctctctagaaaagtttcttcct	tcctgaaaacattttttttgttgtgtgtga	07/27/00	10/10/03	85	Genomic	unknown
ss12935374	SC_SNP\|NT_008470.15_3339483	rev/B	C/G	tcacacacaacaaaaaaaatgttttcagga	aggaagaaacttttctagagagagcagtgc	10/21/03	10/31/03	119	Genomic	unknown
ss17257093	CSHL-HAPMAP\|CSHL-HuAA-200402.chr9.NT_008470.16_3174592	rev/B	C/G	tcacacacaacaaaaaaaatgttttcagga	aggaagaaacttttctagagagagcagtgc	02/17/04	05/17/04	120	Genomic	unknown
ss24042168	PERLEGEN\|afd2465624	rev/B	C/G	tcacacacaacaaaaaaaatgttttcagga	aggaagaaacttttctagagagagcagtgc	08/10/04	09/13/04	123	Genomic	unknown
ss43945681	ABI\|hCV1386247	rev/	C/G	tcacacacaacaaaaaaaatgttttcagga	aggaagaaacttttctagagagagcagtgc	07/18/05	07/18/05	126	Genomic	unknown

Fasta sequence (Legend)

 AAAAATTTGT CTAAATGTGT AGGTTTTCAT TTTGCAAGCC TAGATTGATC TCTTGCACTG
 AGACAGTTGA GGAAATAGAA TTCGTGCTTA GCGGGATTAG TTCAGTTTGT TATTGTGAAA
 TCCTGGGGAC TTATGGCTTG CTTTGTTATG ATAGAATTTT GTAATTTTGA GCACTGCTCT
 CTCTAGAAAA GTTTCTTCCT
 S
 TCCTGAAAAC ATTTTTTTTG TTGTGTGTGA TTGACTGGCA GACTTATAGG CTTAAAGTGA
 GCTAATAGTA AACCCTAAGG AACCTGTGTT ATGTGTCTGG ATCTAGGGTC AGTGGTGGTC
 TGAGAGAGTT GCTATGTGTT TAAAAGCATT CAGATTCACA TTAAAAAAAG AATACTGTTC
 TGcagtttgg cacttcctca aaatattaaa tatagagtta ccgtgtgacc cagcagtcct
 actcctaggt atattcccaa gagaaatgaa gacatgtgtc cacacagaaa cttgtacaca
 aatgcttgta gcaacattat tcatgaaagc caaactgtgg atacgaccca aatgtccatc
 gactaatgaa tggataaata aaatatgcct gtgccatgga atgttatttg gccatgaaaa
 gaatgaaata ctggcacatg ctgcaacgtg gatgaacctg aacacatctt gctaagtgga
 agaaaccagt cacaaaaggc

GeneView

GeneView via analysis of contig annotation: ANKS6 ankyrin repeat and sterile alpha motif domain containing 6

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_008470->NM_173551

function

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


reference	NT_008470->NM_173551->NP_775822	8834269	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs180039 maps exactly once on NCBI human chromosome 9

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
9	NW_001839236.2	18267294	71112447	plus	C	alt_assembly_8	HuRef	HuRef	view	200
9	NW_924539.1	1736674	72026970	minus	G	alt_assembly_1	Celera	Celera	view	200
9	NT_008470.18	8834269	100552885	minus	G	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_008470 AC007800 AL353782

dbSNP Blast Analysis
GenBank HTGS Finished:
AL353782.23

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/G	G/G	HWP	C	G
ss17257093	HapMap-CEU	European	120	IG	0.883	0.117		0.655	0.942	0.058

	HapMap-YRI	Sub-Saharan African	120	IG	0.533	0.450	0.017	0.100	0.758	0.242

ss24042168	AFD_EUR_PANEL	European	48	IG	0.833	0.167		0.752	0.917	0.083

	AFD_AFR_PANEL	African American	38	IG	0.895	0.105		1.000	0.947	0.053

	AFD_CHN_PANEL	Asian	48	IG	0.542	0.417	0.042	0.655	0.750	0.250

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.247+/-0.250	242	170	9	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 .