Reference SNP(refSNP) Cluster Report: rs247446

Reference SNP(refSNP) Cluster Report: rs247446

refSNP ID: rs247446
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:	A/G
Ancestral Allele:	A
Clinical Association:	unknown

HGVS Names
NM_145254.1:c.304+1326T>C
NT_010498.15:g.29098440A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss90446210 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs247446 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
ss319467	KWOK\|OVLP-000621-18231	fwd/T	A/G	atttatgtttacatctatacctaaaaaaag	aatacacaccaagatgtaaactgtggctat	06/30/00	10/10/03	79	Genomic	99 %
ss620862	SC_JCM\|AC026419.2_59087	rev/B	C/T	atagccacagtttacatcttggtgtgtatt	ctttttttaggtatagatgtaaacataaat	07/12/00	10/25/06	80	Genomic	unknown
ss1100776	KWOK\|OVLP-000804-193802	fwd/T	A/G	atttatgtttacatctatacctaaaaaaag	aatacacaccaagatgtaaactgtggctat	09/02/00	10/10/03	86	Genomic	99 %
ss1587306	KWOK\|OVLP-000925-213911	fwd/T	A/G	atttatgtttacatctatacctaaaaaaag	aatacacaccaagatgtaaactgtggctat	10/04/00	10/10/03	87	Genomic	99 %
ss24677804	PERLEGEN\|afd3189191	fwd/T	A/G	atttatgtttacatctatacctaaaaaaag	aatacacaccaagatgtaaactgtggctat	08/10/04	09/13/04	123	Genomic	unknown
ss75063966	ILLUMINA\|ILMN_Human_1M_rs247446	fwd/T	A/G	atttatgtttacatctatacctaaaaaaag	aatacacaccaagatgtaaactgtggctat	08/28/07	08/29/07	129	Genomic	unknown
ss90446210	BCMHGSC_JDW\|JWB-0966579	fwd/T	A/G	atttatgtttacatctatacctaaaaaaag	aatacacaccaagatgtaaactgtggctat	02/26/08	02/29/08	129	Genomic	unknown

Fasta sequence (Legend)

 TAGCAGCCAG TCATCCTGGG GCAGAGGGTC TCCAAAGCAG CAGTAGGTGA TACAGTTAGA
 ACACAGAGAA ACTAGGCCAC TTTCTCTCAA AAAAAAAAAA AAAAAACACC TCAAGTCAAA
 GACATAGAGG GCGATTTCTG CTTGATGCTA AGGTTTCAAT TCACAGTGAA AAAAAGTTAC
 AAATCAGTAG GAATATTACA TTTCTATATT ATAAAAATGT ATTTATGTTT ACATCTATAC
 CTAAAAAAAG
 R
 AATACACACC AAGATGTAAA CTGTGGCTAT TATTTAGGGA TGAGAAAATG GAGGATTTTA
 CATTTTAATT ACTTAGAATT TTCAGTTTAT ATAAAATACA CATTTATATT TATGCATGAG
 CTTTGAAATG ATTTAAACTT ATTGTTCTCA TTTCTGTAAC TGTTTCTTAT CCCATAAGCA
 AAAGCCATAA CAAACCAAAC GCCCCAAAAA CAAGCCTGAA AATAATTCAT AACATCATGT
 TACTCCAATT

GeneView

GeneView via analysis of contig annotation: TMEM170A transmembrane protein 170A

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_010498->NM_145254

function

HuRef

NW_001838327->NM_145254

function

Celera

NW_926528->NM_145254

function

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


reference	NT_010498->NM_145254->NP_660297	29098440	reverse	intron

HuRef	NW_001838327->NM_145254->NP_660297	1059179	reverse	intron

Celera	NW_926528->NM_145254->NP_660297	1018464	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs247446 maps exactly once on NCBI human chromosome 16

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
16	NW_926528.1	1018464	59778550	plus	A	alt_assembly_1	Celera	Celera	view	250
16	NW_001838327.1	1059179	61235716	plus	A	alt_assembly_8	HuRef	HuRef	view	250
16	NT_010498.15	29098440	74041742	plus	A	ref_assembly	reference	reference	view	250

NCBI Resource Links

Submitter-Referenced
GenBank
NC_000016.5 AC009105 AC009163 AC026419.2

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC009163.6 NC_000016.8	AC009105.7

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss24677804	AFD_EUR_PANEL	European	46	IG	0.870	0.130		0.752	0.935	0.065

	AFD_AFR_PANEL	African American	44	IG	1.000				1.000

	AFD_CHN_PANEL	Asian	46	IG	0.957	0.043		1.000	0.978	0.022

ss620862	HapMap-CEU	European	120	IG	0.917	0.067	0.017	0.025	0.950	0.050

	HapMap-HCB	Asian	88	IG	0.955	0.045		1.000	0.977	0.023

	HapMap-JPT	Asian	90	IG	0.800	0.200		0.479	0.900	0.100

	HapMap-YRI	Sub-Saharan African	120	IG	1.000				1.000

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.073+/-0.176	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: PERLEGEN

UNKNOWN

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Revised: May 25, 2006 1:38 PM .