Reference SNP(refSNP) Cluster Report: rs732756

Reference SNP(refSNP) Cluster Report: rs732756

refSNP ID: rs732756
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:	C
Clinical Association:	unknown

HGVS Names
NM_153609.2:c.363+36A>G
NT_011520.11:g.16884935T>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss78403 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs732756 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
ss78403	TSC-CSHL\|TSC0022174	fwd/B	C/T	tcagaccccacccctctcttttcaccccca	attccctccctctcatcccccagatccttt	09/06/00	10/25/06	86	Genomic	95 %
ss3208069	YUSUKE\|IMS-JST068153	fwd/B	C/T	tcagaccccacccctctcttttcaccccca	attccctccctctcatcccccagatccttt	09/05/01	10/10/03	100	Genomic	unknown
ss21841227	SSAHASNP\|WGSA-200403-chr22.chr22.NT_011520.9_16803474	fwd/B	C/T	tcagaccccacccctctcttttcaccccca	attccctccctctcatcccccagatccttt	03/20/04	03/20/04	121	Genomic	unknown
ss44294560	ABI\|hCV2403469	fwd/B	C/T	tcagaccccacccctctcttttcaccccca	attccctccctctcatcccccagatccttt	07/18/05	11/03/06	126	Genomic	unknown
ss75042931	ILLUMINA\|ILMN_Human_1M_rs732756	fwd/B	C/T	tcagaccccacccctctcttttcaccccca	attccctccctctcatcccccagatccttt	08/28/07	08/29/07	129	Genomic	unknown
ss77326510	HGSV\|Cor12156_SNV_20070510.chr22_35818920	fwd/B	C/T	tcagaccccacccctctcttttcaccccca	attccctccctctcatcccccagatccttt	10/09/07	10/12/07	129	Genomic	unknown

Fasta sequence (Legend)

 TGCACTGTGG GACCTTTCCC AAGGTCATGC TCCACCCCTG GTAAGAGGCA TGATCAGGAT
 CTAATCCGAG TGCTATTGAC CCAAACATCC ACTAACTTTC CCATGACCCT CAACCTCATC
 TGCTTCCATG GTGCCTGGAG CAGGGCTGTG GTCCCTGTGA ATGCTCCAGA TGGGTTGACC
 AACTGGCTCC ATGTGATCAG ACCCCACCCC TCTCTTTTCA CCCCCA
 Y
 ATTCCCTCCC TCTCATCCCC CAGATCCTTT CCTACCATCT TCTGGGCTTT GGCGGTTTCA
 CTGCGGAAGG CACTAGATTC CCGGCGGGTA AGATCCTGGG AGAAGTGGCG ATTGAGTACA
 CGCAGACTGC CTGAGTACAC CTGGCTGACC ATCACCTCCG CCTTGTACCC TGCCCAGGAA
 GGAACCAGCA GGGTTAGTGG AGGAAGCAGG TGGGAAAGTC TCCTGTCTCT TCCATGCCTT
 CTCCTGCCAC CCACACCCTC AGCTCAGCCT CAGTGTCTTG GGTCTCCATG Gcaccatcaa
 tgtcatcatc atcatctttg tcactcccat tgtcatcatg gtcatcTAAA GTTTATTGGA
 TGACAAACTG GCTGCAAGGT ACCAGGGAGG TGAAAGGCTC CCAGATGGAT GGTGTCCTAC
 AGGTTCCCAG GGAGAGGCTG ACACAGTGAC C

GeneView

GeneView via analysis of contig annotation: TMPRSS6 transmembrane protease, serine 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_011520->NM_153609

function

HuRef

NW_001838745->NM_153609

function

Celera

NW_927628->NM_153609

function

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


reference	NT_011520->NM_153609->NP_705837	16884935	reverse	intron

HuRef	NW_001838745->NM_153609->NP_705837	15586651	reverse	intron

Celera	NW_927628->NM_153609->NP_705837	15561693	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs732756 maps exactly once on NCBI human chromosome 22

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
22	NW_001838745.1	15586651	20459518	plus	C	alt_assembly_8	HuRef	HuRef	view	226
22	NW_927628.1	15561693	21295499	plus	T	alt_assembly_1	Celera	Celera	view	226
22	NT_011520.11	16884935	35824366	plus	T	ref_assembly	reference	reference	view	226

NCBI Resource Links

Submitter-Referenced
GenBank
NT_011520 AL022314.1

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AL022314.1 NC_000022.9	AC008048.17

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss3208069	JBIC-allele		1498	AF					0.143	0.857

ss44294560	AoD_African_American		90	AF					0.070	0.930

	AoD_Caucasian		92	AF					0.200	0.800

	AoD_Chinese		90	AF					0.220	0.780

	AoD_Japanese		90	AF					0.110	0.890

ss78403	TSC_42_AA		82	AF					0.049	0.951

	TSC_42_C		80	AF					0.263	0.737

	TSC_42_A		76	AF					0.092	0.908

	HapMap-HCB	Asian	90	IG	0.089	0.356	0.556	0.584	0.267	0.733

	HapMap-JPT	Asian	88	IG	0.023	0.364	0.614	0.439	0.205	0.795

	HapMap-YRI	Sub-Saharan African	120	IG		0.167	0.833	0.527	0.083	0.917

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.288+/-0.247	180	150	0	0

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

DoubleHit found by: BCM_SSAHASNP, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .