Reference SNP(refSNP) Cluster Report: rs17788373

Reference SNP(refSNP) Cluster Report: rs17788373

refSNP ID: rs17788373
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	123/129
Map to Genome Build:	36.3

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

HGVS Names
NM_003234.1:c.*2223C>T
NT_029928.12:g.396324G>A

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss52974763 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs17788373 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
ss24608617	PERLEGEN\|afd0794337	fwd/T	A/G	tgaacatgccacatgctttcatttaagtac	tgtgcgtaacacccgaaccaggaatctcag	08/10/04	09/13/04	123	Genomic	unknown
ss52974763	RSG_UW\|TFRC-034365	rev/B	C/T	ctgagattcctggttcgggtgttacgcaca	gtacttaaatgaaagcatgtggcatgttca	06/06/06	12/16/06	127	Genomic	unknown
ss76551504	AFFY\|AFFY_6_1M_SNP_A-8412514	rev/B	C/T	tcgggtgttacgcaca	gtacttaaatgaaagc	08/28/07	08/30/07	129	Genomic	unknown

Fasta sequence (Legend)

 ACTCATTCAT TTTATCCTTT ACCTCCAAAA GGCCCATCTC CTTAACGAGA AGACATCTCA
 AGACCAGGAG CTTGTCACTA GTCTGATATT TCATTCAGGA ATATTGAGCC TGTTAGCACG
 TACTGGCTTG ATAGGAAGTA ACTCAACCCT AACTGTAGAA AAGGGTTTTC TGAAGAGACT
 CACTGCTGCA AAATGCATGC CCTGTATTCA TATTGTGTTA TACGATGAAC ATGCCACATG
 CTTTCATTTA AGTAC
 R
 TGTGCGTAAC ACCCGAACCA GGAATCTCAG CTATGACCTT TTCACTTAGC TACGCTAAAT
 GTCAGTCCAA GATAAAAGAG GAGATTAAAG ATAAAACTGA AGATTAAAGA GACTGTGAGT
 AGTGACACAT TCAAGTGAGG CTGTAAATCT AGGTAAGTGA CACTAAGAAC CTGAAGAGAC
 CCTATGAACT TTTCCCTAGG AGGCCGTTTC CAACTGCCCT ATGACAAACA GCTGATCATC
 ACGTTTATAA TGATG

GeneView

GeneView via analysis of contig annotation: TFRC transferrin receptor (p90, CD71)

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_029928->NM_003234

function

HuRef

NW_001838889->NM_003234

function

Celera

NW_921873->NM_003234

function

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


reference	NT_029928->NM_003234->	396324	reverse	4769	3' UTR

HuRef	NW_001838889->NM_003234->	109103	reverse	4769	3' UTR

Celera	NW_921873->NM_003234->	42520	reverse	4769	3' UTR

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs17788373 maps exactly once on NCBI human chromosome 3

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
3	NW_001838889.1	109103	193077352	plus	G	alt_assembly_8	HuRef	HuRef	view	255
3	NW_921873.1	42520	194361040	plus	G	alt_assembly_1	Celera	Celera	view	255
3	NT_029928.12	396324	197260987	plus	G	ref_assembly	reference	reference	view	255

NCBI Resource Links

Submitter-Referenced
GenBank
NC_000003.6

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank HTGS Finished:	GenBank HTGS Draft:	GenBank mRNA:
NM_003234.1	AC024937.21 NC_000003.10	AC016953.13	BC001188.1 BX537966.1 X01060.1

UniGene Cluster ID
529618

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss24608617	AFD_EUR_PANEL	European	48	IG		0.083	0.917	1.000	0.042	0.958

	AFD_AFR_PANEL	African American	42	IG		0.048	0.952	1.000	0.024	0.976

	AFD_CHN_PANEL	Asian	44	IG			1.000			1.000

ss52974763	HapMap-CEU	European	116	IG	0.828	0.172			0.914	0.086

	HapMap-HCB	Asian	90	IG	1.000				1.000

	HapMap-JPT	Asian	90	IG	1.000				1.000

	HapMap-YRI	Sub-Saharan African	120	IG	0.933	0.067			0.967	0.033

	MCL_HISP-PANEL		90	IG		0.044	0.956	1.000	0.022	0.978

	MCL_AD-PANEL		48	IG		0.042	0.958	1.000	0.021	0.979

	MCL_ASIAN-PANEL		90	IG			1.000			1.000

	MCL_CEPH-PANEL		86	IG		0.186	0.814	0.527	0.093	0.907

	MCL_YORUB-PANEL		48	IG			1.000			1.000

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.496+/-0.044	522	450	9	0

Validation Summary:

Validation status	Marker displays Mendelian segregation	PCR results confirmed in multiple reactions	Homozygotes detected in individual genotype data
	UNKNOWN	UNKNOWN	YES

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Revised: May 25, 2006 1:38 PM .