Reference SNP(refSNP) Cluster Report: rs6763092

Reference SNP(refSNP) Cluster Report: rs6763092

refSNP ID: rs6763092
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	116/129
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_003234.1:c.-24+678T>C
NT_029928.12:g.427758A>G

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss52974522 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs6763092 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
ss10013656	BCM_SSAHASNP\|chr3.NT_029928.10_427758	fwd/T	A/G	tgacacaatcggcctctccggcgcccatca	tccagcacagccctctgaccacaccgctaa	06/27/03	10/10/03	116	Genomic	unknown
ss46539763	PERLEGEN\|PS00794277	fwd/T	A/G	tgacacaatcggcctctccggcgcccatca	tccagcacagccctctgaccacaccgctaa	08/01/05	08/01/05	126	Genomic	unknown
ss52974522	RSG_UW\|TFRC-002925	rev/B	C/T	ttagcggtgtggtcagagggctgtgctgga	tgatgggcgccggagaggccgattgtgtca	06/06/06	12/16/06	127	Genomic	unknown
ss92429905	BCMHGSC_JDW\|JWB-1722001	fwd/T	A/G	tgacacaatcggcctctccggcgcccatca	tccagcacagccctctgaccacaccgctaa	02/26/08	03/03/08	129	Genomic	unknown

Fasta sequence (Legend)

 CACAGTAAGC TTAGCATATA AGCATGGGGT AGCCAAATAC AATTTCCTAC TTTAATCCTC
 TTATCAACGG GGAAGAAAAT GGAAAAAGCT GCAGAATCCA GTCCCCCGGG TAAGTGAGGT
 CTCTACAAGC AGTAAGCAGA GGGAAAGCGT TATCCGAAAA GAGCCGAATC AGAATGTATT
 TTCTTACCCA CCCTCCCAAC CTTAAAAGAA CTGTCCAGCA GAATGTGACA CAATCGGCCT
 CTCCGGCGCC CATCA
 R
 TCCAGCACAG CCCTCTGACC ACACCGCTAA TCTCCAAGTA TCTTTCACAA ATAAGTCACT
 CCTATGGCTC CCGTCTTGTA GTGAGAACTG CTAGCAATAT TCTTAATGTG AACACCTGCG
 GCGTTCAGTC GGATTCTGCC TTGAGAAAAC AGAATCCACA CACAAGGCGA ACAGGCAGAG
 CATGGCAAGA TCAGGTTGTA CCAGAGCCGA AGGGTAAGTT TACAGAAACC CGTATCTAAT
 TAATGCCTGT AACAC

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	Function


reference	NT_029928->NM_003234->NP_003225	427758	reverse	intron

HuRef	NW_001838889->NM_003234->NP_003225	140118	reverse	intron

Celera	NW_921873->NM_003234->NP_003225	73949	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs6763092 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	140118	193108367	plus	A	alt_assembly_8	HuRef	HuRef	view	255
3	NW_921873.1	73949	194392469	plus	A	alt_assembly_1	Celera	Celera	view	255
3	NT_029928.12	427758	197292421	plus	A	ref_assembly	reference	reference	view	255

NCBI Resource Links

Submitter-Referenced
GenBank
NT_029928

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss52974522	MCL_HISP-PANEL		94	IG	0.766	0.213	0.021	1.000	0.872	0.128

	MCL_AD-PANEL		46	IG	0.913	0.087		1.000	0.957	0.043

	MCL_ASIAN-PANEL		94	IG	0.638	0.340	0.021	0.527	0.809	0.191

	MCL_CEPH-PANEL		94	IG	0.809	0.191		0.479	0.904	0.096

	MCL_YORUB-PANEL		48	IG	0.958	0.042		1.000	0.979	0.021

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.198+/-0.245	190	190	0	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 .