Reference SNP(refSNP) Cluster Report: rs3827555

Reference SNP(refSNP) Cluster Report: rs3827555

refSNP ID: rs3827555
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	107/129
Map to Genome Build:	36.3

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

HGVS Names
NT_029928.12:g.428814G>C

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44417721 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3827555 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
ss5014045	YUSUKE\|IMS-JST188970	fwd/B	C/G	cccgcccgctgcgcgcgcatccccgccccc	gggcgatctgtcagagcacctcgcgagcgt	08/12/02	10/10/03	107	Genomic	unknown
ss14167197	BCM_SSAHASNP\|chr3.NT_029928.11_428814	rev/T	C/G	acgctcgcgaggtgctctgacagatcgccc	gggggcggggatgcgcgcgcagcgggcggg	11/05/03	11/22/03	119	Genomic	unknown
ss28460971	KYUGEN\|QH05793	fwd/	C/G	cccgcccgctgcgcgcgcatccccgccccc	gggcgatctgtcagagcacctcgcgagcgt	07/07/04	05/13/05	123	Genomic	unknown
ss44417721	ABI\|hCV26292714	rev/	C/G	acgctcgcgaggtgctctgacagatcgccc	gggggcggggatgcgcgcgcagcgggcggg	07/18/05	07/18/05	126	Genomic	unknown
ss52974511	RSG_UW\|TFRC-001854	fwd/	C/G	cccgcccgctgcgcgcgcatccccgccccc	gggcgatctgtcagagcacctcgcgagcgt	06/06/06	12/16/06	127	Genomic	unknown
ss78249417	HGSV\|Cor12878_SNV_20070510.chr3_197297390	rev/	C/G	acgctcgcgaggtgctctgacagatcgccc	gggggcggggatgcgcgcgcagcgggcggg	10/17/07	10/18/07	129	Genomic	unknown
ss83022934	HGSV\|Cor19240_SNV_20070510.chr3_197297390	rev/	C/G	acgctcgcgaggtgctctgacagatcgccc	gggggcggggatgcgcgcgcagcgggcggg	11/30/07	12/04/07	130	Genomic	unknown

Fasta sequence (Legend)

 AGTTACCTAA CATTCCATCC TGCACGTACA TTTCAAGGCA CTGCCGCAGT GCAATATCCA
 ACATTTAAGC GTCAACGCCA ACAGATTGGA CCTAGCACTG CAGGGACTGG AGGTTGGTCA
 AGGTCAGGCG GAGGCTGCCA GGCTACCAGG GTGGAGGAAG GCGCCGAGGC AGAGGCCAGT
 GCGCCCATCG CGCGGCTCCT CGGGGCACCT GCTGCCTTGG CGCCTTTTCC CTTGGCCTTC
 GCCTCGCCCG CAGCGCCCTC CGCATAGGGC CCCGCCCGCT GCGCGCGCAT CCCCGCCCCC
 S
 GGGCGATCTG TCAGAGCACC TCGCGAGCGT ACGTGCCTCA GGAAGTGACG CACAGCCCCC
 CTGGGGGCCG GGGGCGGGGC CAGGCTATAA ACCGCCGGTT AGGGGCCGCC ATCCCCTCAG
 AGCGTCGGGA TATCGGGTGG CGGCTCGGGA CGGAGGACGC GCTAGTGTGA GTGCGGGCTT
 CTAGAACTAC ACCGACCCTC GTGTCCTCCC TTCATCCTGC GGGGCTGGCT GGAGCGGCCG
 CTCCGGTGCT GTCCAGCAGC CATAGGGAGC CGCACGGGGA GCGGGAAAGC GGTCGCGGCC

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	428814	reverse	5' near gene

HuRef	NW_001838889->NM_003234->NP_003225	141174	reverse	5' near gene

Celera	NW_921873->NM_003234->NP_003225	75005	reverse	5' near gene

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs3827555 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	141174	193109423	minus	C	alt_assembly_8	HuRef	HuRef	view	300
3	NW_921873.1	75005	194393525	minus	G	alt_assembly_1	Celera	Celera	view	300
3	NT_029928.12	428814	197293477	minus	G	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_029928.11

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/G	G/G	HWP	C	G
ss52974511	MCL_HISP-PANEL		84	IG	0.429	0.357	0.214	0.150	0.607	0.393

	MCL_AD-PANEL		42	IG	0.381	0.476	0.143	1.000	0.619	0.381

	MCL_ASIAN-PANEL		94	IG	0.702	0.298		0.251	0.851	0.149

	MCL_CEPH-PANEL		94	IG	0.149	0.596	0.255	0.200	0.447	0.553

	MCL_YORUB-PANEL		46	IG	0.391	0.478	0.130	1.000	0.630	0.370

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.464+/-0.129	190	190	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

UNKNOWN

YES

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Revised: May 25, 2006 1:38 PM .