Reference SNP(refSNP) Cluster Report: rs17290117

Reference SNP(refSNP) Cluster Report: rs17290117

refSNP ID: rs17290117
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:	C/T
Ancestral Allele:	C
Clinical Association:	unknown

HGVS Names
NM_005228.3:c.1722+68T>C
NM_201282.1:c.1722+68T>C
NM_201284.1:c.1722+68T>C
NT_033968.5:g.4820953T>C

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss24778867 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs17290117 during BLAST analysis for the current build.

NCBI Assay ID	Handle\|Submitter ID	Validation Status	ss to rs Orientation /Strand	Alleles	5' Near Seq 30 bp	3' Near Seq 30 bp	Entry Date	Update Date	Build Added	Molecule Type	Freq Warning	Ancestral Allele	Success Rate
ss24778867	EGP_SNPS\|EGFR-146716		fwd/B	C/T	ggaagggccttcacagaagccgaacagtga	gatggcccagggcatcctgtgtgggcagga	06/04/04	08/05/04	123	Genomic			unknown

Fasta sequence (Legend)

 CATTACCTCA AGTTATTTGG AATTTTGAAG AGGTGATTTG TGTTCCTGCA ATAATGTCTC
 AGGGGTGGGC TGACGGGTTT CCTCTTCCTC CTCTCAGTGA GCCAAGGGAG TTTGTGGAGA
 ACTCTGAGTG CATACAGTGC CACCCAGAGT GCCTGCCTCA GGCCATGAAC ATCACCTGCA
 CAGGACGGGT AAGAGCCCCT TGCTGCTATC CACGTCCATT TCATGGGAAG GGCCTTCACA
 GAAGCCGAAC AGTGA
 Y
 GATGGCCCAG GGCATCCTGT GTGGGCAGGA CGGCCATCAG AGCCACTTCC CAGAGGAGAC
 GGCAGGCGCT GACAGCGCTG TCCGGGCAGG GTGTCGGTGA CATTAGCACA CACATTAGCC
 TGCGATGAAC ATTCACTCTT TCTGCTGACA CCCCCAACCT TATCTAAGCT TATCAAATCC
 TCACATTTAA CGGAGGCTGT TTTCACCTGG TTTCCCCCAT CCCTGACCTA GTCAGCATTG
 CTTTATCGCT TTCAT

GeneView

GeneView via analysis of contig annotation: EGFR epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)

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_033968->NM_005228

function

reference

NT_033968->NM_201282

function

reference

NT_033968->NM_201284

function

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


reference	NT_033968->NM_005228->NP_005219	4820953	forward	intron

reference	NT_033968->NM_201282->NP_958439	4820953	forward	intron

reference	NT_033968->NM_201284->NP_958441	4820953	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs17290117 maps exactly once on NCBI human chromosome 7

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
7	NW_001839007.1	4816338	55070156	plus	T	alt_assembly_8	HuRef	HuRef	view	255
7	NT_033968.5	4820953	55199078	plus	T	ref_assembly	reference	reference	view	255
7	NT_079592.2	55187375	55237375	plus	T	alt_assembly_2	CRA_TCAGchr7v2	CRA_TCAGchr7v2	view	255
7	NW_923284.1	921319	55337203	plus	T	alt_assembly_1	Celera	Celera	view	255

NCBI Resource Links

Submitter-Referenced
GenBank
AY588246

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/T	T/T	HWP	C	T
ss24778867	PDR90	Global	178	IG	0.045	0.955	1.000	0.022	0.978

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.044+/-0.142	90	90	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 .