Reference SNP(refSNP) Cluster Report: rs984654

Reference SNP(refSNP) Cluster Report: rs984654

refSNP ID: rs984654
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:	T
Clinical Association:	unknown

HGVS Names
NM_005228.3:c.88+57098T>C
NM_201282.1:c.88+57098T>C
NM_201283.1:c.88+57098T>C
NM_201284.1:c.88+57098T>C
NT_033968.5:g.4733525T>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss1439146 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs984654 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
ss1439146	TSC-CSHL\|TSC0301964	fwd/B	C/T	tgttaggcatattaactttaatgattacaa	ttttaggacactctgtggcctagacttaga	09/06/00	04/07/04	86	Genomic	95 %
ss6845328	WI_SSAHASNP\|NT_033968.2_4668969	fwd/B	C/T	tgttaggcatattaactttaatgattacaa	ttttaggacactctgtggcctagacttaga	02/12/03	10/10/03	111	Genomic	unknown
ss22645696	SSAHASNP\|WGSA-200403-chr7.chr7.NT_033968.5_4733525	fwd/B	C/T	tgttaggcatattaactttaatgattacaa	ttttaggacactctgtggcctagacttaga	03/21/04	03/21/04	121	Genomic	unknown
ss24464435	PERLEGEN\|afd0565930	fwd/B	C/T	tgttaggcatattaactttaatgattacaa	ttttaggacactctgtggcctagacttaga	08/10/04	09/13/04	123	Genomic	unknown
ss24778610	EGP_SNPS\|EGFR-059287	fwd/B	C/T	tgttaggcatattaactttaatgattacaa	ttttaggacactctgtggcctagacttaga	06/04/04	08/05/04	126	Genomic	unknown
ss44823028	ABI\|hCV2678604	fwd/B	C/T	tgttaggcatattaactttaatgattacaa	ttttaggacactctgtggcctagacttaga	07/19/05	07/19/05	126	Genomic	unknown
ss66548285	ILLUMINA\|HumanHap300v1.1_rs984654	fwd/B	C/T	tgttaggcatattaactttaatgattacaa	ttttaggacactctgtggcctagacttaga	11/09/06	11/09/06	127	Genomic	unknown
ss67951545	ILLUMINA\|HumanHap550v1.1_rs984654	fwd/B	C/T	tgttaggcatattaactttaatgattacaa	ttttaggacactctgtggcctagacttaga	11/14/06	11/15/06	127	Genomic	unknown
ss68063331	ILLUMINA\|HumanHap650Yv1.0_rs984654	fwd/B	C/T	tgttaggcatattaactttaatgattacaa	ttttaggacactctgtggcctagacttaga	11/14/06	11/15/06	127	Genomic	unknown
ss71628156	ILLUMINA\|HumanHap650Yv3.0_rs984654	fwd/B	C/T	tgttaggcatattaactttaatgattacaa	ttttaggacactctgtggcctagacttaga	04/23/07	04/23/07	127	Genomic	unknown
ss75619594	ILLUMINA\|ILMN_Human_1M_rs984654	fwd/B	C/T	tgttaggcatattaactttaatgattacaa	ttttaggacactctgtggcctagacttaga	08/28/07	08/29/07	129	Genomic	unknown
ss78623384	HGSV\|Cor12878_SNV_20070510.chr7_54918365	fwd/B	C/T	tgttaggcatattaactttaatgattacaa	ttttaggacactctgtggcctagacttaga	10/17/07	10/20/07	129	Genomic	unknown
ss79305816	ILLUMINA\|HumanHap300v2.0_rs984654	fwd/B	C/T	tgttaggcatattaactttaatgattacaa	ttttaggacactctgtggcctagacttaga	04/18/07	11/18/07	130	Genomic	unknown
ss80868807	HGSV\|Cor18507_SNV_20070510.chr7_54918365	fwd/B	C/T	tgttaggcatattaactttaatgattacaa	ttttaggacactctgtggcctagacttaga	11/26/07	11/27/07	130	Genomic	unknown
ss83643309	KRIBB_YJKIM\|KHS508819	fwd/B	C/T	tgttaggcatattaactttaatgattacaa	ttttaggacactctgtggcctagacttaga	12/04/07	12/05/07	130	Genomic	unknown
ss83918772	HGSV\|Cor18555_SNV_20070510.chr7_54918365	fwd/B	C/T	tgttaggcatattaactttaatgattacaa	ttttaggacactctgtggcctagacttaga	11/27/07	12/06/07	130	Genomic	unknown
ss98293449	ILLUMINA\|HumanHap550v3.0__rs984654	rev/T	A/G	tctaagtctaggccacagagtgtcctaaaa	ttgtaatcattaaagttaatatgcctaaca	04/20/07	03/31/08	130	Genomic	unknown

Fasta sequence (Legend)

 ATTGTCCATT AGTAATTTGT TATAAATGAG ACATTTGGTA TTAAAGCATC TCTTTGGGAT
 ACTGGTATGG TTTATTATAA CATTCTGTTA GTAGTGTTGT ACAAGCTTGA GATGTATTAA
 TACGAAATCC AAGCTGCATG AGGGCTTTAT TTTTCAAGCC TACACCTTGC TGAAATTCTG
 AATTAAAATA TGATTCTCAG TACAAATGAA TAAATCAACA GAAATGGTAA CGCATGTCAA
 ATATTCTTAA AACCCAAGAA AGCCTTGTAA CTTCCTTCAA TCTAATGGGA AATGCAGGCA
 AATACAAGAC TGATGTCCTT GAGTTTTATT ATCAAGACTC AAGGGCACCA GTAAAATCTA
 GTTTCATTGG TTGGAAAAAA AATCCTGATA AGCACTGTTA GGCATATTAA CTTTAATGAT
 TACAA
 Y
 TTTTAGGACA CTCTGTGGCC TAGACTTAGA AACACAACTA ATGTCCAGAA AAAGATTCCT
 CTTTTTATTC CATCATCTGA TAGGCCTATT TTTACACATA CACACCAACC AAAAGTAGCC
 AAGCAAACAA AACAACATAC TCACACCCCT TCGCCTATTA TCATCTAGGT GATTTTCAA

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_201283

function

reference

NT_033968->NM_201284

function

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


reference	NT_033968->NM_005228->NP_005219	4733525	forward	intron

reference	NT_033968->NM_201282->NP_958439	4733525	forward	intron

reference	NT_033968->NM_201283->NP_958440	4733525	forward	intron

reference	NT_033968->NM_201284->NP_958441	4733525	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs984654 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	4728918	54982736	plus	C	alt_assembly_8	HuRef	HuRef	view	425
7	NT_033968.5	4733525	55111650	plus	T	ref_assembly	reference	reference	view	425
7	NT_079592.2	55099951	55149951	plus	T	alt_assembly_2	CRA_TCAGchr7v2	CRA_TCAGchr7v2	view	425
7	NW_923284.1	833894	55249778	plus	C	alt_assembly_1	Celera	Celera	view	425

NCBI Resource Links

Submitter-Referenced
GenBank
NT_033968

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail							Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	C/C	C/T	G/G	T/T	HWP	C	T
ss1439146	SC_12_A	Asian	22	AF	0.091				0.909		0.001	0.910	0.090

	SC_12_AA	African American	24	AF	0.917	0.083					0.001	0.040	0.960

	SC_12_C	European	24	AF	0.857	0.143					0.010	0.170	0.830

	SC_95_C	European	92	IG			0.065	0.283		0.652	0.371	0.207	0.793

	HapMap-CEU	European	120	IG			0.150	0.283		0.567	0.020	0.292	0.708

	HapMap-HCB	Asian	90	IG			0.756	0.244			0.371	0.878	0.122

	HapMap-JPT	Asian	90	IG			0.778	0.200		0.022		0.878	0.122

	HapMap-YRI	Sub-Saharan African	120	IG			0.017	0.017		0.967	0.001	0.025	0.975

ss24464435	AFD_EUR_PANEL	European	48	IG			0.125	0.375		0.500	0.584	0.312	0.688

	AFD_AFR_PANEL	African American	44	IG			0.045	0.182		0.773	0.294	0.136	0.864

	AFD_CHN_PANEL	Asian	46	IG			0.696	0.304			0.403	0.848	0.152

ss24778610	PDR90	Global	176	IG			0.216	0.330		0.455	0.005	0.381	0.619

Concordant Genotype	Total Sample	A/A	A/G	C/C	C/T	G/G	T/T
ss1439146	338	12	1	81	71	10	155
ss24464435	65			20	19		24
ss24778610	90			19	29		40

RefSNP Genotype Summary	Total Individual	A/A	A/G	C/C	C/T	G/G	T/T
rs984654	491	12	1	119	114	10	211

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
114	ss1439146	A/A	TSC-CSHL	SC_12_C	CEPH1331.12		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE	3477455
114	ss1439146	T/T	TSC-CSHL	SC_95_C	CEPH1331.12		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE	3477455
229	ss1439146	A/A	TSC-CSHL	SC_12_C	CEPH1347.02		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE	3477455
229	ss1439146	T/T	TSC-CSHL	SC_95_C	CEPH1347.02		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE	3477455
229	ss1439146	T/T	CSHL-HAPMAP	HapMap-CEU	NA10859	CEPH1347.02	r23_ch7_CEU_perlegen:genotyping_1.0.0	3477455
230	ss1439146	A/G	TSC-CSHL	SC_12_C	CEPH1347.03		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE	3477455
230	ss1439146	T/T	TSC-CSHL	SC_95_C	CEPH1347.03		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE	3477455
231	ss1439146	A/G	TSC-CSHL	SC_12_C	CEPH1347.04		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE	3477455
231	ss1439146	T/T	TSC-CSHL	SC_95_C	CEPH1347.04		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE	3477455
429	ss1439146	A/A	TSC-CSHL	SC_12_C	CEPH1416.01		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE	3477455
429	ss1439146	C/T	TSC-CSHL	SC_95_C	CEPH1416.01		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE	3477455
429	ss1439146	C/T	CSHL-HAPMAP	HapMap-CEU	NA10835	CEPH1416.01	r23_ch7_CEU_perlegen:genotyping_1.0.0	3477455
430	ss1439146	A/G	TSC-CSHL	SC_12_C	CEPH1416.02		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE	3477455
430	ss1439146	C/T	TSC-CSHL	SC_95_C	CEPH1416.02		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE	3477455
840	ss1439146	A/A	TSC-CSHL	SC_12_AA	NA17109		TSC-SANGER-SC_12_AA-Sep-18-2003-GENOTYPE	3477455
840	ss24464435	T/T	PERLEGEN	AFD_AFR_PANEL	NA17109		71_IND_CHR_7
842	ss1439146	A/A	TSC-CSHL	SC_12_AA	NA17111		TSC-SANGER-SC_12_AA-Sep-18-2003-GENOTYPE	3477455
842	ss24464435	T/T	PERLEGEN	AFD_AFR_PANEL	NA17111		71_IND_CHR_7
845	ss1439146	A/A	TSC-CSHL	SC_12_AA	NA17114		TSC-SANGER-SC_12_AA-Sep-18-2003-GENOTYPE	3477455
845	ss24464435	T/T	PERLEGEN	AFD_AFR_PANEL	NA17114		71_IND_CHR_7
846	ss1439146	A/A	TSC-CSHL	SC_12_AA	NA17115		TSC-SANGER-SC_12_AA-Sep-18-2003-GENOTYPE	3477455
846	ss24464435	T/T	PERLEGEN	AFD_AFR_PANEL	NA17115		71_IND_CHR_7
865	ss1439146	A/A	TSC-CSHL	SC_12_AA	NA17134		TSC-SANGER-SC_12_AA-Sep-18-2003-GENOTYPE	3477455
865	ss24464435	T/T	PERLEGEN	AFD_AFR_PANEL	NA17134		71_IND_CHR_7
867	ss1439146	A/G	TSC-CSHL	SC_12_AA	NA17136		TSC-SANGER-SC_12_AA-Sep-18-2003-GENOTYPE	3477455
867	ss24464435	C/T	PERLEGEN	AFD_AFR_PANEL	NA17136		71_IND_CHR_7

Genotype data submitted for	562	samples from	491	individuals	Individual with multiple genotypes submission:	63

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: PERLEGEN

DoubleHit found by: BCM_SSAHASNP, NCBI

UNKNOWN

YES

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Revised: May 25, 2006 1:38 PM .