Reference SNP(refSNP) Cluster Report: rs2980928

Reference SNP(refSNP) Cluster Report: rs2980928

refSNP ID: rs2980928
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	101/129
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_005218.3:c.62-2071T>C
NT_023736.16:g.6717829A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44893947 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2980928 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
ss4195275	SC_JCM\|AF298854.3_34472	fwd/B	C/T	cagcgtgggttggagtaggcatcctctaag	atctttccagcactgggagcctccagtgca	10/15/01	10/10/03	101	Genomic	unknown
ss7987372	IIPGA-WEISS-MARTINEZ\|IIPGA-DEFB1_7526	fwd/B	C/T	cagngtgggttggagtaggcatcctctaag	atctttccagcactgggagcctccagtgca	04/10/03	04/07/04	114	Genomic	unknown
ss14353882	WI_SSAHASNP\|chr8.NT_023736.16_6717829	rev/T	A/G	tgcactggaggctcccagtgctggaaagat	cttagaggatgcctactccaacccacactg	11/05/03	11/22/03	119	Genomic	unknown
ss17994334	CSHL-HAPMAP\|CSHL-HuCC-200402.chr8.NT_023736.16_6717829	rev/T	A/G	tgcactggaggctcccagtgctggaaagat	cttagaggatgcctactccaacccacactg	02/19/04	03/04/04	120	Genomic	unknown
ss22772628	SSAHASNP\|WGSA-200403-chr8.chr8.NT_023736.16_6717829	rev/T	A/G	tgcactggaggctcccagtgctggaaagat	cttagaggatgcctactccaacccacactg	03/21/04	03/21/04	121	Genomic	unknown
ss24374017	PERLEGEN\|afd1856320	rev/T	A/G	tgcactggaggctcccagtgctggaaagat	cttagaggatgcctactccaacccacactg	08/10/04	09/13/04	123	Genomic	unknown
ss44893947	ABI\|hCV15883919	rev/T	A/G	tgcactggaggctcccagtgctggaaagat	cttagaggatgcctactccaacccacgctg	07/19/05	07/19/05	126	Genomic	unknown

Fasta sequence (Legend)

 GGACCTTGTT CCTTCATCTG GGGAGAGGAT CACAGAAAGG TTGAATTAAT TGAGTTCCGA
 AGTCCATCCT GGCTCTAAAA AGCTACATCC ATATTAAATT TGGGCCTCCT CTGCTTACTC
 AGCATATATA TACCCAACCA TTTGATTACT GAGAAGAACA ATCAAGAACA AAGGTGTATA
 AACCTTCTCG ATTTCAAAGT GCTTTCAAAT TTATATGCTC AGTTGATCTC TCTAATAACA
 GATAATCACT TGGAGAGGTT CCATCTTTCG CAGCGTGGGT TGGAGTAGGC ATCCTCTAAG
 Y
 ATCTTTCCAG CACTGGGAGC CTCCAGTGCA GGGAGACTAA AGCAGAAAGT GGAGACTTTG
 GCAGAGTCTA GCTGGTCATG ATCTTACTTG AGGTCAACAT TATGGCGAGA TTATTAAAAC
 ATAGTACAAT CTCAGACAGC CTCATTAGGA ATCAGTCAGA GAAAAAGAAT ATAAGCTGGC
 AATCAAGAGA CTGTGTTTTG TATGAACAAA TGAGTGGCCT TGGCCCAAGA TGCTTCCCTG
 AGTACTGGGA TGGGAGAACC AGAGTGCCTC TCAATTCCCT TCCATCTCCA CAGCAACACA

GeneView

GeneView via analysis of contig annotation: DEFB1 defensin, beta 1

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_023736->NM_005218

function

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


reference	NT_023736->NM_005218->NP_005209	6717829	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs2980928 maps exactly once on NCBI human chromosome 8

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
8	NW_001839109.2	328147	6510563	plus	T	alt_assembly_8	HuRef	HuRef	view	300
8	NW_923840.1	4526748	6707845	minus	G	alt_assembly_1	Celera	Celera	view	300
8	NT_023736.16	6717829	6717829	minus	A	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_023736.12 AF205406 AF233439

dbSNP Blast Analysis
GenBank HTGS Finished:
AF205406.5 AF233439.7 AF298854.5

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss24374017	AFD_EUR_PANEL	European	48	IG	0.625	0.333	0.042	1.000	0.792	0.208

	AFD_AFR_PANEL	African American	46	IG	0.826	0.130	0.043	0.150	0.891	0.109

	AFD_CHN_PANEL	Asian	48	IG	0.833	0.167		0.752	0.917	0.083

ss7987372	D-0	African American	48	IG	0.833	0.125	0.042	0.150	0.896	0.104

	E-0	European	40	IG	0.600	0.350	0.050	1.000	0.775	0.225

	E-1	European	6	IG	0.667	0.333			0.833	0.167

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.247+/-0.250	72	51	46	0

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

UNKNOWN

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Revised: May 25, 2006 1:38 PM .