Reference SNP(refSNP) Cluster Report: rs9804310

Reference SNP(refSNP) Cluster Report: rs9804310

refSNP ID: rs9804310
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	119/129
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_014974.1:c.3925-8367T>C
NT_077567.3:g.304399A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss38582600 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs9804310 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
ss13634073	BCM_SSAHASNP\|chr10.NT_077567.3_304399	fwd/T	A/G	tgctggtggggaagtctcgtgtccaggaac	aggtcagcagtgcagacttcaaggtgtggt	11/05/03	11/22/03	119	Genomic	unknown
ss15593379	SC_SNP\|NT_077567.3_304399	fwd/T	A/G	tgctggtggggaagtctcgtgtccaggaac	aggtcagcagtgcagacttcaaggtgtggt	11/17/03	11/22/03	120	Genomic	unknown
ss20626972	SSAHASNP\|WGSA-200403-chr10.chr10.NT_077567.3_304399	fwd/T	A/G	tgctggtggggaagtctcgtgtccaggaac	aggtcagcagtgcagacttcaaggtgtggt	03/18/04	03/18/04	121	Genomic	unknown
ss38582600	ABI\|hCV2060297	fwd/T	A/G	tgctggtggggaaggctcgtgtccaggaac	aggtcagcagtgcagacttcaaggtgtggt	07/15/05	03/31/08	126	Genomic	unknown
ss66222956	AFFY\|SNP_A-4252062	fwd/T	A/G	tctcgtgtccaggaac	aggtcagcagtgcaga	10/27/06	03/31/08	127	Genomic	unknown
ss76369241	AFFY\|AFFY_6_1M_SNP_A-4252062	fwd/T	A/G	tctcgtgtccaggaac	aggtcagcagtgcaga	08/28/07	08/30/07	129	Genomic	unknown
ss80888184	HGSV\|Cor18507_SNV_20070510.chr10_354399	fwd/T	A/G	tgctggtggggaagtctcgtgtccaggaac	aggtcagcagtgcagacttcaaggtgtggt	11/26/07	11/27/07	130	Genomic	unknown

Fasta sequence (Legend)

 AGCAGCCACC GCTGCCACAC TTTGGTCACC ATACATCTCA ACCGTCCTCC TGTATCGGGA
 GAACTCCTCC ACTTTTTGAG TCCTGTTTGA ATACAGAGCC CTTGTGGCTC TGTAGGAAGT
 AAAAATACCA GAAGTCCCTT CCCAGCCTTC CTGGAAGCTA GGGTGTGGGG AGACGATCAA
 CCAGTCACAT CCATTTACAG CACAAACCAA TCGGGCTCTT GCTGTCGGCA GTGAAGGTGT
 CCAGACACGA TCCAGGTTTG GGGAATGCCA TGCTGGTGGG GAAGGCTCGT GTCCAGGAAC
 R
 AGGTCAGCAG TGCAGACTTC AAGGTGTGGT GTCCTCACAA GAACAAGCTG CTGCACAAGC
 GGTTCCCATA GGCAGGTTCC CAACGCTGGT CCTACTCCCT TGGTGGTTCT GAGAGCCACT
 CACTGGTGCC TCAAACTGCC AAAGGAGGTT TCCATTGCTT ACAGGTCAGA AAGCTGGCTG
 ACGTGCAGGA TACCTGGAAT ATGGTTTCCA TGATCCCCAG CGTGGCTGGG ATGCCGTGTG
 TCAGCAGGAA AGGGCATAAA GTTCCTGCTG ACGGTGGCTC ATTCCCTGAG GCTTTCAAAA

GeneView

GeneView via analysis of contig annotation: DIP2C DIP2 disco-interacting protein 2 homolog C (Drosophila)

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_077567->NM_014974

function

HuRef

NW_001837930->NM_014974

function

Celera

NW_924584->NM_014974

function

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


reference	NT_077567->NM_014974->NP_055789	304399	reverse	intron

HuRef	NW_001837930->NM_014974->NP_055789	5034712	forward	intron

Celera	NW_924584->NM_014974->NP_055789	318976	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs9804310 maps exactly once on NCBI human chromosome 10

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
10	NW_001837930.2	5034712	308887	minus	C	alt_assembly_8	HuRef	HuRef	view	300
10	NW_924584.1	318976	318976	plus	A	alt_assembly_1	Celera	Celera	view	300
10	NT_077567.3	304399	354399	plus	A	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_077567

dbSNP Blast Analysis
GenBank HTGS Finished:
AL603831.23

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss38582600	HapMap-CEU	European	114	IG	0.719	0.281			0.860	0.140

	HapMap-HCB	Asian	82	IG	0.439	0.512	0.049		0.695	0.305

	HapMap-JPT	Asian	90	IG	0.711	0.222	0.067		0.822	0.178

	HapMap-YRI	Sub-Saharan African	118	IG	0.542	0.339	0.119		0.712	0.288

ss66222956	HapMap-CEU	European	118	GF	0.729	0.271			0.864	0.136

	HapMap-HCB	Asian	90	GF	0.489	0.467	0.044		0.722	0.278

	HapMap-JPT	Asian	90	GF	0.689	0.244	0.067		0.811	0.189

	HapMap-YRI	Sub-Saharan African	120	GF	0.533	0.350	0.117		0.708	0.292

Concordant Genotype	Total Sample	A/A	A/G	G/G
ss38582600	269	161	86	13
ss66222956	268	168	87	13

RefSNP Genotype Summary	Total Individual	A/A	A/G	G/G
rs9804310	270	169	87	13

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
5229	ss38582600	A/A	CSHL-HAPMAP	HapMap-JPT	NA18992	JA18992	r23_ch10_JPT_affymetrix:genotype_protocol_1
5229	ss66222956	A/G	CSHL-HAPMAP	HapMap-JPT	NA18992	JA18992	chr10-HapMap-JPT

Genotype data submitted for	270	samples from	270	individuals	Individual with multiple genotypes submission:	269

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

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Revised: May 25, 2006 1:38 PM .