Reference SNP(refSNP) Cluster Report: rs4384829

Reference SNP(refSNP) Cluster Report: rs4384829

refSNP ID: rs4384829
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	111/129
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_030915.3:c.129+9429G>A
NT_022184.14:g.9282735G>A

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss7876357 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs4384829 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
ss5852350	SC_JCM\|NT_034478.1_290364	fwd/T	A/G	ctctccaagggtctaggtgctttgcaacac	tagacagcccaggccagtgctctagcaggg	01/10/03	10/10/03	111	Genomic	unknown
ss7876357	DEVINE_LAB\|DB_1_188435	fwd/T	A/G	ctctccaagggtctaggtgctttgcaacac	tagacagcccaggccagtgctctagcaggg	03/16/03	10/25/06	113	Genomic	96 %
ss9950585	BCM_SSAHASNP\|chr2.NT_022184.12_9282735	fwd/T	A/G	ctctccaagggtctaggtgctttgcaacac	tagacagcccaggccagtgctctagcaggg	06/27/03	10/10/03	116	Genomic	unknown
ss21635259	SSAHASNP\|WGSA-200403-chr2.chr2.NT_022184.13_9282735	fwd/T	A/G	ctctccaagggtctaggtgctttgcaacac	tagacagcccaggccagtgctctagcaggg	03/20/04	03/20/04	121	Genomic	unknown
ss23694619	PERLEGEN\|afd4496756	fwd/T	A/G	ctctccaagggtctaggtgctttgcaacac	tagacagcccaggccagtgctctagcaggg	08/10/04	09/13/04	123	Genomic	unknown
ss44292363	ABI\|hCV98602	fwd/T	A/G	ctctccaagggtctaggtgctttgcaacac	tagacagcccaggccagtgctctagcaggg	07/18/05	07/18/05	126	Genomic	unknown
ss66323121	AFFY\|SNP_A-1902519	rev/B	C/T	tggcctgggctgtcta	gtgttgcaaagcacct	10/29/06	03/31/08	127	Genomic	unknown
ss68808203	PERLEGEN\|PGP04496756	fwd/T	A/G	ctctccaagggtctaggtgctttgcaacac	tagacagcccaggccagtgctctagcaggg	01/30/07	03/31/08	127	Genomic	unknown
ss76013451	AFFY\|AFFY_6_1M_SNP_A-1902519	rev/B	C/T	tggcctgggctgtcta	gtgttgcaaagcacct	08/28/07	08/29/07	130	Genomic	unknown

Fasta sequence (Legend)

 tttttttttt tttgagatgg aatcttgctc tgtcacctgg gcttgagtgc agtggcacga
 tctcagctca ctgcaacctc cgcctccctg gttcaagtga ttttcctgcc tcagttccct
 cagtagctgg gattacaggc acccactaca tgcccagcta gtttttgcat ttttagtgga
 gacgggtttc tccatgttgg ccaggctgtt ctcgaactcc tgacctcagg tgatccacct
 gcctcagcct cccaaattgc tgggattaca gacgtgagcc actgcgcctg gccTGGGCTG
 GACTCTTAAA AGTAGATCTT AACATAATGG AAGTCTTGGA CCCAGTGTCG AAGGGCCACG
 TACCCAACAA CTCTCCAAGG GTCTAGGTGC TTTGCAACAC
 R
 TAGACAGCCC AGGCCAGTGC TCTAGCAGGG TCCACATACT CCTGATGGTT TACAAAGTTC
 ATTTAGGTGC TATACAGACA GCTTGAAAAA TGTAAGACTA GTTTTCCATT TATGTAGTGG
 TAGATTTTTA AACAAGTATG TTTTAAATAA ATGAGTGGAG GAAACTAAGA CATGTATGTG
 GACATAACAG GGATGATGAA GGTGATATCA CAAGGCTGAC ACATACCAGC TTACATGAGT
 GTGAAATTCC ACAGCACAAT CCTTTTAGGA TCCTCTAAAA TGGGTATCTC TTTGGTCATG
 TGCCCCTCGG GTATGGCAGT TGAAGCATCA GGAACCTTCC TGACTGTTTT CATTGGCAGT
 TGAGTGTTAG AGATTTGTAT GCCAAATTAC TTCTTAATAA

GeneView

GeneView via analysis of contig annotation: LBH limb bud and heart development homolog (mouse)

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_022184->NM_030915

function

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


reference	NT_022184->NM_030915->NP_112177	9282735	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs4384829 maps exactly once on NCBI human chromosome 2

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
2	NW_001838769.1	301586	30205342	plus	A	alt_assembly_8	HuRef	HuRef	view	400
2	NW_927719.1	30241563	30309628	plus	A	alt_assembly_1	Celera	Celera	view	400
2	NT_022184.14	9282735	30320306	plus	G	ref_assembly	reference	reference	view	400

NCBI Resource Links

Submitter-Referenced
GenBank
NT_034478.1

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss23694619	AFD_EUR_PANEL	European	46	IG	0.174	0.478	0.348	1.000	0.413	0.587

	AFD_AFR_PANEL	African American	46	IG	0.304	0.565	0.130	0.439	0.587	0.413

	AFD_CHN_PANEL	Asian	48	IG		0.375	0.625	0.273	0.188	0.812

ss66323121	HapMap-CEU	European	118	GF	0.237	0.525	0.237		0.500	0.500

	HapMap-HCB	Asian	90	GF	0.022	0.356	0.622		0.200	0.800

	HapMap-JPT	Asian	90	GF	0.022	0.400	0.578		0.222	0.778

	HapMap-YRI	Sub-Saharan African	120	GF	0.167	0.383	0.450		0.358	0.642

ss68808203	HapMap-CEU	European	120	GF	0.250	0.517	0.233		0.508	0.492

	HapMap-HCB	Asian	90	GF	0.022	0.333	0.644		0.189	0.811

	HapMap-JPT	Asian	90	GF	0.022	0.378	0.600		0.211	0.789

	HapMap-YRI	Sub-Saharan African	120	GF	0.167	0.383	0.450		0.358	0.642

ss7876357	HapMap-CEU	European	118	IG	0.254	0.525	0.220	0.752	0.517	0.483

	HapMap-HCB	Asian	90	IG	0.022	0.378	0.600	0.371	0.211	0.789

	HapMap-JPT	Asian	88	IG	0.023	0.409	0.568	0.294	0.227	0.773

	HapMap-YRI	Sub-Saharan African	120	IG	0.167	0.383	0.450	0.200	0.358	0.642

	CHMJ	Asian	74	IG					0.324	0.676

Concordant Genotype	Total Sample	A/A	A/G	G/G
ss23694619	70	10	33	26
ss66323121	264
ss68808203	265	37	110	118
ss7876357	265	37	110	115

RefSNP Genotype Summary	Total Individual	A/A	A/G	G/G
rs4384829	332	45	141	141

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
188	ss7876357	A/A	CSHL-HAPMAP	HapMap-CEU	NA10851	CEPH1344.01	r23_ch2_CEU_perlegen:genotyping_1.0.0	1985928
188	ss23694619	A/A	PERLEGEN	AFD_EUR_PANEL	NA10851		71_IND_CHR_2
188	ss66323121	T/T	CSHL-HAPMAP	HapMap-CEU	NA10851	CEPH1344.01	chr2-HapMap-CEU
188	ss68808203	A/G	CSHL-HAPMAP	HapMap-CEU	NA10851	CEPH1344.01	chr2-HapMap-CEU
5148	ss7876357	A/G	CSHL-HAPMAP	HapMap-HCB	NA18526	CH18526	r23_ch2_HCB_perlegen:genotyping_1.0.0	1985928
5148	ss66323121	C/T	CSHL-HAPMAP	HapMap-HCB	NA18526	CH18526	chr2-HapMap-HCB
5148	ss68808203	G/G	CSHL-HAPMAP	HapMap-HCB	NA18526	CH18526	chr2-HapMap-HCB
5163	ss7876357	A/G	CSHL-HAPMAP	HapMap-HCB	NA18609	CH18609	r23_ch2_HCB_perlegen:genotyping_1.0.0	1985928
5163	ss66323121	C/T	CSHL-HAPMAP	HapMap-HCB	NA18609	CH18609	chr2-HapMap-HCB
5163	ss68808203	G/G	CSHL-HAPMAP	HapMap-HCB	NA18609	CH18609	chr2-HapMap-HCB
5184	ss7876357	A/G	CSHL-HAPMAP	HapMap-HCB	NA18579	CH18579	r23_ch2_HCB_perlegen:genotyping_1.0.0	1985928
5184	ss66323121	C/C	CSHL-HAPMAP	HapMap-HCB	NA18579	CH18579	chr2-HapMap-HCB
5184	ss68808203	A/G	CSHL-HAPMAP	HapMap-HCB	NA18579	CH18579	chr2-HapMap-HCB
5222	ss7876357	A/G	CSHL-HAPMAP	HapMap-JPT	NA18981	JA18981	r23_ch2_JPT_perlegen:genotyping_1.0.0	1985928
5222	ss66323121	C/T	CSHL-HAPMAP	HapMap-JPT	NA18981	JA18981	chr2-HapMap-JPT
5222	ss68808203	G/G	CSHL-HAPMAP	HapMap-JPT	NA18981	JA18981	chr2-HapMap-JPT

Genotype data submitted for	341	samples from	332	individuals	Individual with multiple genotypes submission:	270

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 .