Reference SNP(refSNP) Cluster Report: rs327512

Reference SNP(refSNP) Cluster Report: rs327512

refSNP ID: rs327512
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	79/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	A/G
Ancestral Allele:	G
Clinical Association:	unknown

HGVS Names

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss1682909 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs327512 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
ss418711	KWOK\|OVLP-000621-292208	rev/B	C/T	attccaaactctttgtaattatttgtttca	tggtgctagtctcttttctccagttgctct	06/30/00	10/10/03	79	Genomic	99 %
ss827139	SC_JCM\|AC000359.1_32719	fwd/T	A/G	agagcaactggagaaaagagactagcacca	tgaaacaaataattacaaagagtttggaat	07/27/00	10/10/03	83	Genomic	unknown
ss962103	KWOK\|OVLP-000804-466888	fwd/T	A/G	agagcaactggagaaaagagactagcacca	tgaaacaaataattacaaagagtttggaat	09/01/00	10/10/03	86	Genomic	99 %
ss1035311	KWOK\|OVLP-000804-468503	fwd/T	A/G	agagcaactggagaaaagagactagcacca	tgaaacaaagaattacaaagagtttggaat	09/02/00	10/10/03	86	Genomic	97 %
ss1421573	TSC-CSHL\|TSC0281359	fwd/T	A/G	agagcaactggagaaaagagactagcacca	tgaaacaaagaattacaaagagtttggaat	09/06/00	10/10/03	86	Genomic	95 %
ss1682909	KWOK\|OVLP-000925-249536	fwd/T	A/G	agagcaactggagaaaagagactagcacca	tgaaacaaagaattacaaagagtttggaat	10/05/00	10/25/06	89	Genomic	99 %
ss1683223	KWOK\|OVLP-000925-252095	fwd/T	A/G	agagcaactggagaaaagagactagcacca	tgaaacaaataattacaaagagtttggaat	10/05/00	10/10/03	87	Genomic	99 %
ss6521566	WI_SSAHASNP\|NT_007933.10_52433765	fwd/T	A/G	agagcaactggagaaaagagactagcacca	tgaaacaaagaattacaaagagtttggaat	02/12/03	10/10/03	111	Genomic	unknown
ss11873221	WI_SSAHASNP\|chr7.NT_007933.12_52433919	fwd/T	A/G	agagcaactggagaaaagagactagcacca	tgaaacaaagaattacaaagagtttggaat	07/04/03	10/10/03	116	Genomic	unknown
ss14561952	WUGSC_SSAHASNP\|chr7.NT_007933.13_52433919	fwd/T	A/G	agagcaactggagaaaagagactagcacca	tgaaacaaagaattacaaagagtttggaat	11/05/03	11/22/03	120	Genomic	unknown
ss44822296	ABI\|hCV2280176	fwd/T	A/G	agagcaactggagaaaagagactagcacca	tgaaacaaagaattacaaagagtttggaat	07/19/05	07/19/05	126	Genomic	unknown
ss77620044	HGSV\|Cor12156_SNV_20070510.chr7_126851202	fwd/T	A/G	agagcaactggagaaaagagactagcacca	tgaaacaaagaattacaaagagtttggaat	10/09/07	10/13/07	129	Genomic	unknown
ss80227016	HGSV\|Cor18507_SNV_20070510.chr7_126851202	fwd/T	A/G	agagcaactggagaaaagagactagcacca	tgaaacaaagaattacaaagagtttggaat	11/23/07	11/25/07	130	Genomic	unknown
ss93763402	BCMHGSC_JDW\|JWB-2371588	fwd/T	A/G	agagcaactggagaaaagagactagcacca	tgaaacaaagaattacaaagagtttggaat	02/26/08	03/05/08	129	Genomic	unknown

Fasta sequence (Legend)

 TCTCTAACCT GCTGAGATTG TTCATTCTGT TCATTCTCTG AAGAGTTCTA GATCTCACAG
 TGAAGCTTCA ATTTCAGAGA CGATGTTTCT GGTATCAGAC ACTCATTCAT TCAACTAACA
 TTTATCAAAG GCATATTGAA GGGAATGAGA AGCAGGAGAA GACTGTCCGC TGAGCAACAT
 AGAAACCGTC ATGAGCCCAA GCGAGTCTCT GAGCAGCAAG GGACACAGGT CCCACAGGCC
 ACCATACCTC TTCTACTTTC ATTAGTAATC AATGGGAGTT GAAGATGCCT CCTTTCATGC
 CTGGAACCCT GGTAGTGCTG GAGATCACCC CAAGGAACAG CTTATGCACA GAACTTTCTT
 ATAATAAGCG TGCCATCTGG GCTTAGTTAA TTCATCTGCA GTTGTATGCT GAATAAGATA
 TTAAGCATGA GCACATTGCT GGTTGTTCAG GATGAAGGCA GTAAACAGAA AAGGGTAAAG
 TCTTTGCTCT CCAACACATT ACAGAGCAAC TGGAGAAAAG AGACTAGCAC CA
 R
 TGAAACAAAG AATTACAAAG AGTTTGGAAT CCAGAGTCTA CTTATTAAGT TCAGTCGCTA
 AATTGGCTTT TACTCACTTG TTTCTAGGTA GGTAGAGGCA CAGACCCCTT CAAATTCTCA
 TCTTTCCAAA AAGTCGGGAA AGAAGGCAGA GGTTTTCCAA AGAGAAAACT GAGGCACAGA
 TTGGCATTGC CACAAGTCAG GGGCTGTCCA GAGAGTAAAA TTCAAGGTTT AGAAGCCAGT
 TCCTCATCAG AAGCTACAAT TTCTGGCTCC TAATCCTGGG

GeneView

GeneView via analysis of contig annotation: PAX4 paired box 4

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

HuRef

NW_001839071->NM_006193

function

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


HuRef	NW_001839071->NM_006193->NP_006184	4036358	forward	5' near gene

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs327512 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_001839071.2	4036358	121618156	minus	T	alt_assembly_8	HuRef	HuRef	view	532
7	NW_923640.1	24819731	122060980	plus	G	alt_assembly_1	Celera	Celera	view	532
7	NT_079596.2	26676265	126640697	plus	G	alt_assembly_2	CRA_TCAGchr7v2	CRA_TCAGchr7v2	view	532
7	NT_007933.14	52440827	127044487	plus	G	ref_assembly	reference	reference	view	532

NCBI Resource Links

Submitter-Referenced
GenBank
NT_007933 AC013686 AC013686.4 AC073934.1

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
ss1682909	HapMap-CEU	European	108	IG	0.519	0.426	0.056	0.584	0.731	0.269

	HapMap-HCB	Asian	86	IG	0.186	0.349	0.465	0.150	0.360	0.640

	HapMap-JPT	Asian	84	IG	0.095	0.476	0.429		0.333	0.667

	HapMap-YRI	Sub-Saharan African	114	IG	0.333	0.491	0.175	1.000	0.579	0.421

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.499+/-0.020	270	210	0	0

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, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .