Reference SNP(refSNP) Cluster Report: rs10224297

Reference SNP(refSNP) Cluster Report: rs10224297

refSNP ID: rs10224297
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:	C/T
Ancestral Allele:	C
Clinical Association:	unknown

HGVS Names
NM_007349.3:c.2434+403G>A
NT_034885.3:g.381566C>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss14094045 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs10224297 during BLAST analysis for the current build.

NCBI Assay ID	Handle\|Submitter ID	Validation Status	ss to rs Orientation /Strand	Alleles	5' Near Seq 30 bp	3' Near Seq 30 bp	Entry Date	Update Date	Build Added	Molecule Type	Freq Warning	Ancestral Allele	Success Rate
ss14094045	WUGSC_SSAHASNP\|chr7.NT_034885.3_381566		fwd/B	C/T	gagaggcaagactatcaaaaagctttcaag	gctccttccatctctaagagttcatcaaaa	11/05/03	10/25/06	119	Genomic			unknown
ss76799723	AFFY\|AFFY_6_1M_SNP_A-8661251		rev/T	A/G	tagagatggaaggagc	cttgaaagctttttga	08/28/07	08/30/07	130	Genomic			unknown

Fasta sequence (Legend)

 CTAGCAGGCA CAAACCTTCT TGCCTTATCA CAGGAGCCAT GATGGCATCC AAGATGTAAC
 AGCAAGTCAG TCAAAGCTCA ATAGTGACAA AGAGGACAGA CGTCAATTCT AGGAAAGCAG
 GGAATGTTCT GTAGGGTAGG GAGCAATTTG GACAAAAGAT TAACTGGCCT GAGAGGCAAG
 ACTATCAAAA AGCTTTCAAG
 Y
 GCTCCTTCCA TCTCTAAGAG TTCATCAAAA GCAAACAAAA ATACTAAACC Atggcacatg
 cctgtagtcc cagctacttg ggagggtgag gtagggaaat cacccgagcc caggagatcg
 agctgcagtg agtcatgatc acaccactgc attccaacct gggtgacaaa gcgagaccct
 gtctcaaaac aaaaacaaaa acaaaaacaa aaaCCAACCA ACAAAAATCC TGGGCAGAGT
 GGGGAGAAAG AAGAAAGAGT ATAGAAAAGA AATTGGAAAT GAGTCAAAAA CTAATTAGAA
 AGCTCAAGCC AGGCCTGGTA ATTAGTATGA ATAAAAAGAT GGTAGAAGTA ATGCTAATGA
 TTTTATTTAA GTAAGA

GeneView

GeneView via analysis of contig annotation: PAXIP1 PAX interacting (with transcription-activation domain) protein 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_034885->NM_007349

function

HuRef

NW_001839099->NM_007349

function

Celera

NW_923796->NM_007349

function

CRA_TCAGchr7v2

NT_079596->NM_007349

function

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


reference	NT_034885->NM_007349->NP_031375	381566	reverse	intron

HuRef	NW_001839099->NM_007349->NP_031375	357246	forward	intron

Celera	NW_923796->NM_007349->NP_031375	788347	reverse	intron

CRA_TCAGchr7v2	NT_079596->NM_007349->NP_031375	54015790	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs10224297 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_001839099.2	357246	148485225	minus	G	alt_assembly_8	HuRef	HuRef	view	200
7	NW_923796.1	788347	149169356	plus	C	alt_assembly_1	Celera	Celera	view	200
7	NT_079596.2	54015790	153980222	plus	C	alt_assembly_2	CRA_TCAGchr7v2	CRA_TCAGchr7v2	view	200
7	NT_034885.3	381566	154383133	plus	C	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_034885

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC093726.3 NC_000007.12	AC073077.5

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss14094045	HapMap-CEU	European	116	IG	1.000				1.000

	HapMap-HCB	Asian	90	IG	0.533	0.378	0.089	0.752	0.722	0.278

	HapMap-JPT	Asian	88	IG	0.682	0.318		0.251	0.841	0.159

	HapMap-YRI	Sub-Saharan African	116	IG	0.759	0.224	0.017	1.000	0.871	0.129

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.229+/-0.249	270	210	0	0

Validation Summary:

Validation status	Marker displays Mendelian segregation	PCR results confirmed in multiple reactions	Homozygotes detected in individual genotype data
	UNKNOWN	UNKNOWN	UNKNOWN

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Revised: May 25, 2006 1:38 PM .