Reference SNP(refSNP) Cluster Report: rs197147

Reference SNP(refSNP) Cluster Report: rs197147

refSNP ID: rs197147
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
NT_011255.14:g.4907407C>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss1631502 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs197147 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
ss259449	KWOK\|OVLP-000621-100189	fwd/T	A/G	aaaataaatatggaaacacacacagaaacc	gtatcatgaggttaagagcacacaagcttg	06/30/00	10/10/03	79	Genomic	97 %
ss686965	SC_JCM\|AC019114.5_61839	fwd/T	A/G	aaaataaatatggaaacacacacagaaacc	gtatcatgaggttaagagcacacaagcttg	07/27/00	10/10/03	85	Genomic	unknown
ss1255019	KWOK\|OVLP-000804-567505	fwd/T	A/G	aaaataaatatggaaacacacacagaaacc	gtatcatgaggttaagagcacacaagcttg	09/02/00	10/10/03	86	Genomic	97 %
ss1631502	KWOK\|OVLP-000925-123622	fwd/T	A/G	aaaataaatatggaaacacacacagaaacc	gtatcatgaggttaagagcacacaagcttg	10/04/00	10/25/06	87	Genomic	97 %
ss75178762	ILLUMINA\|ILMN_Human_1M_rs197147	fwd/T	A/G	aaaataaatatggaaacacacacagaaacc	gtatcatgaggttaagagcacacaagcttg	08/28/07	08/29/07	129	Genomic	unknown
ss76797015	AFFY\|AFFY_6_1M_SNP_A-8658535	rev/B	C/T	cttaacctcatgatac	ggtttctgtgtgtgtt	08/28/07	08/30/07	129	Genomic	unknown

Fasta sequence (Legend)

 ATCAGTGGGG GATTAGAGAA GTAACTTAAT AGCAATCAGT ACTCTGGAAT ACTTACTATG
 TAGCAATTGA AAAGGAGGCC AGGCCCGGTG CTGTGGCTCG ggcgactcac acctgtaatc
 ccagcacttt gggaggtcga gtcgggtgga acacctgagg tccagagttc gagaccagcc
 tggccaacat ggcaaaaacc tgtctctatt aacaaataca aaattagcca ggcatggtgg
 cgcatgcctg taatcccagc tactccagag gctgaggcgg aggttgcagt gagtcgagat
 cactgcactt cagcctgggc aacagggtga gactctgtct caaaaaagga aagaaaagaa
 aaaagagaaG GCCGATCTGT TTGCAAACAT GAAATATCTC CCAACCGCTG AGCTAGGGAC
 AGTGGTCCAG AATCCTGTAC TCAATAAAAT AAATATGGAA ACACACACAG AAACC
 R
 GTATCATGAG GTTAAGAGCA CACAAGCTTG TCAATGCACA GAAAAAGGTA CTCCTAAACT
 GAAGAAACGA ACTTAATCCT TGGGGAGAGA AGGAAAGCTG CACACTGGTA AAAAGAGAAG
 TCAAAGGAGA ATTTAAGAAG CTCTGGGTGT TTTAAATTCT TATGGGACCA TATTCATATA
 TTCCACATGG AGTTGAGATT

GeneView

GeneView via analysis of contig annotation: JMJD2B jumonji domain containing 2B

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_011255->NM_015015

function

Celera

NW_927173->NM_015015

function

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


reference	NT_011255->NM_015015->NP_055830	4907407	forward	5' near gene

Celera	NW_927173->NM_015015->NP_055830	4163318	forward	5' near gene

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs197147 maps exactly once on NCBI human chromosome 19

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
19	NW_001838477.2	1495034	4729208	plus	G	alt_assembly_8	HuRef	HuRef	view	475
19	NW_927173.1	4163318	4904594	minus	C	alt_assembly_1	Celera	Celera	view	475
19	NT_011255.14	4907407	4918407	minus	C	ref_assembly	reference	reference	view	475

NCBI Resource Links

Submitter-Referenced
GenBank
AC019114.5 AC053467 AC053467.1

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/G	G/G	HWP	A	G
ss1631502	CEPH		184	AF					1.000

	HapMap-CEU	European	120	IG		1.000			1.000

	HapMap-HCB	Asian	90	IG		1.000			1.000

	HapMap-JPT	Asian	88	IG		1.000			1.000

	HapMap-YRI	Sub-Saharan African	120	IG	0.100	0.900	0.752	0.050	0.950

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.028+/-0.116	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 .