Reference SNP(refSNP) Cluster Report: rs197142

Reference SNP(refSNP) Cluster Report: rs197142

refSNP ID: rs197142
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
NM_015015.1:c.-109+21305T>C
NT_011255.14:g.4930546T>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss90888806 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs197142 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
ss259444	KWOK\|OVLP-000621-100181	fwd/T	A/G	caatactcatgacctctagatgagctctcc	cggccccaggatcccaggcacagccctccc	06/30/00	10/10/03	79	Genomic	97 %
ss751200	SC_JCM\|AC019114.5_40128	fwd/T	A/G	caatactcatgacctctagatgagctctcc	cggccccaggatcccaggcacagccctccc	07/27/00	10/25/06	85	Genomic	unknown
ss1255045	KWOK\|OVLP-000804-567544	fwd/T	A/G	caatactcatgacctctagatgagctctcc	cggccccaggatcccaggcacagccctccc	09/02/00	10/10/03	86	Genomic	97 %
ss1631528	KWOK\|OVLP-000925-123661	fwd/T	A/G	caatactcatgacctctagatgagctctcc	cggccccaggatcccaggcacagccctccc	10/04/00	10/10/03	87	Genomic	97 %
ss10932982	BCM_SSAHASNP\|chr19.NT_011255.13_4930546	rev/B	C/T	gggagggctgtgcctgggatcctggggccg	ggagagctcatctagaggtcatgagtattg	06/30/03	10/10/03	116	Genomic	unknown
ss23572023	PERLEGEN\|afd4181248	rev/B	C/T	gggagggctgtgcctgggatcctggggccg	ggagagctcatctagaggtcatgagtattg	08/10/04	09/13/04	123	Genomic	unknown
ss75128897	ILLUMINA\|ILMN_Human_1M_rs197142	fwd/T	A/G	caatactcatgacctctagatgagctctcc	cggccccaggatcccaggcacagccctccc	08/28/07	08/29/07	129	Genomic	unknown
ss78503778	HGSV\|Cor18507_SNV_20070510.chr19_4941546	rev/B	C/T	gggagggctgtgcctgggatcctggggccg	ggagagctcatctagaggtcatgagtattg	10/19/07	10/19/07	129	Genomic	unknown
ss81597668	HGSV\|Cor18956_SNV_20070510.chr19_4941546	rev/B	C/T	gggagggctgtgcctgggatcctggggccg	ggagagctcatctagaggtcatgagtattg	11/30/07	11/30/07	130	Genomic	unknown
ss90888806	BCMHGSC_JDW\|JWB-1138667	rev/B	C/T	gggagggctgtgcctgggatcctggggccg	ggagagctcatctagaggtcatgagtattg	02/26/08	03/01/08	129	Genomic	unknown

Fasta sequence (Legend)

 CTAAGAAGGG CCTTATCCAT CCGGGTTTAT AAATATCCTT CAAAATGCAC AGTGTTAGAA
 TTACGGGCCA TCTCATCGAA TATTCTCCCC AAAACAAAGG CCGGAGAGGC GACCAGAACT
 AGTTCAGTGT TTGTACAACA CAGATCTAAA AGAGACACTG GATTACCCCC AGGCCAACTT
 CCATAATGAC AGTATTAAAA CACGGCATGT GAGCTTTGCC CAATACTCAT GACCTCTAGA
 TGAGCTCTCC
 R
 CGGCCCCAGG ATCCCAGGCA CAGCCCTCCC ATCTCCTCGC CACGCTGCCT TCAGACTCAG
 GTAACAGATG CATCCTGCCA GAGGCCACCT GCCCCAGGCC CTCATTCCAG TACAGAAACC
 TGCACTGCTA AGTCAGGGCA TGTCTGCCTC GGGCTCCACA CAAGTGTCTC CCTTTCTAAG
 TCCCTGTTTT TGGGTGGAAG TGAACTGCTC TAACACCAAG GTTCTGACCC TCTTTTTGTG
 GGGCGGGGAC

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

HuRef

NW_001838477->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	4930546	forward	intron

HuRef	NW_001838477->NM_015015->NP_055830	1472086	reverse	intron

Celera	NW_927173->NM_015015->NP_055830	4186460	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs197142 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	1472086	4752156	plus	A	alt_assembly_8	HuRef	HuRef	view	250
19	NW_927173.1	4186460	4927736	minus	T	alt_assembly_1	Celera	Celera	view	250
19	NT_011255.14	4930546	4941546	minus	T	ref_assembly	reference	reference	view	250

NCBI Resource Links

Submitter-Referenced
GenBank
NT_011255 AC053467 AC053467.1

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
ss23572023	AFD_EUR_PANEL	European	46	IG	0.870	0.087	0.043	0.050	0.913	0.087

	AFD_AFR_PANEL	African American	40	IG	0.200	0.650	0.150	0.200	0.525	0.475

	AFD_CHN_PANEL	Asian	44	IG	0.045	0.455	0.500	0.527	0.273	0.727

ss751200	HapMap-CEU	European	120	IG	0.600	0.400		0.100	0.800	0.200

	HapMap-HCB	Asian	90	IG	0.044	0.467	0.489	0.294	0.278	0.722

	HapMap-JPT	Asian	88	IG	0.045	0.455	0.500	0.343	0.273	0.727

	CHMJ	Asian	74	IG					0.243	0.757

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.500+/-0.014	242	200	9	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

UNKNOWN

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Revised: May 25, 2006 1:38 PM .