Reference SNP(refSNP) Cluster Report: rs2927707

Reference SNP(refSNP) Cluster Report: rs2927707

refSNP ID: rs2927707
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	101/129
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_016579.2:c.143-881G>A
NT_077812.2:g.974917C>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss90898136 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2927707 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
ss4129102	SC_JCM\|AC022146.6_158596	fwd/T	A/G	ggtgaggagctgacacatttaggatgggga	agtgataggtctgggaggaattcaggaggc	10/15/01	04/07/04	101	Genomic	unknown
ss4972976	YUSUKE\|IMS-JST143326	rev/B	C/T	gcctcctgaattcctcccagacctatcact	tccccatcctaaatgtgtcagctcctcacc	08/12/02	10/10/03	108	Genomic	unknown
ss21535142	SSAHASNP\|WGSA-200403-chr19.chr19.NT_077812.2_974917	rev/B	C/T	gcctcctgaattcctcccagacctatcact	tccccatcctaaatgtgtcagctcctcacc	03/20/04	03/20/04	121	Genomic	unknown
ss24089581	PERLEGEN\|afd1597130	rev/B	C/T	gcctcctgaattcctcccagacctatcact	tccccatcctaaatgtgtcagctcctcacc	08/10/04	09/13/04	123	Genomic	unknown
ss66583997	ILLUMINA\|HumanHap300v1.1_rs2927707	fwd/B	A/G	ggtgaggagctgacacatttaggatgggga	agtgataggtctgggaggaattcaggaggc	11/09/06	11/09/06	127	Genomic	unknown
ss67283646	ILLUMINA\|HumanHap550v1.1_rs2927707	fwd/T	A/G	ggtgaggagctgacacatttaggatgggga	agtgataggtctgggaggaattcaggaggc	11/14/06	11/14/06	127	Genomic	unknown
ss67686097	ILLUMINA\|HumanHap650Yv1.0_rs2927707	fwd/T	A/G	ggtgaggagctgacacatttaggatgggga	agtgataggtctgggaggaattcaggaggc	11/14/06	11/14/06	127	Genomic	unknown
ss69223674	PERLEGEN\|PGP01597130	rev/B	C/T	gcctcctgaattcctcccagacctatcact	tccccatcctaaatgtgtcagctcctcacc	01/30/07	03/31/08	127	Genomic	unknown
ss70762171	ILLUMINA\|HumanHap550v3.0__rs2927707	rev/B	C/T	gcctcctgaattcctcccagacctatcact	tccccatcctaaatgtgtcagctcctcacc	04/20/07	03/30/08	130	Genomic	unknown
ss71336171	ILLUMINA\|HumanHap650Yv3.0_rs2927707	fwd/T	A/G	ggtgaggagctgacacatttaggatgggga	agtgataggtctgggaggaattcaggaggc	04/23/07	04/23/07	127	Genomic	unknown
ss74943734	ILLUMINA\|ILMN_Human_1M_rs2927707	fwd/T	A/G	ggtgaggagctgacacatttaggatgggga	agtgataggtctgggaggaattcaggaggc	08/28/07	08/29/07	129	Genomic	unknown
ss79154115	ILLUMINA\|HumanHap300v2.0_rs2927707	fwd/T	A/G	ggtgaggagctgacacatttaggatgggga	agtgataggtctgggaggaattcaggaggc	04/18/07	11/18/07	129	Genomic	unknown
ss79851901	HGSV\|Cor18507_SNV_20070510.chr19_8276921	rev/B	C/T	gcctcctgaattcctcccagacctatcact	tccccatcctaaatgtgtcagctcctcacc	11/23/07	11/23/07	130	Genomic	unknown
ss82888173	HGSV\|Cor18555_SNV_20070510.chr19_8276921	rev/B	C/T	gcctcctgaattcctcccagacctatcact	tccccatcctaaatgtgtcagctcctcacc	11/27/07	12/03/07	130	Genomic	unknown
ss83203844	HGSV\|Cor18956_SNV_20070510.chr19_8276921	rev/B	C/T	gcctcctgaattcctcccagacctatcact	tccccatcctaaatgtgtcagctcctcacc	11/30/07	12/04/07	130	Genomic	unknown
ss84124696	KRIBB_YJKIM\|KHS640583	fwd/T	A/G	ggtgaggagctgacacatttaggatgggga	agtgataggtctgggaggaattcaggaggc	12/04/07	12/06/07	130	Genomic	unknown
ss85349585	HGSV\|Cor19129_SNV_20070510.chr19_8276921	rev/B	C/T	gcctcctgaattcctcccagacctatcact	tccccatcctaaatgtgtcagctcctcacc	12/06/07	12/09/07	130	Genomic	unknown
ss85486477	HGSV\|Cor18517_SNV_20070510.chr19_8276921	rev/B	C/T	gcctcctgaattcctcccagacctatcact	tccccatcctaaatgtgtcagctcctcacc	12/06/07	12/09/07	130	Genomic	unknown
ss90898136	BCMHGSC_JDW\|JWB-1142116	rev/B	C/T	gcctcctgaattcctcccagacctatcact	tccccatcctaaatgtgtcagctcctcacc	02/26/08	03/01/08	129	Genomic	unknown

Fasta sequence (Legend)

 TGTCCAGTCT GTGGGTGGAC AGGCATGACC AGGGCTTTAA GGACAGTTGT TAGACATGGG
 AGGCAGTGCT TCCTAGGTCT CCAAGAGGGA CATGAGAACC CTCCCAGGAA ATCAGCTGAG
 ATCTGAAAAT TGAGGGGAAA ACACAGGGTG TAGGGAGGAG AGAGGGAAAG GCAAGTCTCT
 GGTGTCCTAA TGGACCTTGG GGCCTGGGGC CTGGGGCTCT GGTGAGGAGC TGACACATTT
 AGGATGGGGA
 R
 AGTGATAGGT CTGGGAGGAA TTCAGGAGGC GGGGCAACAG GACTTGGTGA CTGAGCAGAT
 TTTCTACCCA GTGCCTCAGT TTCCCACCCA CTGCCTCAGT TTCCCTTTTG CTACGCAGAG
 GAGATAGACC CTCCCTGCTG ACCTGAGCCC GGGAGCCTGA CCCAGGGCAT GTGGAAAAAT
 GGCCCGTCCC TCAGTCTCTT TAACCACTGA GTTTGGAGGT CTCCCTGGCA GATCATCTCG
 CTATGAGGAG

GeneView

GeneView via analysis of contig annotation: CD320 CD320 molecule

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_077812->NM_016579

function

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


reference	NT_077812->NM_016579->NP_057663	974917	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs2927707 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_001838480.2	321655	8024954	plus	A	alt_assembly_8	HuRef	HuRef	view	200
19	NW_927173.1	7486171	8227447	minus	T	alt_assembly_1	Celera	Celera	view	200
19	NT_077812.2	974917	8276921	minus	C	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_077812 AC010323 AC092310 AC093233

dbSNP Blast Analysis

UniGene Cluster ID
333427

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G	N
ss24089581	AFD_EUR_PANEL	European	48	IG	0.625	0.292	0.083	0.403	0.771	0.229

	AFD_AFR_PANEL	African American	46	IG	0.739	0.261		0.479	0.870	0.130

	AFD_CHN_PANEL	Asian	48	IG	0.333	0.583	0.083	0.251	0.625	0.375

ss4129102	HapMap-CEU	European	120	IG	0.483	0.367	0.150	0.150	0.667	0.333

	HapMap-HCB	Asian	90	IG	0.422	0.422	0.156	0.584	0.633	0.367

	HapMap-JPT	Asian	90	IG	0.289	0.556	0.156	0.479	0.567	0.433

	HapMap-YRI	Sub-Saharan African	120	IG	0.667	0.317	0.017	0.479	0.825	0.175

	CHMJ	Asian	74	IG					0.622	0.297	0.081

ss4972976	JBIC-allele		1488	AF					0.594	0.407

ss69223674	HapMap-CEU	European	120	GF	0.483	0.367	0.150		0.667	0.333

	HapMap-HCB	Asian	90	GF	0.422	0.422	0.156		0.633	0.367

	HapMap-JPT	Asian	90	GF	0.289	0.556	0.156		0.567	0.433

	HapMap-YRI	Sub-Saharan African	120	GF	0.667	0.317	0.017		0.825	0.175

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.425+/-0.178	332	260	270	0

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: PERLEGEN

UNKNOWN

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Revised: May 25, 2006 1:38 PM .