Reference SNP(refSNP) Cluster Report: rs819171

Reference SNP(refSNP) Cluster Report: rs819171

refSNP ID: rs819171
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	86/129
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
NT_028392.5:g.3064076C>T

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss8411596 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs819171 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
ss1087821	KWOK\|OVLP-000804-111494	rev/T	A/G	gggttatagttgtgctgatgaagcattcac	gggtactctgcagtggaacggctgtctgtg	09/02/00	10/10/03	86	Genomic	99 %
ss1729860	KWOK\|OVLP-000925-293591	fwd/B	C/T	cacagacagccgttccactgcagagtaccc	gtgaatgcttcatcagcacaactataaccc	10/05/00	10/10/03	87	Genomic	97 %
ss3942575	SC_JCM\|AL356299.16_9555	fwd/B	C/T	cacagacagccgttccactgcagagtaccc	gtgaatgcttcatcagcacaactataaccc	09/25/01	10/10/03	100	Genomic	unknown
ss6788131	WI_SSAHASNP\|NT_028392.4_3034752	fwd/B	C/T	cacagacagccgttccactgcagagtaccc	gtgaatgcttcatcagcacaactataaccc	02/12/03	10/10/03	111	Genomic	unknown
ss8411596	SC_SNP\|NT_028392.4_3034752	fwd/B	C/T	cacagacagccgttccactgcagagtaccc	gtgaatgcttcatcagcacaactataaccc	04/17/03	05/16/04	114	Genomic	unknown
ss12499344	WI_SSAHASNP\|chr20.NT_028392.4_3034752	fwd/B	C/T	cacagacagccgttccactgcagagtaccc	gtgaatgcttcatcagcacaactataaccc	07/04/03	10/10/03	116	Genomic	unknown
ss19483147	CSHL-HAPMAP\|CSHL-HuDD-200402.chr20.NT_028392.4_3034752	fwd/B	C/T	cacagacagccgttccactgcagagtaccc	gtgaatgcttcatcagcacaactataaccc	02/20/04	03/04/04	120	Genomic	unknown
ss20130452	CSHL-HAPMAP\|CSHL-HuFF-200402.chr20.NT_028392.4_3034752	fwd/B	C/T	cacagacagccgttccactgcagagtaccc	gtgaatgcttcatcagcacaactataaccc	02/21/04	03/04/04	120	Genomic	unknown
ss21802188	SSAHASNP\|WGSA-200403-chr20.chr20.NT_028392.4_3034752	fwd/B	C/T	cacagacagccgttccactgcagagtaccc	gtgaatgcttcatcagcacaactataaccc	03/20/04	03/20/04	121	Genomic	unknown
ss23559786	PERLEGEN\|afd0397785	fwd/B	C/T	cacagacagccgttccactgcagagtaccc	gtgaatgcttcatcagcacaactataaccc	08/10/04	09/13/04	123	Genomic	unknown
ss41415598	ABI\|hCV7593561	fwd/B	C/T	cacagacagccgttccactgcagagtaccc	gtgaatgcttcatcagcacgactataaccc	07/17/05	07/17/05	126	Genomic	unknown
ss48292467	SNP500CANCER\|AHCY-19	rev/T	A/G	gggttatagtygtgctgatgaagcattcac	gggtactctgcagtggaacggctgtctgtg	08/19/05	11/03/06	126	Genomic	unknown
ss69379304	SI_EXO\|NT_028392.5_3064076	fwd/B	C/T	cacagacagccgttccactgcagagtaccc	gtgaatgcttcatcagcacaactataaccc	04/12/07	04/12/07	127	Genomic	unknown
ss91687879	BCMHGSC_JDW\|JWB-1437847	fwd/B	C/T	cacagacagccgttccactgcagagtaccc	gtgaatgcttcatcagcacaactataaccc	02/26/08	03/02/08	129	Genomic	unknown

Fasta sequence (Legend)

 GACATTGTAT CTTTAGAACT TAATGTGAGT CCCCACTTAG TGCACTTTTA AAAATACTGC
 AAACagccgg gcacagtggc tcacgcctat aatcccaggc agatcacttg aggtcaggag
 ttcaagatca gcctggctaa catggtaaaa ccccgtctct actaaaaata ccaaaaaaaa
 attagctggg tgtgatctca actactcagg aggctgaggc aggaggatcg cttgaaccca
 ggaggcgaag gttgcattga gctgagattg catcactgca ctccagcctg ggtgacggag
 cgagactctg tctcaaaaaa aaaCGAAAGA GTTCCCTCTT CACTTTACCC ATTCTTTCAA
 GCCTAAGGAC CACAGACAGC CGTTCCACTG CAGAGTACCC
 Y
 GTGAATGCTT CATCAGCACA ACTATAACCC CCTATTCATG GCATACATTG TTGGCAGAGG
 ATTATCTATA AAATAAAGGC TCAAAATTCT TCCAGGCACC AAGATTTTTA TTTACCCACC
 TTCCTGCTTT CTTTTAACAT TATAGGCCAA ATTATTCTCT TTTTGACCCA GGGTTGTGAA
 AGGAACCATC TGGTTATAAA GTGGTGGCAG ATTTCACGAA ATCTGCCTGC ATTCATGTTT
 TTCTGGCCCC TCTCAACCCC TAGCTGTCAC TTCTCTGTTC TTTCTCAGTT GCCCCTTAAC
 AGTCTATTCT AACCCCTGTA AAACAGGGAC TAAAAGTACT AACCTCATTG TAATGAGGTT
 TAAGAGAAGG CCCAGCACTA AGCCAGGCTC TCAGGAAAAT

GeneView

GeneView via analysis of contig annotation: AHCY S-adenosylhomocysteine hydrolase

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_028392->NM_000687

function

HuRef

NW_001838664->NM_000687

function

Celera

NW_927339->NM_000687

function

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


reference	NT_028392->NM_000687->NP_000678	3064076	reverse	3' near gene

HuRef	NW_001838664->NM_000687->NP_000678	2030203	forward	3' near gene

Celera	NW_927339->NM_000687->NP_000678	3120573	reverse	3' near gene

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs819171 maps exactly once on NCBI human chromosome 20

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
20	NW_927339.1	3120573	29617464	plus	T	alt_assembly_1	Celera	Celera	view	400
20	NW_001838664.2	2030203	29649787	minus	A	alt_assembly_8	HuRef	HuRef	view	400
20	NT_028392.5	3064076	32331645	plus	C	ref_assembly	reference	reference	view	400

NCBI Resource Links

Submitter-Referenced
GenBank
NT_028392.5 AL137253 AL356299.12 AL356299.16

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AL356299.16 NC_000020.9	AL137253.8

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss23559786	AFD_EUR_PANEL	European	48	IG	0.042	0.333	0.625	1.000	0.208	0.792

	AFD_AFR_PANEL	African American	44	IG	0.091	0.682	0.227	0.100	0.432	0.568

	AFD_CHN_PANEL	Asian	46	IG	0.043	0.348	0.609	1.000	0.217	0.783

ss48292467	P1		198	AF	0.111	0.283	0.606	0.020	0.253	0.747

	CAUC1		60	AF	0.067	0.333	0.600	0.752	0.233	0.767

	AFR1		46	AF	0.261	0.348	0.391	0.150	0.435	0.565

	HISP1		44	AF	0.091	0.136	0.773	0.025	0.159	0.841

	PAC1		48	AF	0.041	0.292	0.667	1.000	0.187	0.813

ss8411596	CEPH		184	AF					0.210	0.790

	CHMJ	Asian	74	IG					0.149	0.851

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.385+/-0.210	71	50	0	0

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: PERLEGEN

DoubleHit found by: BCM_SSAHASNP, NCBI

UNKNOWN

Disclaimer Privacy statement

Revised: May 25, 2006 1:38 PM .