Reference SNP(refSNP) Cluster Report: rs200955

Reference SNP(refSNP) Cluster Report: rs200955

refSNP ID: rs200955
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:	C/T
Ancestral Allele:	T
Clinical Association:	unknown

HGVS Names
NT_007592.14:g.18697563T>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss1845428 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs200955 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
ss263945	KWOK\|OVLP-000621-128418	fwd/B	C/T	ctcggcctcaccagagcctgtggacactca	tgtgctacttgttcccttcagtaggggcag	06/30/00	10/10/03	79	Genomic	97 %
ss735481	SC_JCM\|Z98744.1_35275	fwd/B	C/T	ctcggcctcaccagagcctgtggacactca	tgtgctacttgttcccttcagtaggggcag	07/27/00	10/10/03	87	Genomic	unknown
ss1257131	KWOK\|OVLP-000804-586977	fwd/B	C/T	ctcggcctcaccagagcctgtggacactca	tgtgctacttgttcccttcagtaggggcag	09/02/00	10/10/03	86	Genomic	97 %
ss1845428	KWOK\|OVLP-000925-710072	fwd/B	C/T	ctcggcctcaccagagcctgtggacactca	tgtgctacttgttcccttcagtaggggcag	10/05/00	10/25/06	87	Genomic	97 %
ss2315637	TSC-CSHL\|TSC0722776	fwd/B	C/T	ctcggcctcaccagagcctgtggacactca	tgtgctacttgttcccttcagtaggggcag	10/20/00	10/10/03	88	Genomic	95 %
ss11810093	WI_SSAHASNP\|chr6.NT_007592.13_18697563	fwd/B	C/T	ctcggcctcaccagagcctgtggacactca	tgtgctacttgttcccttcagtaggggcag	07/04/03	10/10/03	116	Genomic	unknown
ss65841035	KRIBB_YJKIM\|KHS16828	fwd/B	C/T	ctcggcctcaccagagcctgtggacactca	tgtgctacttgttcccttcagtaggggcag	10/17/06	11/15/06	127	Genomic	unknown
ss66277004	AFFY\|SNP_A-1787205	rev/T	A/G	gggaacaagtagcaca	tgagtgtccacaggct	10/29/06	08/14/07	127	Genomic	unknown
ss75929851	AFFY\|AFFY_6_1M_SNP_A-1787205	rev/T	A/G	gggaacaagtagcaca	tgagtgtccacaggct	08/28/07	08/29/07	129	Genomic	unknown

Fasta sequence (Legend)

 AAGGTCCACT TAGAGCTAGA AGTTCATTTC ATAGATGACA GCATGCAGTA GGTTAAAGTA
 TCCCTCCTCA GAGGCCCACT ACCTAACACA TGGCTTGCTA AACATTACAT TGAAACAGAA
 CAAAAGTGTC GAGCTTTTTG TCAAAACTGT TACTTGCATg gggtacgatg gcaactttgt
 tatgtgcata tgctccaagg tggtcaagtt acatgggcta tacaagagct aaatagctta
 cattgtacca attaagtaac ttatcattca ttctttcctc ccttctgagt ccttattgtc
 tattgttcca ctctCATGTG TGTAGTTTTT AGAGCCTGTT Gttttttgta tttttgaggc
 ggagtctcgc tctgtagccc aggctggagg gcagtggcgc gatctcggct cactgcaacc
 tctgcctgcc aggttcaagc gatcctcctg cctcagcctc ccgagtagct gggactacag
 gcgcgtgcca ccacggccgg cagtcttttt tttagtggac aggggggttt caccgtgtta
 gccaggatgg tcttgatctc ctgaccttgt gatccgcctg cctcggcctc accagagCCT
 GTGGACACTC A
 Y
 TGTGCTACTT GTTCCCTTCA GTAGGGGCAG GTAGATACGC AGGAGACACA TTCCTCAAGG
 ATAAAAACAG GAATACTTTT CAAAACTAAA CTTCATCTGT AAAATTGACC CCATGACATG
 TCTTTTTTGA GTGATAATCC TTATCAGTAG GAACAGGTTC TGTATGTGAA ATTGATTTAG
 CATACCAACA GCCTGTGACC

GeneView

GeneView via analysis of contig annotation: HIST1H4L histone cluster 1, H4l

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

GeneView via analysis of contig annotation: HIST1H3I histone cluster 1, H3i

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_007592->NM_003546

function

reference

NT_007592->NM_003533

function

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


reference	NT_007592->NM_003546->NP_003537	18697563	reverse	3' near gene

reference	NT_007592->NM_003533->NP_003524	18697563	reverse	3' near gene

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs200955 maps exactly once on NCBI human chromosome 6

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
6	NW_001838980.1	919305	27646996	plus	T	alt_assembly_8	HuRef	HuRef	view	611
6	NT_007592.14	18697563	27947291	plus	T	ref_assembly	reference	reference	view	611
6	NW_923073.1	909668	29445347	plus	T	alt_assembly_1	Celera	Celera	view	611

NCBI Resource Links

Submitter-Referenced
GenBank
Z98744 AC024428 Z98744.1

dbSNP Blast Analysis
GenBank HTGS Finished:
Z98744.2

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss1845428	HapMap-CEU	European	120	IG			1.000			1.000

	HapMap-HCB	Asian	90	IG			1.000			1.000

	HapMap-JPT	Asian	86	IG			1.000			1.000

	HapMap-YRI	Sub-Saharan African	116	IG	0.017	0.276	0.707	0.752	0.155	0.845

ss65841035	KHP1		180	AF			1.000			1.000

ss66277004	HapMap-CEU	European	118	GF			1.000			1.000

	HapMap-HCB	Asian	90	GF			1.000			1.000

	HapMap-JPT	Asian	90	GF			1.000			1.000

	HapMap-YRI	Sub-Saharan African	120	GF	0.017	0.283	0.700		0.158	0.842

Concordant Genotype	Total Sample	C/C	C/T	T/T
ss1845428	269	1	27	237
ss66277004	268

RefSNP Genotype Summary	Total Individual	C/C	C/T	T/T
rs200955	270	1	27	237

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
5280	ss1845428	C/T	CSHL-HAPMAP	HapMap-YRI	NA19173	YOR047.01	r23_ch6_YRI_illumina:golden_gate_1.0.0	498545
5280	ss66277004	G/G	CSHL-HAPMAP	HapMap-YRI	NA19173	YOR047.01	chr6-HapMap-YRI

Genotype data submitted for	270	samples from	270	individuals	Individual with multiple genotypes submission:	269

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 .