Reference SNP(refSNP) Cluster Report: rs4712827

Reference SNP(refSNP) Cluster Report: rs4712827

refSNP ID: rs4712827
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	111/129
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_007592.14:g.1544319C>T
XM_371798.5:c.270+1138G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44772569 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs4712827 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
ss6494156	WI_SSAHASNP\|NT_007592.11_1544319	fwd/B	C/T	tacacagacaaatgtagagtagcaagaaca	ccaccacaataatgaaaagtgtaaattcat	02/12/03	05/28/04	111	Genomic	unknown
ss11773331	WI_SSAHASNP\|chr6.NT_007592.13_1544319	fwd/B	C/T	tacacagacaaatgtagagtagcaagaaca	ccaccacaataatgaaaagtgtaaattcat	07/04/03	10/10/03	116	Genomic	unknown
ss12893974	SC_SNP\|NT_007592.13_1544319	fwd/B	C/T	tacacagacaaatgtagagtagcaagaaca	ccaccacaataatgaaaagtgtaaattcat	10/21/03	10/31/03	119	Genomic	unknown
ss17125071	CSHL-HAPMAP\|CSHL-HuAA-200402.chr6.NT_007592.13_1544319	fwd/B	C/T	tacacagacaaatgtagagtagcaagaaca	ccaccacaataatgaaaagtgtaaattcat	02/17/04	03/04/04	120	Genomic	unknown
ss44772569	ABI\|hCV401659	fwd/B	C/T	tacacagacaaatgtagagtagcaagaaca	ccaccacaataatgaaaagtgtaaattcat	07/19/05	11/03/06	126	Genomic	unknown
ss65723362	ILLUMINA\|Human1-rs4712827	fwd/B	C/T	tacacagacaaatgtagagtagcaagaaca	ccaccacaataatgaaaagtgtaaattcat	10/10/06	10/10/06	127	Genomic	unknown
ss66651740	ILLUMINA\|HumanHap300v1.1_rs4712827	fwd/T	C/T	tacacagacaaatgtagagtagcaagaaca	ccaccacaataatgaaaagtgtaaattcat	11/09/06	11/09/06	127	Genomic	unknown
ss67363386	ILLUMINA\|HumanHap550v1.1_rs4712827	fwd/B	C/T	tacacagacaaatgtagagtagcaagaaca	ccaccacaataatgaaaagtgtaaattcat	11/14/06	11/14/06	127	Genomic	unknown
ss67749259	ILLUMINA\|HumanHap650Yv1.0_rs4712827	fwd/B	C/T	tacacagacaaatgtagagtagcaagaaca	ccaccacaataatgaaaagtgtaaattcat	11/14/06	11/14/06	127	Genomic	unknown
ss68965079	PERLEGEN\|PGP04856733	fwd/B	C/T	tacacagacaaatgtagagtagcaagaaca	ccaccacaataatgaaaagtgtaaattcat	01/30/07	03/31/08	127	Genomic	unknown
ss70818288	ILLUMINA\|HumanHap550v3.0__rs4712827	rev/T	A/G	atgaatttacacttttcattattgtggtgg	tgttcttgctactctacatttgtctgtgta	04/20/07	03/30/08	130	Genomic	unknown
ss71399460	ILLUMINA\|HumanHap650Yv3.0_rs4712827	fwd/B	C/T	tacacagacaaatgtagagtagcaagaaca	ccaccacaataatgaaaagtgtaaattcat	04/23/07	04/23/07	127	Genomic	unknown
ss75533770	ILLUMINA\|ILMN_Human_1M_rs4712827	fwd/B	C/T	tacacagacaaatgtagagtagcaagaaca	ccaccacaataatgaaaagtgtaaattcat	08/28/07	08/29/07	129	Genomic	unknown
ss79191085	ILLUMINA\|HumanHap300v2.0_rs4712827	fwd/B	C/T	tacacagacaaatgtagagtagcaagaaca	ccaccacaataatgaaaagtgtaaattcat	04/18/07	11/18/07	130	Genomic	unknown
ss82582565	HGSV\|Cor18956_SNV_20070510.chr6_10794047	fwd/B	C/T	tacacagacaaatgtagagtagcaagaaca	ccaccacaataatgaaaagtgtaaattcat	11/30/07	12/03/07	130	Genomic	unknown
ss84326444	KRIBB_YJKIM\|KHS685011	fwd/B	C/T	tacacagacaaatgtagagtagcaagaaca	ccaccacaataatgaaaagtgtaaattcat	12/04/07	12/07/07	130	Genomic	unknown
ss93390791	BCMHGSC_JDW\|JWB-2097023	fwd/B	C/T	tacacagacaaatgtagagtagcaagaaca	ccaccacaataatgaaaagtgtaaattcat	02/26/08	03/04/08	129	Genomic	unknown

Fasta sequence (Legend)

 TTTAAGGTAA AGATCATCAC ACAAATGGTG TCACTCTGCA TATTAGGAGA CAAGCTGGGG
 TGGGGGAAGT CCGTAACATT TAGACTCCAA AGTGTTAATT TCTCTAACAT GTGAATATCT
 TATGCAGTCA AGCAAGAGGG ACACAACTCA ACAGAAAAAT TAGAAAGAGG ATATCAAAGT
 CACAGAACAC AGATAGCAAT AAACATTTCA AGAGGTATTT GCCCTCAATA ATAGATAAAT
 GCCTCCCTGC CCTATTAGAT TGGCTAATCA TACACAGACA AATGTAGAGT AGCAAGAACA
 Y
 CCACCACAAT AATGAAAAGT GTAAATTCAT GCAGACTTTA GGTAACTTGC TATTAAAATT
 TTTTAATGTT ATATCCTTTA ATCCAGCCCT TCCACATCCA GAATTATATT CTTGGGGAAA
 AAAGCAACAC TCAGACAAAT GCTTGAAGAT AGGTAAGTTT GTTAAAGCCC TGAAAATATT
 TAAAATGTCA GATAAGGGAT GAGCTAAAAA TCGCAATGTA TCTAACTGCG CTCGCTCTGT
 TGCTCAGGCT GGAGTACAAT GGCACAATCA TGGCTCATTG CAGCCTCAAA CTCCCGGACT

GeneView

GeneView via analysis of contig annotation: C6orf52 chromosome 6 open reading frame 52

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->XM_371798

function

HuRef

NW_001838973->XM_001718541

function

Celera

NW_922984->XM_938497

function

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


reference	NT_007592->XM_371798->XP_371798	1544319	reverse	intron

HuRef	NW_001838973->XM_001718541->XP_001718593	6906714	reverse	intron

Celera	NW_922984->XM_938497->XP_943590	10309809	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs4712827 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_001838973.1	6906714	10561677	plus	C	alt_assembly_8	HuRef	HuRef	view	300
6	NT_007592.14	1544319	10794047	plus	C	ref_assembly	reference	reference	view	300
6	NW_922984.1	10309809	11914553	plus	C	alt_assembly_1	Celera	Celera	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_007592

dbSNP Blast Analysis
GenBank HTGS Finished:
AL358777.12 NC_000006.10

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss44772569	HapMap-CEU	European	116	IG	0.190	0.466	0.345	0.752	0.422	0.578

	HapMap-HCB	Asian	86	IG	0.023	0.256	0.721	1.000	0.151	0.849

	HapMap-JPT	Asian	86	IG	0.023	0.256	0.721	1.000	0.151	0.849

	HapMap-YRI	Sub-Saharan African	120	IG	0.200	0.550	0.250	0.439	0.475	0.525

	AoD_African_American		90	AF					0.520	0.480

ss68965079	HapMap-CEU	European	120	GF	0.183	0.467	0.350		0.417	0.583

	HapMap-HCB	Asian	90	GF	0.022	0.311	0.667		0.178	0.822

	HapMap-JPT	Asian	90	GF	0.022	0.289	0.689		0.167	0.833

	HapMap-YRI	Sub-Saharan African	120	GF	0.200	0.567	0.233		0.483	0.517

Concordant Genotype	Total Sample	C/C	C/T	T/T
ss44772569	259	38	109	104
ss68965079	259	38	111	110

RefSNP Genotype Summary	Total Individual	C/C	C/T	T/T
rs4712827	270	38	111	110

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
252	ss44772569	T/T	CSHL-HAPMAP	HapMap-CEU	NA11839	CEPH1349.13	r23_ch6_CEU_illumina:golden_gate_1.0.0	521757
252	ss68965079	C/T	CSHL-HAPMAP	HapMap-CEU	NA11839	CEPH1349.13	chr6-HapMap-CEU
399	ss44772569	T/T	CSHL-HAPMAP	HapMap-CEU	NA10830	CEPH1408.01	r23_ch6_CEU_illumina:golden_gate_1.0.0	521757
399	ss68965079	C/T	CSHL-HAPMAP	HapMap-CEU	NA10830	CEPH1408.01	chr6-HapMap-CEU
5139	ss44772569	C/T	CSHL-HAPMAP	HapMap-YRI	NA19100	YOR105.01	r23_ch6_YRI_illumina:golden_gate_1.0.0	521757
5139	ss68965079	C/C	CSHL-HAPMAP	HapMap-YRI	NA19100	YOR105.01	chr6-HapMap-YRI
5153	ss44772569	T/T	CSHL-HAPMAP	HapMap-HCB	NA18561	CH18561	r23_ch6_HCB_illumina:golden_gate_1.0.0	521757
5153	ss68965079	C/T	CSHL-HAPMAP	HapMap-HCB	NA18561	CH18561	chr6-HapMap-HCB
5169	ss44772569	T/T	CSHL-HAPMAP	HapMap-HCB	NA18564	CH18564	r23_ch6_HCB_illumina:golden_gate_1.0.0	521757
5169	ss68965079	C/T	CSHL-HAPMAP	HapMap-HCB	NA18564	CH18564	chr6-HapMap-HCB
5174	ss44772569	T/T	CSHL-HAPMAP	HapMap-HCB	NA18571	CH18571	r23_ch6_HCB_illumina:golden_gate_1.0.0	521757
5174	ss68965079	C/T	CSHL-HAPMAP	HapMap-HCB	NA18571	CH18571	chr6-HapMap-HCB
5182	ss44772569	C/T	CSHL-HAPMAP	HapMap-HCB	NA18577	CH18577	r23_ch6_HCB_illumina:golden_gate_1.0.0	521757
5182	ss68965079	T/T	CSHL-HAPMAP	HapMap-HCB	NA18577	CH18577	chr6-HapMap-HCB
5191	ss44772569	T/T	CSHL-HAPMAP	HapMap-HCB	NA18593	CH18593	r23_ch6_HCB_illumina:golden_gate_1.0.0	521757
5191	ss68965079	C/T	CSHL-HAPMAP	HapMap-HCB	NA18593	CH18593	chr6-HapMap-HCB
5211	ss44772569	T/T	CSHL-HAPMAP	HapMap-JPT	NA18972	JA18972	r23_ch6_JPT_illumina:golden_gate_1.0.0	521757
5211	ss68965079	C/T	CSHL-HAPMAP	HapMap-JPT	NA18972	JA18972	chr6-HapMap-JPT
5213	ss44772569	T/T	CSHL-HAPMAP	HapMap-JPT	NA18973	JA18973	r23_ch6_JPT_illumina:golden_gate_1.0.0	521757
5213	ss68965079	C/T	CSHL-HAPMAP	HapMap-JPT	NA18973	JA18973	chr6-HapMap-JPT
5294	ss44772569	T/T	CSHL-HAPMAP	HapMap-YRI	NA19160	YOR056.03	r23_ch6_YRI_illumina:golden_gate_1.0.0	521757
5294	ss68965079	C/T	CSHL-HAPMAP	HapMap-YRI	NA19160	YOR056.03	chr6-HapMap-YRI

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

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, NCBI

UNKNOWN

Disclaimer Privacy statement

Revised: May 25, 2006 1:38 PM .