Reference SNP(refSNP) Cluster Report: rs272827

Reference SNP(refSNP) Cluster Report: rs272827

refSNP ID: rs272827
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_018067.3:c.46+5127T>C
NT_032977.8:g.6599109T>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss41137081 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs272827 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
ss354659	KWOK\|OVLP-000621-123311	fwd/T	A/G	ctaatgcttttgtcaggcacagctaaacac	ttaaactcattagttcatttaacctttgcc	06/30/00	10/10/03	79	Genomic	99 %
ss694192	SC_JCM\|AL138901.2_67753	fwd/T	A/G	ctaatgcttttgtcaggcacagctaaacac	ttaaactcattagttcatttaacctttgcc	07/27/00	10/10/03	87	Genomic	unknown
ss983814	KWOK\|OVLP-000804-596889	fwd/T	A/G	ctaatgcttttgtcaggcacagctaaacac	ttaaactcattagttcatttaacctttgcc	09/01/00	10/10/03	86	Genomic	99 %
ss984664	KWOK\|OVLP-000804-601821	fwd/T	A/G	ctaatgcttttgtcaggcacagctaaacac	ttaaactcattagttcatttaacctttgcc	09/01/00	10/10/03	86	Genomic	99 %
ss1586491	KWOK\|OVLP-000925-203441	fwd/T	A/G	ctaatgcttttgtcaggcacagctaaacac	ttaaactcattagttcatttaacctttgcc	10/04/00	10/10/03	87	Genomic	99 %
ss6403898	WI_SSAHASNP\|NT_004511.13_2959510	rev/B	C/T	ggcaaaggttaaatgaactaatgagtttaa	gtgtttagctgtgcctgacaaaagcattag	02/12/03	10/10/03	111	Genomic	unknown
ss9862343	BCM_SSAHASNP\|chr1.NT_004511.15_6408742	rev/B	C/T	ggcaaaggttaaatgaactaatgagtttaa	gtgtttagctgtgcctgacaaaagcattag	06/27/03	10/10/03	116	Genomic	unknown
ss13001469	SC_SNP\|NT_004511.15_6408742	rev/B	C/T	ggcaaaggttaaatgaactaatgagtttaa	gtgtttagctgtgcctgacaaaagcattag	10/22/03	10/31/03	119	Genomic	unknown
ss16434900	CSHL-HAPMAP\|CSHL-HuAA-200402.chr1.NT_079482.1_1328937	rev/B	C/T	ggcaaaggttaaatgaactaatgagtttaa	gtgtttagctgtgcctgacaaaagcattag	02/17/04	03/04/04	120	Genomic	unknown
ss41137081	ABI\|hCV3124849	rev/B	C/T	ggcaaaggttaaatgaactaatgagtttaa	gtgtttagctgtgcctgacaaaagcattag	07/16/05	11/03/06	126	Genomic	unknown
ss66194530	AFFY\|SNP_A-2263904	rev/B	C/T	gaactaatgagtttaa	gtgtttagctgtgcct	10/27/06	08/14/07	127	Genomic	unknown
ss66712158	ILLUMINA\|HumanHap300v1.1_rs272827	fwd/B	A/G	ctaatgcttttgtcaggcacagctaaacac	ttaaactcattagttcatttaacctttgcc	11/09/06	11/09/06	127	Genomic	unknown
ss67270307	ILLUMINA\|HumanHap550v1.1_rs272827	fwd/T	A/G	ctaatgcttttgtcaggcacagctaaacac	ttaaactcattagttcatttaacctttgcc	11/14/06	11/14/06	127	Genomic	unknown
ss67670834	ILLUMINA\|HumanHap650Yv1.0_rs272827	fwd/T	A/G	ctaatgcttttgtcaggcacagctaaacac	ttaaactcattagttcatttaacctttgcc	11/14/06	11/14/06	127	Genomic	unknown
ss68397129	CSHL-HAPMAP\|sanger:assay:4496281:1	rev/B	C/T	ggcaaaggttaaatgaactaatgagtttaa	gtgtttagctgtgcctgacaaaagcattag	01/11/07	01/16/07	127	NA	unknown
ss68763441	PERLEGEN\|PGP06611194	rev/B	C/T	ggcaaaggttaaatgaactaatgagtttaa	gtgtttagctgtgcctgacaaaagcattag	01/30/07	08/14/07	127	Genomic	unknown
ss70748754	ILLUMINA\|HumanHap550v3.0__rs272827	fwd/T	A/G	ctaatgcttttgtcaggcacagctaaacac	ttaaactcattagttcatttaacctttgcc	04/20/07	03/30/08	130	Genomic	unknown
ss71320841	ILLUMINA\|HumanHap650Yv3.0_rs272827	fwd/T	A/G	ctaatgcttttgtcaggcacagctaaacac	ttaaactcattagttcatttaacctttgcc	04/23/07	04/23/07	127	Genomic	unknown
ss75643611	ILLUMINA\|ILMN_Human_1M_rs272827	fwd/T	A/G	ctaatgcttttgtcaggcacagctaaacac	ttaaactcattagttcatttaacctttgcc	08/28/07	08/29/07	129	Genomic	unknown
ss76274809	AFFY\|AFFY_6_1M_SNP_A-2263904	rev/B	C/T	gaactaatgagtttaa	gtgtttagctgtgcct	08/28/07	08/30/07	129	Genomic	unknown
ss79145074	ILLUMINA\|HumanHap300v2.0_rs272827	fwd/T	A/G	ctaatgcttttgtcaggcacagctaaacac	ttaaactcattagttcatttaacctttgcc	04/18/07	11/18/07	130	Genomic	unknown
ss83409535	KRIBB_YJKIM\|KHS454860	fwd/T	A/G	ctaatgcttttgtcaggcacagctaaacac	ttaaactcattagttcatttaacctttgcc	12/04/07	12/05/07	130	Genomic	unknown
ss87355625	BCMHGSC_JDW\|JWB-0033425	rev/B	C/T	ggcaaaggttaaatgaactaatgagtttaa	gtgtttagctgtgcctgacaaaagcattag	02/26/08	02/26/08	129	Genomic	unknown
ss108121432	1000GENOMES\|CEU.trio.12.15.2008_45598_chr1_36399778	rev/B	C/T	ggcaaaggttaaatgaactaatgagtttaa	gtgtttagctgtgcctgacaaaagcattag	12/15/08	12/15/08	130	Genomic	unknown
ss110294064	1000GENOMES\|NA19240_2008_12_16_43545_chr1_36399778	rev/B	C/T	ggcaaaggttaaatgaactaatgagtttaa	gtgtttagctgtgcctgacaaaagcattag	12/16/08	12/17/08	130	Genomic	unknown

Fasta sequence (Legend)

 ACACACACAC ACATACACAC ACACACATGC AGAGGAAACA GACTTACTGG GATTCAAAAC
 TCTACACATA TCTGAGACAC ACAGATGTAC CCACAGAGTA CGGGGCCAGG TACCTCCTCT
 AAGAAACAGA CAAAGCCTCA GAGACACACA CAGCACACAG AGACACAATG TCCCCGGAAT
 ATTTATACAG CGTCATCCAG GTCACTTCTG CTCCTTCTGA GCAAATTATT TCCCTAGGCC
 CAGAGAAAGT CCGATTAACA GGAGCAACAG CTAATGCTTT TGTCAGGCAC AGCTAAACAC
 R
 TTAAACTCAT TAGTTCATTT AACCTTTGCC ATAATCCTAT GAGGTAGATA TTATTACCCC
 ATTTTACAAA CGAGGAAACA GGTTCAGAGA TTAAGACACT TACTTAAGCT CCACAGCTAG
 TGAGTAGCAA AGCTGGGGTT TGGACCCAAT CAGCATGACG GTCTTTACCC TGCCTGCATC
 CCAGTGGGGA CAGCCTCCTG GGTTCCCTCT CCTGGAGAGA TCTGGGCTGG GAGAATAGGA
 GGTCAGTAGA AAGGGCAAAC TCTGGGGAAT GCCTAATTGT GGGGCCGGGA GAGGAGGGAC

GeneView

GeneView via analysis of contig annotation: MAP7D1 MAP7 domain containing 1

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_032977->NM_018067

function

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


reference	NT_032977->NM_018067->NP_060537	6599109	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs272827 maps exactly once on NCBI human chromosome 1

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
1	NW_001838577.2	6524586	34743912	plus	A	alt_assembly_8	HuRef	HuRef	view	300
1	NW_921351.1	10762529	34901671	minus	C	alt_assembly_1	Celera	Celera	view	300
1	NT_032977.8	6599109	36399778	minus	T	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_079482 AC026653 AL138901.2 AL138901.3 AL360074.3

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
ss41137081	HapMap-CEU	European	120	IG	0.100	0.400	0.500	0.752	0.300	0.700

	HapMap-HCB	Asian	90	IG		0.156	0.844	0.584	0.078	0.922

	HapMap-JPT	Asian	90	IG	0.022	0.244	0.733	1.000	0.144	0.856

	HapMap-YRI	Sub-Saharan African	120	IG		0.100	0.900	0.752	0.050	0.950

ss66194530	HapMap-CEU	European	118	GF	0.102	0.390	0.508		0.297	0.703

	HapMap-HCB	Asian	90	GF		0.156	0.844		0.078	0.922

	HapMap-JPT	Asian	90	GF	0.022	0.244	0.733		0.144	0.856

	HapMap-YRI	Sub-Saharan African	120	GF		0.100	0.900		0.050	0.950

ss68763441	HapMap-CEU	European	120	GF	0.100	0.400	0.500		0.300	0.700

	HapMap-HCB	Asian	90	GF		0.156	0.844		0.078	0.922

	HapMap-JPT	Asian	90	GF	0.022	0.244	0.733		0.144	0.856

	HapMap-YRI	Sub-Saharan African	120	GF		0.100	0.900		0.050	0.950

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.251+/-0.250	270	210	270	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

Disclaimer Privacy statement

Revised: May 25, 2006 1:38 PM .