Reference SNP(refSNP) Cluster Report: rs1211554

Reference SNP(refSNP) Cluster Report: rs1211554

refSNP ID: rs1211554
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	87/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	A/C
Ancestral Allele:	C
Clinical Association:	unknown

HGVS Names
NM_018303.4:c.-43-18282G>T
NM_148959.3:c.802G>T
NP_683762.2:p.D268Y
NT_034880.3:g.596142C>A
NT_034880.3:g.596143C>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss93363914 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1211554 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
ss1752893	KWOK\|OVLP-000925-280222	fwd/T	A/C	aggcaggaatgaaatactgaagagagacat	ttcttgaaccaaaacaagctgaagaagagt	10/05/00	04/07/04	87	Genomic	91 %
ss2624193	SC_JCM\|AL357054.4_201294	fwd/T	A/C	aggcaggaatgaaatactgaagagagacat	ttcttgaaccaaaacaagctgaagaagagt	11/03/00	10/10/03	92	Genomic	unknown
ss10303652	BCM_SSAHASNP\|chr6.NT_034880.2_596143	fwd/T	A/C	aggcaggaatgaaatactgaagagagacat	ttcttgaaccaaaacaagctgaagaagagt	06/27/03	10/10/03	116	Genomic	unknown
ss12922222	SC_SNP\|NT_034880.2_596143	fwd/T	A/C	aggcaggaatgaaatactgaagagagacat	ttcttgaaccaaaacaagctgaagaagagt	10/21/03	10/31/03	119	Genomic	unknown
ss15747848	SC_SNP\|NT_034880.3_596143	fwd/T	A/C	aggcaggaatgaaatactgaagagagacat	ttcttgaaccaaaacaagctgaagaagagt	11/17/03	11/22/03	120	Genomic	unknown
ss19671860	CSHL-HAPMAP\|CSHL-HuDD-200402.chr6.NT_034880.3_596143	fwd/T	A/C	aggcaggaatgaaatactgaagagagacat	ttcttgaaccaaaacaagctgaagaagagt	02/20/04	03/04/04	120	Genomic	unknown
ss20277644	CSHL-HAPMAP\|CSHL-HuFF-200402.chr6.NT_034880.3_596143	fwd/T	A/C	aggcaggaatgaaatactgaagagagacat	ttcttgaaccaaaacaagctgaagaagagt	02/21/04	03/04/04	120	Genomic	unknown
ss22506603	SSAHASNP\|WGSA-200403-chr6.chr6.NT_034880.3_596143	fwd/T	A/C	aggcaggaatgaaatactgaagagagacat	ttcttgaaccaaaacaagctgaagaagagt	03/21/04	03/21/04	121	Genomic	unknown
ss23394992	PERLEGEN\|afd1471421	fwd/T	A/C	aggcaggaatgaaatactgaagagagacat	ttcttgaaccaaaacaagctgaagaagagt	08/10/04	09/13/04	123	Genomic	unknown
ss66604561	ILLUMINA\|HumanHap300v1.1_rs1211554	fwd/B	A/C	aggcaggaatgaaatactgaagagagacat	ttcttgaaccaaaacaagctgaagaagagt	11/09/06	11/09/06	127	Genomic	unknown
ss66982857	ILLUMINA\|HumanHap550v1.1_rs1211554	fwd/T	A/C	aggcaggaatgaaatactgaagagagacat	ttcttgaaccaaaacaagctgaagaagagt	11/14/06	11/14/06	127	Genomic	unknown
ss67156506	ILLUMINA\|HumanHap650Yv1.0_rs1211554	fwd/T	A/C	aggcaggaatgaaatactgaagagagacat	ttcttgaaccaaaacaagctgaagaagagt	11/14/06	11/14/06	127	Genomic	unknown
ss68961751	PERLEGEN\|PGP01471421	fwd/T	A/C	aggcaggaatgaaatactgaagagagacat	ttcttgaaccaaaacaagctgaagaagagt	01/30/07	08/14/07	127	Genomic	unknown
ss70405070	ILLUMINA\|HumanHap300v2.0_rs1211554	fwd/T	A/C	aggcaggaatgaaatactgaagagagacat	ttcttgaaccaaaacaagctgaagaagagt	04/18/07	11/18/07	127	Genomic	unknown
ss70555925	ILLUMINA\|HumanHap550v3.0__rs1211554	fwd/T	A/C	aggcaggaatgaaatactgaagagagacat	ttcttgaaccaaaacaagctgaagaagagt	04/20/07	03/30/08	130	Genomic	unknown
ss71093221	ILLUMINA\|HumanHap650Yv3.0_rs1211554	fwd/T	A/C	aggcaggaatgaaatactgaagagagacat	ttcttgaaccaaaacaagctgaagaagagt	04/23/07	04/23/07	127	Genomic	unknown
ss74811237	AFFY\|SNP_M-185082	fwd/T	A/C	aggcaggaatgaaatactgaagagagacat	ttcttgaaccaaaacaagctgaagaagagt	08/09/07	08/09/07	128	Genomic	unknown
ss75811641	ILLUMINA\|ILMN_Human_1M_rs1211554	fwd/T	A/C	aggcaggaatgaaatactgaagagagacat	ttcttgaaccaaaacaagctgaagaagagt	08/28/07	08/29/07	129	Genomic	unknown
ss77668712	HGSV\|Cor12156_SNV_20070510.chr6_601143	fwd/T	A/C	aggcaggaatgaaatactgaagagagacat	ttcttgaaccaaaacaagctgaagaagagt	10/09/07	10/14/07	129	Genomic	unknown
ss78547980	HGSV\|Cor12878_SNV_20070510.chr6_601143	fwd/T	A/C	aggcaggaatgaaatactgaagagagacat	ttcttgaaccaaaacaagctgaagaagagt	10/17/07	10/19/07	129	Genomic	unknown
ss83700993	KRIBB_YJKIM\|KHS522797	fwd/T	A/C	aggcaggaatgaaatactgaagagagacat	ttcttgaaccaaaacaagctgaagaagagt	12/04/07	12/05/07	130	Genomic	unknown
ss86345357	CANCER-GENOME\|17565	fwd/T	A/C	aggcaggaatgaaatactgaagagagacat	ttcttgaaccaaaacaagctgaagaagagt	01/25/08	01/25/08	129	Genomic	unknown
ss93363914	BCMHGSC_JDW\|JWB-2085729	fwd/T	A/C	aggcaggaatgaaatactgaagagagacat	ttcttgaaccaaaacaagctgaagaagagt	02/26/08	03/04/08	129	Genomic	unknown

Fasta sequence (Legend)

 GAAAAAAACC TGACAAACCC AATAAACAAA ACATGAACTA CCCAACTGTT TTACCAATGC
 TTTAATATAA ATTTTGCAAA GGAGGAAGGG CTCAACAAAA TATACGCCCT GCATAAGTCA
 GTGAAGGTCC AAATTTTCAA CCCAATTAAC TCAGGGTCTG TTTTAGTTTT GAAAAGATCA
 AAACCTTAAA AAAAAAATCT AAGCTGGCTG AATTTTTACA AGGCAGGAAT GAAATACTGA
 AGAGAGACAT
 M
 TTCTTGAACC AAAACAAGCT GAAGAAGAGT ATTGTCCCAA ATATTGCACA GGGCCGTCGT
 AGGATGTATT TGCTGTCCCT CCAAAAACTG CAGAAGCTTC CGATTGTCCA CCCGCACTTG
 CACCATGCTC TCCAGGTCTC TGTTTTCAGG CACACCCACA GCCGACTGGG GAGGGTTTCC
 AAGATTTTTA AAATAACTTT GAATGGACAC CACCTCCGTC TCTATACTCA GGGTCATCCT
 GCCACTGAGG

GeneView

GeneView via analysis of contig annotation: EXOC2 exocyst complex component 2

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

GeneView via analysis of contig annotation: HUS1B HUS1 checkpoint homolog b (S. pombe)

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_034880->NM_018303

function

HuRef

NW_001838972->NM_018303

function

Celera

NW_922984->NM_018303

function

reference

NT_034880->NM_148959

function

HuRef

NW_001838972->NM_148959

function

Celera

NW_922984->NM_148959

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	mRNA pos	Function	dbSNP allele	Protein residue	Codon pos	Amino acid pos


reference	NT_034880->NM_018303->NP_060773	596143	reverse		intron

HuRef	NW_001838972->NM_018303->NP_060773	3128637	forward		intron

Celera	NW_922984->NM_018303->NP_060773	278769	reverse		intron

reference	NT_034880->NM_148959->NP_683762	596143	reverse	822	missense	T	Tyr [Y]	1	268
					contig reference	G	Asp [D]	1	268

HuRef	NW_001838972->NM_148959->NP_683762	3128637	forward	822	missense	G	Asp [D]	1	268
					contig reference	T	Tyr [Y]	1	268

Celera	NW_922984->NM_148959->NP_683762	278769	reverse	822	missense	G	Asp [D]	1	268
					contig reference	T	Tyr [Y]	1	268

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs1211554 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_001838972.2	3128637	526227	minus	T	alt_assembly_8	HuRef	HuRef	view	200
6	NT_034880.3	596143	601143	plus	C	ref_assembly	reference	reference	view	200
6	NW_922984.1	278769	1883513	plus	A	alt_assembly_1	Celera	Celera	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_034880 AL138738 AL357054.4

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank HTGS Finished:	GenBank HTGS Draft:
NM_148959.3	AL357054.14 NC_000006.10	AL138738.3

UniGene Cluster ID
483478

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/C	C/C	HWP	A	C
ss1752893	CEPH		184	AF					0.940	0.060

	HapMap-CEU	European	120	IG	0.800	0.200		0.403	0.900	0.100

	HapMap-HCB	Asian	90	IG	0.756	0.244		0.371	0.878	0.122

	HapMap-JPT	Asian	88	IG	0.682	0.318		0.251	0.841	0.159

	HapMap-YRI	Sub-Saharan African	120	IG	0.083	0.583	0.333	0.100	0.375	0.625

	CHMJ	Asian	74	IG					0.905	0.095

ss23394992	AFD_EUR_PANEL	European	48	IG	0.833	0.167		0.752	0.917	0.083

	AFD_AFR_PANEL	African American	46	IG	0.130	0.565	0.304	0.439	0.413	0.587

	AFD_CHN_PANEL	Asian	46	IG	0.826	0.130	0.043	0.150	0.891	0.109

ss68961751	HapMap-CEU	European	120	GF	0.800	0.200			0.900	0.100

	HapMap-HCB	Asian	90	GF	0.778	0.222			0.889	0.111

	HapMap-JPT	Asian	90	GF	0.667	0.333			0.833	0.167

	HapMap-YRI	Sub-Saharan African	120	GF	0.083	0.583	0.333		0.375	0.625

Concordant Genotype	Total Sample	A/A	A/C	C/C
ss1752893	269	147	89	32
ss23394992	71	42	20	8
ss68961751	269	147	90	32

RefSNP Genotype Summary	Total Individual	A/A	A/C	C/C
rs1211554	332	181	109	40

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
5174	ss1752893	A/C	CSHL-HAPMAP	HapMap-HCB	NA18571	CH18571	r23_ch6_HCB_illumina:golden_gate_1.0.0	499499
5174	ss68961751	A/A	CSHL-HAPMAP	HapMap-HCB	NA18571	CH18571	chr6-HapMap-HCB

Genotype data submitted for	341	samples from	332	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

Validated by: ILLUMINA, PERLEGEN

DoubleHit found by: BCM_SSAHASNP, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .