Reference SNP(refSNP) Cluster Report: rs1128628

Reference SNP(refSNP) Cluster Report: rs1128628

refSNP ID: rs1128628
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/G
Ancestral Allele:	C
Clinical Association:	unknown

HGVS Names
NM_025083.2:c.*1618C>G
NT_010194.16:g.45713653G>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss43714946 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1128628 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
ss1516377	LEE\|191164	fwd/B	C/G	ggccaagcagctcccaagccggggccctct	ttggccaaaatctgaggagcagtctaggtt	09/13/00	05/16/04	86	cDNA	unknown
ss4320850	CGAP-GAI\|237714	rev/T	C/G	aacctagactgctcctcagattttggccaa	agagggccccggcttgggagctgcttggcc	11/28/01	10/10/03	103	cDNA	unknown
ss4409024	LEE\|e191164	fwd/B	C/G	ggccaagcagctcccaagccggggccctct	ttggccaaaatctgaggagcagtctaggtt	04/26/02	10/10/03	108	cDNA	unknown
ss16246253	CGAP-GAI\|1490307	fwd/B	C/G	ggccaagcagctcccaagccggggccctct	ttggccaaaatctgaggagcagtctaggtt	11/18/03	11/22/03	120	cDNA	unknown
ss24179188	PERLEGEN\|afd4223432	rev/T	C/G	aacctagactgctcctcagattttggccaa	agagggccccggcttgggagctgcttggcc	08/10/04	09/13/04	126	Genomic	unknown
ss43714946	ABI\|hCV8870018	rev/	C/G	aacctagactgctcctcagattttggccaa	agagggccccggcttgggagctgcttggcc	07/18/05	11/03/06	126	Genomic	unknown
ss69181358	PERLEGEN\|PGP04223432	rev/	C/G	aacctagactgctcctcagattttggccaa	agagggccccggcttgggagctgcttggcc	01/30/07	08/14/07	127	Genomic	unknown
ss82829697	HGSV\|Cor18956_SNV_20070510.chr15_72710388	rev/	C/G	aacctagactgctcctcagattttggccaa	agagggccccggcttgggagctgcttggcc	11/30/07	12/03/07	130	Genomic	unknown
ss85070154	HGSV\|Cor19129_SNV_20070510.chr15_72710388	rev/	C/G	aacctagactgctcctcagattttggccaa	agagggccccggcttgggagctgcttggcc	12/06/07	12/08/07	130	Genomic	unknown

Fasta sequence (Legend)

 CTCTGTGTCT GCCCAGGCTG GCTGAGCGGG TGGATGGGTG GACAGAAGGG CTCACCAAGG
 ATTGTGGACA TAGGGTAGGC CCTGGTACCA CGGGTTTCAG GCTGTTATCA CTTCCCTTGT
 AGGAACATAG CCAGAAGCAG ATGAGCCAGG GTAGAGGGCT GGCCCCTCCT CTCATCTTCC
 CTTCAGTCTT AAATTGTCTC CAGCGATGGG AAGAGGCCAG GGACTGTAAC CCTTGTGCTG
 TGTATTCTCT GAGCCTCTGC TCACTCTCAG GGCCAAGCAG CTCCCAAGCC GGGGCCCTCT
 S
 TTGGCCAAAA TCTGAGGAGC AGTCTAGGTT ACAGGCTTTT TGGTAGGTAG GTTCTGGCTG
 CCTGTTAATG CAGTTAGGCC CCCTGATTAG GTACAGTGAG AAACAAGCTA GAACAACCCT
 GGCCCAGAAG ACTGTCCACT CCAGCAAGAT CCAGGGATGA TAGCCTTGCA GGGCCACTGG
 GAGTTTGTGC CCAAGCTTCT CCCTCTTCTC TCCCCAGGGG GCACTGGGAC TGGTCCCTGC
 CCTCATCCTT AGCCTGGGCC TTCCCCAGAG GTATTAAAGA GAAGTATGAT TCCTCTGTCT

GeneView

GeneView via analysis of contig annotation: EDC3 enhancer of mRNA decapping 3 homolog (S. cerevisiae)

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_010194->NM_025083

function

HuRef

NW_001838219->NM_025083

function

Celera

NW_925907->NM_025083

function

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


reference	NT_010194->NM_025083->	45713653	reverse	3303	3' UTR

HuRef	NW_001838219->NM_025083->	530387	reverse	3303	3' UTR

Celera	NW_925907->NM_025083->	529831	reverse	3303	3' UTR

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs1128628 maps exactly once on NCBI human chromosome 15

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
15	NW_001838219.1	530387	51721496	minus	G	alt_assembly_8	HuRef	HuRef	view	300
15	NW_925907.1	529831	51873270	minus	G	alt_assembly_1	Celera	Celera	view	300
15	NT_010194.16	45713653	72710388	minus	G	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
dbSTS	GenBank
CGAP-C-23771	NC_000015.8 BF975484 Hs.22208

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank HTGS Finished:	GenBank mRNA:
NM_025083.2	AC100835.2 NC_000015.8	BC011534.1

UniGene Cluster ID
96852

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/G	G/G	HWP	C	G
ss1516377	CEPH		184	AF					0.880	0.120

ss24179188	AFD_EUR_PANEL	European	48	IG	0.917	0.083		1.000	0.958	0.042

	AFD_AFR_PANEL	African American	46	IG	0.696	0.261	0.043	0.752	0.826	0.174

	AFD_CHN_PANEL	Asian	48	IG	0.417	0.458	0.125	1.000	0.646	0.354

ss43714946	HapMap-CEU	European	118	IG	0.847	0.136	0.017	0.343	0.915	0.085

	HapMap-HCB	Asian	86	IG	0.349	0.581	0.070	0.100	0.640	0.360

	HapMap-JPT	Asian	90	IG	0.422	0.489	0.089	0.527	0.667	0.333

	HapMap-YRI	Sub-Saharan African	110	IG	0.655	0.309	0.036	1.000	0.809	0.191

ss69181358	HapMap-CEU	European	120	GF	0.850	0.150			0.925	0.075

	HapMap-HCB	Asian	90	GF	0.378	0.622			0.689	0.311

	HapMap-JPT	Asian	90	GF	0.422	0.578			0.711	0.289

	HapMap-YRI	Sub-Saharan African	120	GF	0.650	0.350			0.825	0.175

Concordant Genotype	Total Sample	C/C	C/G	G/G
ss24179188	71	4	19	48
ss43714946	250		80	161
ss69181358	250		83	167

RefSNP Genotype Summary	Total Individual	C/C	C/G	G/G
rs1128628	332	4	101	207

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
262	ss43714946	C/G	CSHL-HAPMAP	HapMap-CEU	NA11829	CEPH1350.10	r23_ch15_CEU_perlegen:genotyping_1.0.0	5131734
262	ss69181358	G/G	CSHL-HAPMAP	HapMap-CEU	NA11829	CEPH1350.10	chr15-HapMap-CEU
373	ss43714946	G/G	CSHL-HAPMAP	HapMap-CEU	NA12264	CEPH1375.11	r23_ch15_CEU_perlegen:genotyping_1.0.0	5131734
373	ss69181358	C/G	CSHL-HAPMAP	HapMap-CEU	NA12264	CEPH1375.11	chr15-HapMap-CEU
411	ss43714946	G/G	CSHL-HAPMAP	HapMap-CEU	NA12156	CEPH1408.13	r23_ch15_CEU_perlegen:genotyping_1.0.0	5131734
411	ss69181358	C/G	CSHL-HAPMAP	HapMap-CEU	NA12156	CEPH1408.13	chr15-HapMap-CEU
466	ss43714946	C/G	CSHL-HAPMAP	HapMap-CEU	NA12005	CEPH1420.11	r23_ch15_CEU_perlegen:genotyping_1.0.0	5131734
466	ss69181358	G/G	CSHL-HAPMAP	HapMap-CEU	NA12005	CEPH1420.11	chr15-HapMap-CEU
566	ss43714946	C/G	CSHL-HAPMAP	HapMap-CEU	NA12802	CEPH1454.02	r23_ch15_CEU_perlegen:genotyping_1.0.0	5131734
566	ss69181358	G/G	CSHL-HAPMAP	HapMap-CEU	NA12802	CEPH1454.02	chr15-HapMap-CEU
577	ss43714946	C/C	CSHL-HAPMAP	HapMap-CEU	NA12813	CEPH1454.13	r23_ch15_CEU_perlegen:genotyping_1.0.0	5131734
577	ss69181358	C/G	CSHL-HAPMAP	HapMap-CEU	NA12813	CEPH1454.13	chr15-HapMap-CEU
5133	ss43714946	G/G	CSHL-HAPMAP	HapMap-YRI	NA18502	YOR004.02	r23_ch15_YRI_perlegen:genotyping_1.0.0	5131734
5133	ss69181358	C/G	CSHL-HAPMAP	HapMap-YRI	NA18502	YOR004.02	chr15-HapMap-YRI
5134	ss43714946	C/C	CSHL-HAPMAP	HapMap-YRI	NA19127	YOR077.02	r23_ch15_YRI_perlegen:genotyping_1.0.0	5131734
5134	ss69181358	C/G	CSHL-HAPMAP	HapMap-YRI	NA19127	YOR077.02	chr15-HapMap-YRI
5163	ss43714946	C/C	CSHL-HAPMAP	HapMap-HCB	NA18609	CH18609	r23_ch15_HCB_perlegen:genotyping_1.0.0	5131734
5163	ss69181358	C/G	CSHL-HAPMAP	HapMap-HCB	NA18609	CH18609	chr15-HapMap-HCB
5170	ss43714946	C/C	CSHL-HAPMAP	HapMap-HCB	NA18566	CH18566	r23_ch15_HCB_perlegen:genotyping_1.0.0	5131734
5170	ss69181358	C/G	CSHL-HAPMAP	HapMap-HCB	NA18566	CH18566	chr15-HapMap-HCB
5182	ss43714946	C/C	CSHL-HAPMAP	HapMap-HCB	NA18577	CH18577	r23_ch15_HCB_perlegen:genotyping_1.0.0	5131734
5182	ss69181358	C/G	CSHL-HAPMAP	HapMap-HCB	NA18577	CH18577	chr15-HapMap-HCB
5186	ss43714946	C/G	CSHL-HAPMAP	HapMap-HCB	NA18582	CH18582	r23_ch15_HCB_perlegen:genotyping_1.0.0	5131734
5186	ss69181358	G/G	CSHL-HAPMAP	HapMap-HCB	NA18582	CH18582	chr15-HapMap-HCB
5189	ss43714946	C/G	CSHL-HAPMAP	HapMap-HCB	NA18592	CH18592	r23_ch15_HCB_perlegen:genotyping_1.0.0	5131734
5189	ss69181358	G/G	CSHL-HAPMAP	HapMap-HCB	NA18592	CH18592	chr15-HapMap-HCB
5203	ss43714946	C/C	CSHL-HAPMAP	HapMap-JPT	NA18956	JA18956	r23_ch15_JPT_perlegen:genotyping_1.0.0	5131734
5203	ss69181358	C/G	CSHL-HAPMAP	HapMap-JPT	NA18956	JA18956	chr15-HapMap-JPT
5218	ss43714946	C/C	CSHL-HAPMAP	HapMap-JPT	NA18978	JA18978	r23_ch15_JPT_perlegen:genotyping_1.0.0	5131734
5218	ss69181358	C/G	CSHL-HAPMAP	HapMap-JPT	NA18978	JA18978	chr15-HapMap-JPT
5221	ss43714946	C/C	CSHL-HAPMAP	HapMap-JPT	NA18995	JA18995	r23_ch15_JPT_perlegen:genotyping_1.0.0	5131734
5221	ss69181358	C/G	CSHL-HAPMAP	HapMap-JPT	NA18995	JA18995	chr15-HapMap-JPT
5223	ss43714946	C/C	CSHL-HAPMAP	HapMap-JPT	NA18971	JA18971	r23_ch15_JPT_perlegen:genotyping_1.0.0	5131734
5223	ss69181358	C/G	CSHL-HAPMAP	HapMap-JPT	NA18971	JA18971	chr15-HapMap-JPT
5259	ss43714946	G/G	CSHL-HAPMAP	HapMap-YRI	NA18857	YOR023.01	r23_ch15_YRI_perlegen:genotyping_1.0.0	5131734
5259	ss69181358	C/G	CSHL-HAPMAP	HapMap-YRI	NA18857	YOR023.01	chr15-HapMap-YRI
5266	ss43714946	C/C	CSHL-HAPMAP	HapMap-YRI	NA18912	YOR028.02	r23_ch15_YRI_perlegen:genotyping_1.0.0	5131734
5266	ss69181358	C/G	CSHL-HAPMAP	HapMap-YRI	NA18912	YOR028.02	chr15-HapMap-YRI
5310	ss43714946	C/C	CSHL-HAPMAP	HapMap-YRI	NA19129	YOR077.01	r23_ch15_YRI_perlegen:genotyping_1.0.0	5131734
5310	ss69181358	C/G	CSHL-HAPMAP	HapMap-YRI	NA19129	YOR077.01	chr15-HapMap-YRI

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
	UNKNOWN	UNKNOWN	UNKNOWN

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Revised: May 25, 2006 1:38 PM .