Reference SNP(refSNP) Cluster Report: rs3887583

Reference SNP(refSNP) Cluster Report: rs3887583

refSNP ID: rs3887583
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	108/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	G/T
Ancestral Allele:	G
Clinical Association:	unknown

HGVS Names
NM_004933.2:c.42+2666G>T
NT_010542.15:g.801564G>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss43835026 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3887583 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
ss73908	TSC-CSHL\|TSC0028292	fwd/B	G/T	tgtttgtagactgcagcaagcacccagtgt	tgcagagctttcttacacagcagccccttg	09/06/00	10/10/03	108	Genomic	unknown
ss5957271	SC_JCM\|NT_010542.10_46518	fwd/B	G/T	tgtttgtagactgcagcaagcgcccagtgt	tgcagagctttcttacacagcagccccttg	01/10/03	10/10/03	111	Genomic	unknown
ss6603525	WI_SSAHASNP\|NT_010542.11_46842	fwd/B	G/T	tgtttgtagactgcagcaagcgcccagtgt	tgcagagctttcttacacagcagccccttg	02/12/03	10/10/03	111	Genomic	unknown
ss43835026	ABI\|hCV1008243	fwd/B	G/T	tgtttgtagactgcagcaagcgcccagtgt	tgcagagctttcttacacagcagccccttg	07/18/05	11/03/06	126	Genomic	unknown
ss69355300	PERLEGEN\|PGP04624172	fwd/B	G/T	tgtttgtagactgcagcaagcgcccagtgt	tgcagagctttcttacacagcagccccttg	01/30/07	01/30/07	127	Genomic	unknown
ss109572902	1000GENOMES\|CEU.trio.12.15.2008_3351970_chr16_87768448	fwd/B	G/T	tgtttgtagactgcagcaagcgcccagtgt	tgcagagctttcttacacagcagccccttg	12/15/08	12/16/08	130	Genomic	unknown

Fasta sequence (Legend)

 CTGGGGCCAT TCCTGGCATG CCTGGCCATC CAGGAACGGG GTGGCCCCAG ATTCCAGCCT
 GGGGGAGGGG TTGAAGCCTG AGAAGCTTGA GGGGCCTTCG CACTCTCTTC CCAGGCAAAC
 CCACCCACAC GCCACCAAGC GTGTTCCTAG AATCTCGTAG CACCCTTCCT TGGAAAACCG
 GGGGAGCAGG AGTGCAAGGT CGGCCCCAGA ACCGCTCCTC GTTCCCGTCT CGCAGTGGTG
 TTCGTAAACC CCATTCCCAC CTCGCAGTGG TGTTTGTAGA CTGCAGCAAG CGCCCAGTGT
 K
 TGCAGAGCTT TCTTACACAG CAGCCCCTTG GGGTTGAGTG TCAGGCTAGG AGCAGACCTC
 AAGAGAAGCG TTAAGTCCCA GGAGCTTGGC TGCAGGGCGG TGGCCCCAGA CGTCTCAAGG
 GCTTCGAGGT GGTTCCCTCC AGGCTCTTGG CTAAGGGTCC AGTCGAGGAT GAGCTTGGGG
 GTGTCATTGG GGACCCCCTG TGGGGAAGCA GGTCACTAAT GTCCATGGGT CTTGCCTGGC
 TTGGGTGGGG GACAGAGAGG AGTGGACGAG TGTCCACAAA ATCCACCTCC CAGGGTGCTT

GeneView

GeneView via analysis of contig annotation: CDH15 cadherin 15, type 1, M-cadherin (myotubule)

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_010542->NM_004933

function

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


reference	NT_010542->NM_004933->NP_004924	801564	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs3887583 maps exactly once on NCBI human chromosome 16

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
16	NW_926561.1	874551	74306561	plus	G	alt_assembly_1	Celera	Celera	view	300
16	NW_001838336.2	926769	74939813	minus	C	alt_assembly_8	HuRef	HuRef	view	300
16	NT_010542.15	801564	87768448	plus	G	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_010542.10

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	G/G	G/T	T/T	HWP	G	T
ss43835026	HapMap-CEU	European	120	IG	0.883	0.117		0.655	0.942	0.058

	HapMap-HCB	Asian	90	IG	0.644	0.333	0.022	0.584	0.811	0.189

	HapMap-JPT	Asian	88	IG	0.682	0.295	0.023	1.000	0.830	0.170

	HapMap-YRI	Sub-Saharan African	120	IG	1.000				1.000

ss69355300	HapMap-CEU	European	120	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	1.000				1.000

Concordant Genotype	Total Sample	G/G	G/T	T/T
ss43835026	229	228
ss69355300	229	229

RefSNP Genotype Summary	Total Individual	G/G	G/T	T/T
rs3887583	270	229

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
200	ss43835026	G/T	CSHL-HAPMAP	HapMap-CEU	NA12057	CEPH1344.13	r23_ch16_CEU_imsut-riken:genotyping
200	ss69355300	G/G	CSHL-HAPMAP	HapMap-CEU	NA12057	CEPH1344.13	chr16-HapMap-CEU
242	ss43835026	G/T	CSHL-HAPMAP	HapMap-CEU	NA10854	CEPH1349.02	r23_ch16_CEU_imsut-riken:genotyping
242	ss69355300	G/G	CSHL-HAPMAP	HapMap-CEU	NA10854	CEPH1349.02	chr16-HapMap-CEU
253	ss43835026	G/T	CSHL-HAPMAP	HapMap-CEU	NA11840	CEPH1349.14	r23_ch16_CEU_imsut-riken:genotyping
253	ss69355300	G/G	CSHL-HAPMAP	HapMap-CEU	NA11840	CEPH1349.14	chr16-HapMap-CEU
264	ss43835026	G/T	CSHL-HAPMAP	HapMap-CEU	NA11831	CEPH1350.12	r23_ch16_CEU_imsut-riken:genotyping
264	ss69355300	G/G	CSHL-HAPMAP	HapMap-CEU	NA11831	CEPH1350.12	chr16-HapMap-CEU
362	ss43835026	G/T	CSHL-HAPMAP	HapMap-CEU	NA11994	CEPH1362.15	r23_ch16_CEU_imsut-riken:genotyping
362	ss69355300	G/G	CSHL-HAPMAP	HapMap-CEU	NA11994	CEPH1362.15	chr16-HapMap-CEU
429	ss43835026	G/T	CSHL-HAPMAP	HapMap-CEU	NA10835	CEPH1416.01	r23_ch16_CEU_imsut-riken:genotyping
429	ss69355300	G/G	CSHL-HAPMAP	HapMap-CEU	NA10835	CEPH1416.01	chr16-HapMap-CEU
438	ss43835026	G/T	CSHL-HAPMAP	HapMap-CEU	NA12248	CEPH1416.11	r23_ch16_CEU_imsut-riken:genotyping
438	ss69355300	G/G	CSHL-HAPMAP	HapMap-CEU	NA12248	CEPH1416.11	chr16-HapMap-CEU
537	ss43835026	G/T	CSHL-HAPMAP	HapMap-CEU	NA12752	CEPH1447.01	r23_ch16_CEU_imsut-riken:genotyping
537	ss69355300	G/G	CSHL-HAPMAP	HapMap-CEU	NA12752	CEPH1447.01	chr16-HapMap-CEU
545	ss43835026	G/T	CSHL-HAPMAP	HapMap-CEU	NA12760	CEPH1447.09	r23_ch16_CEU_imsut-riken:genotyping
545	ss69355300	G/G	CSHL-HAPMAP	HapMap-CEU	NA12760	CEPH1447.09	chr16-HapMap-CEU
623	ss43835026	G/T	CSHL-HAPMAP	HapMap-CEU	NA12878	CEPH1463.02	r23_ch16_CEU_imsut-riken:genotyping
623	ss69355300	G/G	CSHL-HAPMAP	HapMap-CEU	NA12878	CEPH1463.02	chr16-HapMap-CEU
636	ss43835026	G/T	CSHL-HAPMAP	HapMap-CEU	NA12891	CEPH1463.15	r23_ch16_CEU_imsut-riken:genotyping
636	ss69355300	G/G	CSHL-HAPMAP	HapMap-CEU	NA12891	CEPH1463.15	chr16-HapMap-CEU
5152	ss43835026	G/T	CSHL-HAPMAP	HapMap-HCB	NA18532	CH18532	r23_ch16_HCB_imsut-riken:genotyping
5152	ss69355300	G/G	CSHL-HAPMAP	HapMap-HCB	NA18532	CH18532	chr16-HapMap-HCB
5155	ss43835026	G/T	CSHL-HAPMAP	HapMap-HCB	NA18537	CH18537	r23_ch16_HCB_imsut-riken:genotyping
5155	ss69355300	G/G	CSHL-HAPMAP	HapMap-HCB	NA18537	CH18537	chr16-HapMap-HCB
5156	ss43835026	G/T	CSHL-HAPMAP	HapMap-HCB	NA18603	CH18603	r23_ch16_HCB_imsut-riken:genotyping
5156	ss69355300	G/G	CSHL-HAPMAP	HapMap-HCB	NA18603	CH18603	chr16-HapMap-HCB
5160	ss43835026	G/T	CSHL-HAPMAP	HapMap-HCB	NA18545	CH18545	r23_ch16_HCB_imsut-riken:genotyping
5160	ss69355300	G/G	CSHL-HAPMAP	HapMap-HCB	NA18545	CH18545	chr16-HapMap-HCB
5161	ss43835026	G/T	CSHL-HAPMAP	HapMap-HCB	NA18572	CH18572	r23_ch16_HCB_imsut-riken:genotyping
5161	ss69355300	G/G	CSHL-HAPMAP	HapMap-HCB	NA18572	CH18572	chr16-HapMap-HCB
5162	ss43835026	T/T	CSHL-HAPMAP	HapMap-HCB	NA18547	CH18547	r23_ch16_HCB_imsut-riken:genotyping
5162	ss69355300	G/G	CSHL-HAPMAP	HapMap-HCB	NA18547	CH18547	chr16-HapMap-HCB
5164	ss43835026	G/T	CSHL-HAPMAP	HapMap-HCB	NA18550	CH18550	r23_ch16_HCB_imsut-riken:genotyping
5164	ss69355300	G/G	CSHL-HAPMAP	HapMap-HCB	NA18550	CH18550	chr16-HapMap-HCB
5170	ss43835026	G/T	CSHL-HAPMAP	HapMap-HCB	NA18566	CH18566	r23_ch16_HCB_imsut-riken:genotyping
5170	ss69355300	G/G	CSHL-HAPMAP	HapMap-HCB	NA18566	CH18566	chr16-HapMap-HCB
5171	ss43835026	G/T	CSHL-HAPMAP	HapMap-HCB	NA18563	CH18563	r23_ch16_HCB_imsut-riken:genotyping
5171	ss69355300	G/G	CSHL-HAPMAP	HapMap-HCB	NA18563	CH18563	chr16-HapMap-HCB
5173	ss43835026	G/T	CSHL-HAPMAP	HapMap-HCB	NA18612	CH18612	r23_ch16_HCB_imsut-riken:genotyping
5173	ss69355300	G/G	CSHL-HAPMAP	HapMap-HCB	NA18612	CH18612	chr16-HapMap-HCB
5174	ss43835026	G/T	CSHL-HAPMAP	HapMap-HCB	NA18571	CH18571	r23_ch16_HCB_imsut-riken:genotyping
5174	ss69355300	G/G	CSHL-HAPMAP	HapMap-HCB	NA18571	CH18571	chr16-HapMap-HCB
5177	ss43835026	G/T	CSHL-HAPMAP	HapMap-HCB	NA18594	CH18594	r23_ch16_HCB_imsut-riken:genotyping
5177	ss69355300	G/G	CSHL-HAPMAP	HapMap-HCB	NA18594	CH18594	chr16-HapMap-HCB
5184	ss43835026	G/T	CSHL-HAPMAP	HapMap-HCB	NA18579	CH18579	r23_ch16_HCB_imsut-riken:genotyping
5184	ss69355300	G/G	CSHL-HAPMAP	HapMap-HCB	NA18579	CH18579	chr16-HapMap-HCB
5185	ss43835026	G/T	CSHL-HAPMAP	HapMap-HCB	NA18632	CH18632	r23_ch16_HCB_imsut-riken:genotyping
5185	ss69355300	G/G	CSHL-HAPMAP	HapMap-HCB	NA18632	CH18632	chr16-HapMap-HCB
5187	ss43835026	G/T	CSHL-HAPMAP	HapMap-HCB	NA18633	CH18633	r23_ch16_HCB_imsut-riken:genotyping
5187	ss69355300	G/G	CSHL-HAPMAP	HapMap-HCB	NA18633	CH18633	chr16-HapMap-HCB
5189	ss43835026	G/T	CSHL-HAPMAP	HapMap-HCB	NA18592	CH18592	r23_ch16_HCB_imsut-riken:genotyping
5189	ss69355300	G/G	CSHL-HAPMAP	HapMap-HCB	NA18592	CH18592	chr16-HapMap-HCB
5194	ss43835026	G/T	CSHL-HAPMAP	HapMap-JPT	NA18940	JA18940	r23_ch16_JPT_imsut-riken:genotyping
5194	ss69355300	G/G	CSHL-HAPMAP	HapMap-JPT	NA18940	JA18940	chr16-HapMap-JPT
5198	ss43835026	T/T	CSHL-HAPMAP	HapMap-JPT	NA18944	JA18944	r23_ch16_JPT_imsut-riken:genotyping
5198	ss69355300	G/G	CSHL-HAPMAP	HapMap-JPT	NA18944	JA18944	chr16-HapMap-JPT
5200	ss43835026	G/T	CSHL-HAPMAP	HapMap-JPT	NA18949	JA18949	r23_ch16_JPT_imsut-riken:genotyping
5200	ss69355300	G/G	CSHL-HAPMAP	HapMap-JPT	NA18949	JA18949	chr16-HapMap-JPT
5206	ss43835026	G/T	CSHL-HAPMAP	HapMap-JPT	NA18968	JA18968	r23_ch16_JPT_imsut-riken:genotyping
5206	ss69355300	G/G	CSHL-HAPMAP	HapMap-JPT	NA18968	JA18968	chr16-HapMap-JPT
5208	ss43835026	G/T	CSHL-HAPMAP	HapMap-JPT	NA18969	JA18969	r23_ch16_JPT_imsut-riken:genotyping
5208	ss69355300	G/G	CSHL-HAPMAP	HapMap-JPT	NA18969	JA18969	chr16-HapMap-JPT
5212	ss43835026	G/T	CSHL-HAPMAP	HapMap-JPT	NA18965	JA18965	r23_ch16_JPT_imsut-riken:genotyping
5212	ss69355300	G/G	CSHL-HAPMAP	HapMap-JPT	NA18965	JA18965	chr16-HapMap-JPT
5216	ss43835026	G/T	CSHL-HAPMAP	HapMap-JPT	NA18967	JA18967	r23_ch16_JPT_imsut-riken:genotyping
5216	ss69355300	G/G	CSHL-HAPMAP	HapMap-JPT	NA18967	JA18967	chr16-HapMap-JPT
5218	ss43835026	G/T	CSHL-HAPMAP	HapMap-JPT	NA18978	JA18978	r23_ch16_JPT_imsut-riken:genotyping
5218	ss69355300	G/G	CSHL-HAPMAP	HapMap-JPT	NA18978	JA18978	chr16-HapMap-JPT
5220	ss43835026	G/T	CSHL-HAPMAP	HapMap-JPT	NA18980	JA18980	r23_ch16_JPT_imsut-riken:genotyping
5220	ss69355300	G/G	CSHL-HAPMAP	HapMap-JPT	NA18980	JA18980	chr16-HapMap-JPT
5222	ss43835026	G/T	CSHL-HAPMAP	HapMap-JPT	NA18981	JA18981	r23_ch16_JPT_imsut-riken:genotyping
5222	ss69355300	G/G	CSHL-HAPMAP	HapMap-JPT	NA18981	JA18981	chr16-HapMap-JPT
5228	ss43835026	G/T	CSHL-HAPMAP	HapMap-JPT	NA18994	JA18994	r23_ch16_JPT_imsut-riken:genotyping
5228	ss69355300	G/G	CSHL-HAPMAP	HapMap-JPT	NA18994	JA18994	chr16-HapMap-JPT
5229	ss43835026	G/T	CSHL-HAPMAP	HapMap-JPT	NA18992	JA18992	r23_ch16_JPT_imsut-riken:genotyping
5229	ss69355300	G/G	CSHL-HAPMAP	HapMap-JPT	NA18992	JA18992	chr16-HapMap-JPT
5233	ss43835026	G/T	CSHL-HAPMAP	HapMap-JPT	NA19005	JA19005	r23_ch16_JPT_imsut-riken:genotyping
5233	ss69355300	G/G	CSHL-HAPMAP	HapMap-JPT	NA19005	JA19005	chr16-HapMap-JPT
5236	ss43835026	G/T	CSHL-HAPMAP	HapMap-JPT	NA19003	JA19003	r23_ch16_JPT_imsut-riken:genotyping
5236	ss69355300	G/G	CSHL-HAPMAP	HapMap-JPT	NA19003	JA19003	chr16-HapMap-JPT

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 .