Reference SNP(refSNP) Cluster Report: rs13161905

Reference SNP(refSNP) Cluster Report: rs13161905

refSNP ID: rs13161905
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	121/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	C/T
Ancestral Allele:	Not available
Clinical Association:	unknown

HGVS Names
NM_001044.3:c.928-896G>A
NT_006576.15:g.1407212C>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss42593989 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs13161905 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
ss22254020	SSAHASNP\|WGSA-200403-chr5.chr5.NT_023089.13_1399950	fwd/B	C/T	ccagcttcacaaccccctgagtgtgtcccc	catcccatgtgcgccctgctgcatgatggc	03/21/04	03/21/04	121	Genomic	unknown
ss35033744	EGP_SNPS\|SLC6A3-029378	rev/T	A/G	gccatcatgcagcagggcgcacatgggatg	ggggacacactcagggggttgtgaagctgg	02/09/05	11/02/06	125	Genomic	unknown
ss42593989	ABI\|hCV11363032	fwd/B	C/T	ccagcttcacaaccccctgagtgtgtcccc	catcccatgtgcgccctgctgcatgatggc	07/18/05	11/03/06	126	Genomic	unknown
ss67061053	ILLUMINA\|HumanHap550v1.1_rs13161905	fwd/B	C/T	ccagcttcacaaccccctgagtgtgtcccc	catcccatgtgcgccctgctgcatgatggc	11/14/06	11/14/06	127	Genomic	unknown
ss67388845	ILLUMINA\|HumanHap650Yv1.0_rs13161905	fwd/B	C/T	ccagcttcacaaccccctgagtgtgtcccc	catcccatgtgcgccctgctgcatgatggc	11/14/06	11/14/06	127	Genomic	unknown
ss68146036	ILLUMINA\|HumanHap250Sv1.0_rs13161905	fwd/B	C/T	ccagcttcacaaccccctgagtgtgtcccc	catcccatgtgcgccctgctgcatgatggc	12/06/06	12/07/06	127	Genomic	unknown
ss68923835	PERLEGEN\|PGP08275322	fwd/B	C/T	ccagcttcacaaccccctgagtgtgtcccc	catcccatgtgcgccctgctgcatgatggc	01/30/07	03/31/08	127	Genomic	unknown
ss70596012	ILLUMINA\|HumanHap550v3.0__rs13161905	rev/T	A/G	gccatcatgcagcagggcgcacatgggatg	ggggacacactcagggggttgtgaagctgg	04/20/07	03/30/08	130	Genomic	unknown
ss71140447	ILLUMINA\|HumanHap650Yv3.0_rs13161905	fwd/B	C/T	ccagcttcacaaccccctgagtgtgtcccc	catcccatgtgcgccctgctgcatgatggc	04/23/07	04/23/07	127	Genomic	unknown
ss75512146	ILLUMINA\|ILMN_Human_1M_rs13161905	fwd/B	C/T	ccagcttcacaaccccctgagtgtgtcccc	catcccatgtgcgccctgctgcatgatggc	08/28/07	08/29/07	129	Genomic	unknown
ss77232198	HGSV\|Cor12156_SNV_20070510.chr5_1470212	fwd/B	C/T	ccagcttcacaaccccctgagtgtgtcccc	catcccatgtgcgccctgctgcatgatggc	10/09/07	10/12/07	129	Genomic	unknown
ss85305110	KRIBB_YJKIM\|KHS956366	fwd/B	C/T	ccagcttcacaaccccctgagtgtgtcccc	catcccatgtgcgccctgctgcatgatggc	12/04/07	12/09/07	130	Genomic	unknown
ss92959318	BCMHGSC_JDW\|JWB-1922496	fwd/B	C/T	ccagcttcacaaccccctgagtgtgtcccc	catcccatgtgcgccctgctgcatgatggc	02/26/08	03/03/08	129	Genomic	unknown
ss108733945	1000GENOMES\|CEU.trio.12.15.2008_1186712_chr5_1470212	fwd/B	C/T	ccagcttcacaaccccctgagtgtgtcccc	catcccatgtgcgccctgctgcatgatggc	12/15/08	12/16/08	130	Genomic	unknown

Fasta sequence (Legend)

 CCACACACAA CATGACCGCA GCGTCCTAAT AGCCCTCGGA ACAGCACGGC CTCATCCACA
 CATGACATGA CCGCAGCGTC CTAACAACCC TCGGAACAGC ACAGATTCAT CCACATGCTG
 CATAATGGTG GCACCCTGAT AACCCTCAGA AAGTCATGAA CTCATCCACA CACAACATGA
 CCGCGGCGCC CTGATAACCC TCAGAACAGC ATGGACTTAT CCACACTCAC ACCAGCCCTA
 GCGGGGTCTC CATCCTCCCT TGATCAGGGT CCAGCTTCAC AACCCCCTGA GTGTGTCCCC
 Y
 CATCCCATGT GCGCCCTGCT GCATGATGGC AGTGCCCTGA AACCCTCAGA ACAGCACAGA
 CTCAACCACA GGCTACATGA TGGCGGCTTC CTGATAACCC TCAGAACATC ATGGATCATC
 CACAAGCTGC ATGATGGCGG CACCCTGATA ACCCTCAGAA CAACATAAAC TCATCCTGAG
 GCTACATGAT GGTGGCGCCC TGACAACCCT CAGAACAGCA TGGATCATCC ACATGCTGCA
 TGATGGCAGC ACCCTGATAA CCCTCAGAAA GGCATGGACC CATCCACATG CTACATGATG

GeneView

GeneView via analysis of contig annotation: SLC6A3 solute carrier family 6 (neurotransmitter transporter, dopamine), member 3

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_006576->NM_001044

function

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


reference	NT_006576->NM_001044->NP_001035	1407212	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs13161905 maps exactly once on NCBI human chromosome 5

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
5	NW_001838923.2	724589	1398382	minus	A	alt_assembly_8	HuRef	HuRef	view	300
5	NW_922518.1	557666	1455234	plus	C	alt_assembly_1	Celera	Celera	view	300
5	NT_006576.15	1407212	1470212	plus	C	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_023089

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss35033744	PDR90	Global	176	IG	0.636	0.250	0.114	0.005	0.761	0.239

ss42593989	HapMap-CEU	European	116	IG	0.517	0.397	0.086	1.000	0.716	0.284

	HapMap-HCB	Asian	90	IG	1.000				1.000

	HapMap-JPT	Asian	90	IG	1.000				1.000

	HapMap-YRI	Sub-Saharan African	118	IG	1.000				1.000

ss68923835	HapMap-CEU	European	120	GF	0.517	0.483			0.758	0.242

	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	C/C	C/T
ss35033744	90
ss42593989	257	220	33
ss68923835	257	221	36

RefSNP Genotype Summary	Total Individual	C/C	C/T	T/T
rs13161905	360	221	36

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
159	ss42593989	T/T	CSHL-HAPMAP	HapMap-CEU	NA12146	CEPH1334.12	r23_ch5_CEU_perlegen:genotyping_1.0.0	2947543
159	ss68923835	C/T	CSHL-HAPMAP	HapMap-CEU	NA12146	CEPH1334.12	chr5-HapMap-CEU
174	ss42593989	C/T	CSHL-HAPMAP	HapMap-CEU	NA07048	CEPH1341.01	r23_ch5_CEU_perlegen:genotyping_1.0.0	2947543
174	ss68923835	C/C	CSHL-HAPMAP	HapMap-CEU	NA07048	CEPH1341.01	chr5-HapMap-CEU
229	ss42593989	T/T	CSHL-HAPMAP	HapMap-CEU	NA10859	CEPH1347.02	r23_ch5_CEU_perlegen:genotyping_1.0.0	2947543
229	ss68923835	C/T	CSHL-HAPMAP	HapMap-CEU	NA10859	CEPH1347.02	chr5-HapMap-CEU
242	ss42593989	C/T	CSHL-HAPMAP	HapMap-CEU	NA10854	CEPH1349.02	r23_ch5_CEU_perlegen:genotyping_1.0.0	2947543
242	ss68923835	C/C	CSHL-HAPMAP	HapMap-CEU	NA10854	CEPH1349.02	chr5-HapMap-CEU
348	ss42593989	T/T	CSHL-HAPMAP	HapMap-CEU	NA10860	CEPH1362.01	r23_ch5_CEU_perlegen:genotyping_1.0.0	2947543
348	ss68923835	C/T	CSHL-HAPMAP	HapMap-CEU	NA10860	CEPH1362.01	chr5-HapMap-CEU
360	ss42593989	T/T	CSHL-HAPMAP	HapMap-CEU	NA11992	CEPH1362.13	r23_ch5_CEU_perlegen:genotyping_1.0.0	2947543
360	ss68923835	C/T	CSHL-HAPMAP	HapMap-CEU	NA11992	CEPH1362.13	chr5-HapMap-CEU
408	ss42593989	T/T	CSHL-HAPMAP	HapMap-CEU	NA12154	CEPH1408.10	r23_ch5_CEU_perlegen:genotyping_1.0.0	2947543
408	ss68923835	C/T	CSHL-HAPMAP	HapMap-CEU	NA12154	CEPH1408.10	chr5-HapMap-CEU
466	ss42593989	T/T	CSHL-HAPMAP	HapMap-CEU	NA12005	CEPH1420.11	r23_ch5_CEU_perlegen:genotyping_1.0.0	2947543
466	ss68923835	C/T	CSHL-HAPMAP	HapMap-CEU	NA12005	CEPH1420.11	chr5-HapMap-CEU
537	ss42593989	T/T	CSHL-HAPMAP	HapMap-CEU	NA12752	CEPH1447.01	r23_ch5_CEU_perlegen:genotyping_1.0.0	2947543
537	ss68923835	C/T	CSHL-HAPMAP	HapMap-CEU	NA12752	CEPH1447.01	chr5-HapMap-CEU
545	ss42593989	T/T	CSHL-HAPMAP	HapMap-CEU	NA12760	CEPH1447.09	r23_ch5_CEU_perlegen:genotyping_1.0.0	2947543
545	ss68923835	C/T	CSHL-HAPMAP	HapMap-CEU	NA12760	CEPH1447.09	chr5-HapMap-CEU
565	ss42593989	T/T	CSHL-HAPMAP	HapMap-CEU	NA12801	CEPH1454.01	r23_ch5_CEU_perlegen:genotyping_1.0.0	2947543
565	ss68923835	C/T	CSHL-HAPMAP	HapMap-CEU	NA12801	CEPH1454.01	chr5-HapMap-CEU
566	ss42593989	C/T	CSHL-HAPMAP	HapMap-CEU	NA12802	CEPH1454.02	r23_ch5_CEU_perlegen:genotyping_1.0.0	2947543
566	ss68923835	C/C	CSHL-HAPMAP	HapMap-CEU	NA12802	CEPH1454.02	chr5-HapMap-CEU
577	ss42593989	C/T	CSHL-HAPMAP	HapMap-CEU	NA12813	CEPH1454.13	r23_ch5_CEU_perlegen:genotyping_1.0.0	2947543
577	ss68923835	C/C	CSHL-HAPMAP	HapMap-CEU	NA12813	CEPH1454.13	chr5-HapMap-CEU

Genotype data submitted for	360	samples from	360	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	YES

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Revised: May 25, 2006 1:38 PM .