Reference SNP(refSNP) Cluster Report: rs207961

Reference SNP(refSNP) Cluster Report: rs207961

refSNP ID: rs207961
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:	C/G
Ancestral Allele:	Not available
Clinical Association:	unknown

HGVS Names
NM_013272.2:c.1009+5832C>G
NT_010274.16:g.7619131C>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss1632099 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs207961 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
ss272231	KWOK\|OVLP-000621-170822	fwd/B	C/G	accttaaagcaagaggcagtaacttgatca	atgtgttctgaaaagatcacagcatggaca	06/30/00	10/10/03	79	Genomic	97 %
ss1257778	KWOK\|OVLP-000804-596367	fwd/B	C/G	accttaaagcaagaggcagtaacttgatca	atgtgttctgaaaagatcacagcatggaca	09/02/00	10/10/03	86	Genomic	97 %
ss1314879	TSC-CSHL\|TSC0154961	fwd/B	C/G	accttaaagcaagaggcagtaacttgatca	atgtgttctgaaaagatcacagcatggaca	09/06/00	04/07/04	86	Genomic	95 %
ss1632099	KWOK\|OVLP-000925-137718	fwd/B	C/G	accttaaagcaagaggcagtaacttgatca	atgtgttctgaaaagatcacagcatggaca	10/04/00	10/25/06	87	Genomic	97 %
ss4040300	SC_JCM\|AX081181.1_11952	fwd/B	C/G	accttaaagcaagaggcagtaacttgatca	atgtgttctgaaaagatcacagcatggaca	09/26/01	10/10/03	100	Genomic	unknown
ss5462328	TSC-CSHL\|TSC0189304	fwd/B	C/G	accttaaagcaagaggcagtaacttgatca	atgtgttctgaaaagatcacagcatggaca	09/21/02	10/10/03	110	Genomic	unknown
ss10773979	BCM_SSAHASNP\|chr15.NT_010274.15_7619131	rev/T	C/G	tgtccatgctgtgatcttttcagaacacat	tgatcaagttactgcctcttgctttaaggt	06/30/03	10/10/03	116	Genomic	unknown
ss24665584	PERLEGEN\|afd2558463	rev/T	C/G	tgtccatgctgtgatcttttcagaacacat	tgatcaagttactgcctcttgctttaaggt	08/10/04	09/13/04	123	Genomic	unknown
ss43701046	ABI\|hCV2271353	rev/	C/G	tgtccatgctgtgatcttttcagaacacat	tgatcaagttactgcctcttgctttaaggt	07/18/05	07/18/05	126	Genomic	unknown
ss75927005	AFFY\|AFFY_6_1M_SNP_A-1783247	fwd/	C/G	ggcagtaacttgatca	atgtgttctgaaaaga	08/28/07	08/29/07	129	Genomic	unknown
ss78196439	HGSV\|Cor12878_SNV_20070510.chr15_90454608	rev/	C/G	tgtccatgctgtgatcttttcagaacacat	tgatcaagttactgcctcttgctttaaggt	10/17/07	10/18/07	129	Genomic	unknown
ss90253370	BCMHGSC_JDW\|JWB-0894360	rev/	C/G	tgtccatgctgtgatcttttcagaacacat	tgatcaagttactgcctcttgctttaaggt	02/26/08	02/29/08	129	Genomic	unknown

Fasta sequence (Legend)

 CCAACACAGG TAGTCACATG TGGGCTGGTG GTGGCACTCA GGACACCTGA AGCTCTTGCC
 AAGTCTACGT CCATGGATTG GTCAAACACA GGCCAAAACC CTGAGTGGGA AGTAGGGGGC
 AGGGGAGCTT TAGGGAAAGC GGCAATCCAT TTACTCCCTC Ccctatcaca tagcaggcac
 tgagcacctg ctgtgtacca ggacatgaga aaaaacaact gcagtccctg ccttcatgaa
 gcgtacagag taagtgaata aaggacaatt attcacacat ataaaggaaa attatgatgt
 gccttggaag gggtaccacc aggtcaggaa gatgttccta agaaatgaca catgagctga
 tgtctgaaga tgaaatgaga attccagTAG AGGGAACGAA TGCAGAGTCC TAGGAGGAAA
 GGAGCCTGGG GTATAGGGAG AACTGAAAAG AGACCAGTGA GGTGGGCGTG GAGGGAACAG
 GGCATGACTG GCATGAGAAG GGTTTGGAGG GACTCAGAGA CCATGGAAGG ACTTTGTCTC
 CATACCTTAA AGCAAGAGGC AGTAACTTGA TCA
 S
 ATGTGTTCTG AAAAGATCAC AGCATGGACA ACAGCCTGGA GGGCCCAGGG CATGCTGGAG
 TGTGGAGTGT TACCTTGTTA ATGTTAACAA GGACTCTCAG ATCAACAGAG ATCAAGGGCA
 GGCTGGAGAG AGACTTGGGT GGCAAAATCA GCTGAACTCC AGGATGGACT GCATTGCTGG
 AGGGGAGGGG AGGTTACAAG

GeneView

GeneView via analysis of contig annotation: SLCO3A1 solute carrier organic anion transporter family, member 3A1

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_010274->NM_013272

function

HuRef

NW_001838222->NM_013272

function

Celera

NW_925940->NM_013272

function

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


reference	NT_010274->NM_013272->NP_037404	7619131	forward	intron

HuRef	NW_001838222->NM_013272->NP_037404	7644837	forward	intron

Celera	NW_925940->NM_013272->NP_037404	7558392	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs207961 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_001838222.1	7644837	68792874	minus	C	alt_assembly_8	HuRef	HuRef	view	573
15	NW_925940.1	7558392	69065572	minus	C	alt_assembly_1	Celera	Celera	view	573
15	NT_010274.16	7619131	90454608	minus	C	ref_assembly	reference	reference	view	573

NCBI Resource Links

Submitter-Referenced
GenBank
NT_010274 AC005319 AC068012 AC068012.1

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC005319.1 AC113190.8 NC_000015.8	AC135631.2 AC135719.2 AC136685.2 AC136691.2

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/G	G/G	HWP	C	G
ss1314879	WICGR6_caucasian_pooled		96	AF					0.210	0.790

ss1632099	HapMap-CEU	European	120	IG	0.033	0.533	0.433	0.050	0.300	0.700

	HapMap-HCB	Asian	88	IG	0.023	0.364	0.614	0.439	0.205	0.795

	HapMap-JPT	Asian	90	IG	0.044	0.333	0.622		0.211	0.789

	HapMap-YRI	Sub-Saharan African	120	IG	0.033	0.433	0.533	0.251	0.250	0.750

ss24665584	AFD_EUR_PANEL	European	44	IG	0.045	0.455	0.500	0.527	0.273	0.727

	AFD_AFR_PANEL	African American	44	IG		0.364	0.636	0.317	0.182	0.818

	AFD_CHN_PANEL	Asian	48	IG	0.083	0.292	0.625	0.403	0.229	0.771

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.367+/-0.221	332	260	9	0

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: PERLEGEN

DoubleHit found by: BCM_SSAHASNP, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .