Reference SNP(refSNP) Cluster Report: rs315988

Reference SNP(refSNP) Cluster Report: rs315988

refSNP ID: rs315988
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/T
Ancestral Allele:	C
Clinical Association:	unknown

HGVS Names
NM_003058.2:c.1501+1812A>G
NT_007422.13:g.2948035T>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss2015711 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs315988 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
ss404951	KWOK\|OVLP-000621-256572	fwd/B	C/T	aggacagagggtttgatgggtacctcctca	gatgaaaagagggttctgaggacagtttcc	06/30/00	10/10/03	79	Genomic	99 %
ss719363	SC_JCM\|AC024253.3_69325	rev/T	A/G	ggaaactgtcctcagaaccctcttttcatc	tgaggaggtacccatcaaaccctctgtcct	07/27/00	10/10/03	85	Genomic	unknown
ss965623	KWOK\|OVLP-000804-485690	fwd/B	C/T	aggacagagggtttgatgggtacctcctca	gatgaaaagagggttctgaggacagtttcc	09/01/00	10/10/03	86	Genomic	99 %
ss967455	KWOK\|OVLP-000804-495606	rev/T	A/G	ggaaactgtcctcagaaccctcttttcatc	tgaggaggtacccatcaaaccctctgtcct	09/01/00	10/10/03	86	Genomic	99 %
ss2015711	KWOK\|OVLP-000925-508401	fwd/B	C/T	aggacagagggtttgatgggtacctcctca	gatgaaaagagggttctgaggacagtttcc	10/06/00	05/16/04	87	Genomic	99 %
ss2516111	SC_JCM\|AC024253.4_52791	rev/T	A/G	ggaaactgtcctcagaaccctcttttcatc	tgaggaggtacccatcaaaccctctgtcct	11/03/00	10/10/03	89	Genomic	unknown
ss12830299	SC_SNP\|NT_007422.12_2948035	fwd/B	C/T	aggacagagggtttgatgggtacctcctca	gatgaaaagagggttctgaggacagtttcc	10/21/03	10/31/03	119	Genomic	unknown
ss44736522	ABI\|hCV928552	fwd/B	C/T	aggacagagggtttgatgggtacctcctca	gatgaaaagagggttctgaggacagtttcc	07/19/05	07/19/05	126	Genomic	unknown
ss66478122	AFFY\|SNP_A-2286899	fwd/B	C/T	gatgggtacctcctca	gatgaaaagagggttc	10/29/06	08/14/07	127	Genomic	unknown
ss75267532	ILLUMINA\|ILMN_Human_1M_rs315988	fwd/B	C/T	aggacagagggtttgatgggtacctcctca	gatgaaaagagggttctgaggacagtttcc	08/28/07	08/29/07	129	Genomic	unknown
ss76291358	AFFY\|AFFY_6_1M_SNP_A-2286899	fwd/B	C/T	gatgggtacctcctca	gatgaaaagagggttc	08/28/07	08/30/07	129	Genomic	unknown
ss83653157	HGSV\|Cor18555_SNV_20070510.chr6_160631105	fwd/B	C/T	aggacagagggtttgatgggtacctcctca	gatgaaaagagggttctgaggacagtttcc	11/27/07	12/05/07	130	Genomic	unknown
ss84500069	HGSV\|Cor19240_SNV_20070510.chr6_160631105	fwd/B	C/T	aggacagagggtttgatgggtacctcctca	gatgaaaagagggttctgaggacagtttcc	11/30/07	12/07/07	130	Genomic	unknown
ss85665946	HGSV\|Cor19129_SNV_20070510.chr6_160631105	fwd/B	C/T	aggacagagggtttgatgggtacctcctca	gatgaaaagagggttctgaggacagtttcc	12/06/07	12/09/07	130	Genomic	unknown
ss93593898	BCMHGSC_JDW\|JWB-2245298	fwd/B	C/T	aggacagagggtttgatgggtacctcctca	gatgaaaagagggttctgaggacagtttcc	02/26/08	03/04/08	129	Genomic	unknown

Fasta sequence (Legend)

 TGTAGTTATA ATCCTTTATC TTTCCTGCAG GAAGGTGTCA GGCAGGAACA AGGGTCAATA
 AAGTACTATT TGTTAAATAG TACTTAGAGA AACATGAAGT tgtcaaagtt gtttgaacca
 gagtgactcc gtcttggata ggggctgggt aaaatggggc ggagacctac tgggctgcat
 tcccaggagg ttaggcattc ttagtcacag gatgatagga ggtcagcaaa agacacaggg
 tcacaaagac cttggtgata aaacaggaag tggtaaagaa gctggcccaa acccaccaaa
 accaagatgg cgatggaagt gacctctggt catcctcact actcattata cactaattat
 aatgcattag catgttaaaa gacactccca ccagcaccat gacagtttac agatgccaga
 tgccatggtg atgtccggaa gtcaccctat atagtctgaa aaggggagga accctcagtt
 ccaggaactg cccatccctt tcctggaaaa ctcacgaata atccactcct tgtttagcat
 ataatccaga agtaactata ggttactcaa ctgagcagcc catgctgctg ttctgcctat
 ggagtagcca ttctttattc ctttactttc ttaataaact tgctttcctt ttactctatg
 gattgacctc gaattctttc ttgtgcaaga tccaagaacc ccctcttggg gtctgggtca
 ggacctcttt ccagtaacGA AGTAACCATC TGCTATCCAG AAATGTCCTG CTGACCCATT
 AGTCACCCAC TGTCCACCTA AGGGAGTGGC CAAGATTGAG TGGTCTCTAA CTTCCTCCAT
 GGCAGGAAGG AGGACAGAGG GTTTGATGGG TACCTCCTCA
 Y
 GATGAAAAGA GGGTTCTGAG GACAGTTTCC TTAGCCAGTG TTGGGGGAGA AAGAAATAGG
 GGTCACATAT GTCTCAGGAG TAGCACCAGC TACTCTGTGG CCAAGTTATC TCAGGATAAA
 GAGCTTGTGC TCTGTCAACT TTGGCCATCT TATTGCTATT AAACTGGATC ATGGAGGAAT
 TCATTGCATC TGTTTTGCAG

GeneView

GeneView via analysis of contig annotation: SLC22A2 solute carrier family 22 (organic cation transporter), member 2

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_007422->NM_003058

function

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


reference	NT_007422->NM_003058->NP_003049	2948035	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs315988 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_001838991.2	374176	158135148	minus	A	alt_assembly_8	HuRef	HuRef	view	880
6	NT_007422.13	2948035	160580684	plus	T	ref_assembly	reference	reference	view	880
6	NW_923184.1	93378559	161309955	plus	T	alt_assembly_1	Celera	Celera	view	880

NCBI Resource Links

Submitter-Referenced
GenBank
NT_007422 AL162582 AL162582.4 AL162582.5

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AL162582.30	AL645523.3

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss2015711	CEPH		184	AF					0.640	0.360

	HapMap-CEU	European	120	IG	0.667	0.267	0.067		0.800	0.200

	HapMap-HCB	Asian	90	IG	0.644	0.311	0.044		0.800	0.200

	HapMap-JPT	Asian	90	IG	0.756	0.222	0.022		0.867	0.133

	HapMap-YRI	Sub-Saharan African	120	IG	0.200	0.450	0.350		0.425	0.575

ss66478122	HapMap-CEU	European	118	GF	0.661	0.288	0.051		0.805	0.195

	HapMap-HCB	Asian	90	GF	0.644	0.311	0.044		0.800	0.200

	HapMap-JPT	Asian	90	GF	0.756	0.222	0.022		0.867	0.133

	HapMap-YRI	Sub-Saharan African	120	GF	0.200	0.450	0.350		0.425	0.575

Concordant Genotype	Total Sample	C/C	C/T	T/T
ss2015711	269	141	85	43
ss66478122	268	140	85	43

RefSNP Genotype Summary	Total Individual	C/C	C/T	T/T
rs315988	270	141	85	43

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
618	ss2015711	T/T	CSHL-HAPMAP	HapMap-CEU	NA12872	CEPH1459.09	r23_ch6_CEU_affymetrix:genechip500k	3108914
618	ss66478122	C/T	CSHL-HAPMAP	HapMap-CEU	NA12872	CEPH1459.09	chr6-HapMap-CEU

Genotype data submitted for	270	samples from	270	individuals	Individual with multiple genotypes submission:	269

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

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Revised: May 25, 2006 1:38 PM .