Reference SNP(refSNP) Cluster Report: rs4386668

Reference SNP(refSNP) Cluster Report: rs4386668

refSNP ID: rs4386668
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	111/129
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_053039.1:c.1002+84C>G
NT_077444.3:g.811833C>G

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss7847902 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs4386668 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
ss5855602	SC_JCM\|NT_030640.5_1036431	fwd/T	C/G	actgtatttggctgtaaagagttcagtcta	ccttaatattctttctgtgtagatctcaaa	01/10/03	10/10/03	111	Genomic	unknown
ss7847902	DEVINE_LAB\|DB_1_22478	fwd/T	C/G	actgtatttggctgtaaagagttcagtcta	ccttaatattctttctgtgtagatctcaaa	03/16/03	10/25/06	113	Genomic	96 %
ss16999844	CSHL-HAPMAP\|CSHL-HuAA-200402.chr4.NT_077444.2_811833	rev/B	C/G	tttgagatctacacagaaagaatattaagg	tagactgaactctttacagccaaatacagt	02/17/04	03/04/04	120	Genomic	unknown
ss22083047	SSAHASNP\|WGSA-200403-chr4.chr4.NT_077444.2_811833	rev/B	C/G	tttgagatctacacagaaagaatattaagg	tagactgaactctttacagccaaatacagt	03/20/04	03/20/04	121	Genomic	unknown
ss42318412	ABI\|hCV26031611	rev/	C/G	tttgagatctacacagaaagaatattaagg	tagactgaactctttacagccaaatacagt	07/17/05	07/17/05	126	Genomic	unknown
ss52078867	SI_EXO\|NT_077444.3_811833	rev/	C/G	tttgagatctacacagaaagaatattaagg	tagactgaactctttacagccaaatacagt	03/29/06	03/29/06	127	Genomic	unknown
ss68901452	PERLEGEN\|PGP04218331	rev/	C/G	tttgagatctacacagaaagaatattaagg	tagactgaactctttacagccaaatacagt	01/30/07	03/31/08	127	Genomic	unknown
ss77297692	HGSV\|Cor12156_SNV_20070510.chr4_70333445	rev/	C/G	tttgagatctacacagaaagaatattaagg	tagactgaactctttacagccaaatacagt	10/09/07	10/12/07	129	Genomic	unknown
ss92629810	BCMHGSC_JDW\|JWB-1797030	rev/	C/G	tttgagatctacacagaaagaatattaagg	tagactgaactctttacagccaaatacagt	02/26/08	03/03/08	129	Genomic	unknown

Fasta sequence (Legend)

 GAAAACAGCT TTGAAGAAAA TGATCATAAG TCTTCCTTGT ATTTCTACAA AGATGCAGTT
 CTGGATATAT ATTTTTAGTT GAAAACACTT GAAAGTCATC TAAAGACTAC ATTAGGCACC
 ATTTTCACTT ACCTGAAATA TATTGAGTTA ATTTCAGCCA TATGTATGAC TGTTAATATC
 AGAAATTAAA AATAATCATG GGTCTCAAGT TCCCTTTTGT GGATACATAT GGAGTACTGA
 GTTCCCACTG GTAGTAATAG GAACCACTCA TGCATACCAA GGGTAGTAAC ACCCCCAGGG
 CCACATGTAA CCACTAAGTC TGAGGCACAA CTATGACTTG TGTCGGTGGA AGCTACACAA
 GATATTTAAG ACTGTATTTG GCTGTAAAGA GTTCAGTCTA
 S
 CCTTAATATT CTTTCTGTGT AGATCTCAAA CTTTAACAGC CTCTTTCAGT AGTTTTCCAC
 ACCAGTAAGG CACTTTATCT TACCTTTTGT GGGATCTTGG CAAGGGCTGT TGCAATTACG
 TTGGCCCTTT CTGCTGTCAT GTTACTTATC ACTGACCCCA GAGAAAACAC CACAACACCA
 TTTTCACCAG AGCTCTGTAC AAATTCCTCC ATTTCCTGTG AAAAAAAATT GTTTAATCAC
 AAAAGAGTAT CACCACAGCA GGCACTACTA AAGAATTGGT ACCAAATATT AAAGAGAGAA
 AATCAAGTAT TTTGAGGAAT TATTGGAGTA AATAATATTT TTTAACTGAC TCAATCACTC
 AGGTTCTTTA CAAGAAGATG TTTGAGGTAG TTGGCCTCTG

GeneView

GeneView via analysis of contig annotation: UGT2B28 UDP glucuronosyltransferase 2 family, polypeptide B28

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_077444->NM_053039

function

HuRef

NW_001838914->NM_053039

function

Celera

NW_922162->NM_053039

function

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


reference	NT_077444->NM_053039->NP_444267	811833	forward	intron

HuRef	NW_001838914->NM_053039->NP_444267	10252877	forward	intron

Celera	NW_922162->NM_053039->NP_444267	17321018	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs4386668 maps exactly once on NCBI human chromosome 4

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
4	NW_001838914.1	10252877	65951163	minus	G	alt_assembly_8	HuRef	HuRef	view	400
4	NW_922162.1	17321018	67496044	minus	G	alt_assembly_1	Celera	Celera	view	400
4	NT_077444.3	811833	70187274	minus	C	ref_assembly	reference	reference	view	400

NCBI Resource Links

Submitter-Referenced
GenBank
NT_077444.3

dbSNP Blast Analysis
GenBank HTGS Finished:
AC114786.4 NC_000004.10

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/G	G/G	HWP	C	G
ss68901452	HapMap-CEU	European	120	GF	0.417	0.333	0.250		0.583	0.417

	HapMap-HCB	Asian	90	GF	0.267	0.489	0.244		0.511	0.489

	HapMap-JPT	Asian	90	GF	0.533	0.333	0.133		0.700	0.300

	HapMap-YRI	Sub-Saharan African	120	GF	0.300	0.217	0.483		0.408	0.592

ss7847902	HapMap-CEU	European	114	IG	0.316	0.351	0.333	0.025	0.491	0.509

Concordant Genotype	Total Sample	C/C	C/G	G/G
ss68901452	249	76	83	90
ss7847902	69	28	21	16

RefSNP Genotype Summary	Total Individual	C/C	C/G	G/G
rs4386668	270	104	83	106

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
157	ss7847902	C/G	CSHL-HAPMAP	HapMap-CEU	NA12144	CEPH1334.10	r23_ch4_CEU_wicgr:genotype_protocol_1
157	ss68901452	G/G	CSHL-HAPMAP	HapMap-CEU	NA12144	CEPH1334.10	chr4-HapMap-CEU
174	ss7847902	G/G	CSHL-HAPMAP	HapMap-CEU	NA07048	CEPH1341.01	r23_ch4_CEU_wicgr:genotype_protocol_1
174	ss68901452	C/G	CSHL-HAPMAP	HapMap-CEU	NA07048	CEPH1341.01	chr4-HapMap-CEU
185	ss7847902	G/G	CSHL-HAPMAP	HapMap-CEU	NA07055	CEPH1341.12	r23_ch4_CEU_wicgr:genotype_protocol_1
185	ss68901452	G/G	CSHL-HAPMAP	HapMap-CEU	NA07055	CEPH1341.12	chr4-HapMap-CEU
200	ss7847902	C/G	CSHL-HAPMAP	HapMap-CEU	NA12057	CEPH1344.13	r23_ch4_CEU_wicgr:genotype_protocol_1
200	ss68901452	G/G	CSHL-HAPMAP	HapMap-CEU	NA12057	CEPH1344.13	chr4-HapMap-CEU
203	ss7847902	C/G	CSHL-HAPMAP	HapMap-CEU	NA07348	CEPH1345.02	r23_ch4_CEU_wicgr:genotype_protocol_1
203	ss68901452	G/G	CSHL-HAPMAP	HapMap-CEU	NA07348	CEPH1345.02	chr4-HapMap-CEU
226	ss7847902	G/G	CSHL-HAPMAP	HapMap-CEU	NA12044	CEPH1346.12	r23_ch4_CEU_wicgr:genotype_protocol_1
226	ss68901452	C/G	CSHL-HAPMAP	HapMap-CEU	NA12044	CEPH1346.12	chr4-HapMap-CEU
242	ss7847902	G/G	CSHL-HAPMAP	HapMap-CEU	NA10854	CEPH1349.02	r23_ch4_CEU_wicgr:genotype_protocol_1
242	ss68901452	C/G	CSHL-HAPMAP	HapMap-CEU	NA10854	CEPH1349.02	chr4-HapMap-CEU
265	ss7847902	C/G	CSHL-HAPMAP	HapMap-CEU	NA11832	CEPH1350.13	r23_ch4_CEU_wicgr:genotype_protocol_1
265	ss68901452	G/G	CSHL-HAPMAP	HapMap-CEU	NA11832	CEPH1350.13	chr4-HapMap-CEU
348	ss7847902	C/G	CSHL-HAPMAP	HapMap-CEU	NA10860	CEPH1362.01	r23_ch4_CEU_wicgr:genotype_protocol_1
348	ss68901452	G/G	CSHL-HAPMAP	HapMap-CEU	NA10860	CEPH1362.01	chr4-HapMap-CEU
349	ss7847902	G/G	CSHL-HAPMAP	HapMap-CEU	NA10861	CEPH1362.02	r23_ch4_CEU_wicgr:genotype_protocol_1
349	ss68901452	G/G	CSHL-HAPMAP	HapMap-CEU	NA10861	CEPH1362.02	chr4-HapMap-CEU
360	ss7847902	C/G	CSHL-HAPMAP	HapMap-CEU	NA11992	CEPH1362.13	r23_ch4_CEU_wicgr:genotype_protocol_1
360	ss68901452	G/G	CSHL-HAPMAP	HapMap-CEU	NA11992	CEPH1362.13	chr4-HapMap-CEU
363	ss7847902	G/G	CSHL-HAPMAP	HapMap-CEU	NA11995	CEPH1362.16	r23_ch4_CEU_wicgr:genotype_protocol_1
363	ss68901452	C/G	CSHL-HAPMAP	HapMap-CEU	NA11995	CEPH1362.16	chr4-HapMap-CEU
400	ss7847902	C/G	CSHL-HAPMAP	HapMap-CEU	NA10831	CEPH1408.02	r23_ch4_CEU_wicgr:genotype_protocol_1
400	ss68901452	G/G	CSHL-HAPMAP	HapMap-CEU	NA10831	CEPH1408.02	chr4-HapMap-CEU
410	ss7847902	C/G	CSHL-HAPMAP	HapMap-CEU	NA12155	CEPH1408.12	r23_ch4_CEU_wicgr:genotype_protocol_1
410	ss68901452	G/G	CSHL-HAPMAP	HapMap-CEU	NA12155	CEPH1408.12	chr4-HapMap-CEU
457	ss7847902	G/G	CSHL-HAPMAP	HapMap-CEU	NA10839	CEPH1420.02	r23_ch4_CEU_wicgr:genotype_protocol_1
457	ss68901452	C/G	CSHL-HAPMAP	HapMap-CEU	NA10839	CEPH1420.02	chr4-HapMap-CEU
466	ss7847902	G/G	CSHL-HAPMAP	HapMap-CEU	NA12005	CEPH1420.11	r23_ch4_CEU_wicgr:genotype_protocol_1
466	ss68901452	C/G	CSHL-HAPMAP	HapMap-CEU	NA12005	CEPH1420.11	chr4-HapMap-CEU
535	ss7847902	G/G	CSHL-HAPMAP	HapMap-CEU	NA12750	CEPH1444.13	r23_ch4_CEU_wicgr:genotype_protocol_1
535	ss68901452	C/G	CSHL-HAPMAP	HapMap-CEU	NA12750	CEPH1444.13	chr4-HapMap-CEU
537	ss7847902	G/G	CSHL-HAPMAP	HapMap-CEU	NA12752	CEPH1447.01	r23_ch4_CEU_wicgr:genotype_protocol_1
537	ss68901452	C/G	CSHL-HAPMAP	HapMap-CEU	NA12752	CEPH1447.01	chr4-HapMap-CEU
538	ss7847902	G/G	CSHL-HAPMAP	HapMap-CEU	NA12753	CEPH1447.02	r23_ch4_CEU_wicgr:genotype_protocol_1
538	ss68901452	C/G	CSHL-HAPMAP	HapMap-CEU	NA12753	CEPH1447.02	chr4-HapMap-CEU
546	ss7847902	C/G	CSHL-HAPMAP	HapMap-CEU	NA12761	CEPH1447.10	r23_ch4_CEU_wicgr:genotype_protocol_1
546	ss68901452	G/G	CSHL-HAPMAP	HapMap-CEU	NA12761	CEPH1447.10	chr4-HapMap-CEU
610	ss7847902	G/G	CSHL-HAPMAP	HapMap-CEU	NA12864	CEPH1459.01	r23_ch4_CEU_wicgr:genotype_protocol_1
610	ss68901452	C/G	CSHL-HAPMAP	HapMap-CEU	NA12864	CEPH1459.01	chr4-HapMap-CEU

Genotype data submitted for	270	samples from	270	individuals	Individual with multiple genotypes submission:	90

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

UNKNOWN

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Revised: May 25, 2006 1:38 PM .