Reference SNP(refSNP) Cluster Report: rs327072

Reference SNP(refSNP) Cluster Report: rs327072

refSNP ID: rs327072
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:	G/T
Ancestral Allele:	Not available
Clinical Association:	unknown

HGVS Names
NM_005245.3:c.3580+7333G>T
NT_022792.17:g.19989060C>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss2004279 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs327072 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
ss418208	KWOK\|OVLP-000621-290874	rev/T	A/C	ggtacgaccgccagtacctgaaagtacctg	aaaggcagtttggtacttccccaagaggag	06/30/00	10/10/03	79	Genomic	99 %
ss419729	KWOK\|OVLP-000621-294561	fwd/B	G/T	ctcctcttggggaagtaccaaactgccttt	caggtactttcaggtactggcggtcgtacc	06/30/00	10/10/03	85	Genomic	99 %
ss633929	SC_JCM\|AC040966.2_58101	rev/T	A/C	ggtacgaccgccagtacctgaaagtacctg	aaaggcagtttggtacttccccaagaggag	07/12/00	10/10/03	87	Genomic	unknown
ss961531	KWOK\|OVLP-000804-463201	fwd/B	G/T	ctcctcttggggaagtaccaaactgccttt	caggtactttcaggtactggcggtcgtacc	09/01/00	10/10/03	86	Genomic	99 %
ss961965	KWOK\|OVLP-000804-466421	fwd/B	G/T	ctcctcttggggaagtaccaaactgccttt	caggtactttcaggtactggcggtcgtacc	09/01/00	10/10/03	86	Genomic	99 %
ss2004279	KWOK\|OVLP-000925-342658	fwd/B	G/T	ctcctcttggggaagtaccaaactgccttt	caggtactttcaggtactggcggtcgtacc	10/06/00	10/25/06	87	Genomic	99 %
ss2004592	KWOK\|OVLP-000925-346266	fwd/B	G/T	ctcctcttggggaagtaccaaactgccttt	caggtactttcaggtactggcggtcgtacc	10/06/00	10/10/03	87	Genomic	99 %
ss6718270	WI_SSAHASNP\|NT_022792.13_8352026	rev/T	A/C	ggtacgaccgccagtacctgaaagtacctg	aaaggcagtttggtacttccccaagaggag	02/12/03	10/10/03	111	Genomic	unknown
ss24179948	PERLEGEN\|afd4041917	rev/T	A/C	ggtacgaccgccagtacctgaaagtacctg	aaaggcagtttggtacttccccaagaggag	08/10/04	09/13/04	123	Genomic	unknown
ss68922750	PERLEGEN\|PGP04041917	rev/T	A/C	ggtacgaccgccagtacctgaaagtacctg	aaaggcagtttggtacttccccaagaggag	01/30/07	08/14/07	127	Genomic	unknown
ss77392434	HGSV\|Cor12156_SNV_20070510.chr4_187952269	rev/T	A/C	ggtacgaccgccagtacctgaaagtacctg	aaaggcagtttggtacttccccaagaggag	10/09/07	10/12/07	129	Genomic	unknown
ss81400153	HGSV\|Cor18507_SNV_20070510.chr4_187952269	rev/T	A/C	ggtacgaccgccagtacctgaaagtacctg	aaaggcagtttggtacttccccaagaggag	11/26/07	11/29/07	130	Genomic	unknown
ss82592844	HGSV\|Cor18555_SNV_20070510.chr4_187952269	rev/T	A/C	ggtacgaccgccagtacctgaaagtacctg	aaaggcagtttggtacttccccaagaggag	11/27/07	12/03/07	130	Genomic	unknown
ss92934614	BCMHGSC_JDW\|JWB-1914076	rev/T	A/C	ggtacgaccgccagtacctgaaagtacctg	aaaggcagtttggtacttccccaagaggag	02/26/08	03/03/08	129	Genomic	unknown

Fasta sequence (Legend)

 GCAAGGCCGG AAGGCAGATG TGTGTTTGTG ACGTGTGTTT GTGATGTATG TGTATGTGTG
 GGTAGCACAC CTCATAAATT CTATCACTTG TTTTAAATGG GTAATGCAAT CACATGGCAC
 AACGTGCAAA TAGTACAGGA AGATACCCAG TCAGGTTTTA CTTTCACCCA GTTCTCCAGA
 CACTCCGTTC CCTTCCTTAG tatattaact ctcttttctt attttctgta tcctgaatgc
 tgtggcatct gggccctcat tgagtgggga aggactgccc cttccaggac tcgggatagc
 agatgactgg tgcaggaccg tgcttttcat atgcaagctg accagtccag agtcccactc
 cacaccacca tctgtgtcac gcccaagtca tatcagagcc agtgctagac aactggggac
 agctatgccc cagagccttt gaaattactt aaaccagcca gtcctgagcg tctcaccttg
 cctttctgtg agatcctcag tcaagctttc ccggttcctt ccacctccag accaaccctg
 gcatggtccc gtatggccca gcacggcctt cggcctttgc caccttcagt ggcggtggta
 tggcctcctc ttggggaagt accaaactgc cttt
 K
 caggtacttt caggtactgg cggtcgtacc tgatctgttg cctcaccata cctgaataat
 aaaatctacT TAGAGGCAAC TAGTGTTTGC ATTTTCTTTC ACTTGTATAT AAGCAAGAAA
 GAATATGTTG GTTTTTTCCT CATCTTTTTA TACAGATAGC ATACTGTATA CATGGATATG
 CATCTTGGGT TTTTCCATAA CAGTATTGGA TGCTGTGCTT TTAAGAGCAC CTTggctggg
 tgtggtggct cgtgcctgta atcccagcac ttcgggaggc tgaggcttgt ggatcacttg
 aggtcaggag ttcgagacca gcttggccaa catggcaaaa ccccatgtct gctaaaaaca
 aaaattagct gggtgtggtg gtgcacacct gtaatcccag ctacttggga ggctgaggca
 tgagaatagc ttgaacccag gaggcagagg ttgcagcgag ccgagatcac tccactgcac
 tccaacctag gcaacagtga gattgcatct caaaaaaaaa aaaaTCACCT TATTGTGGTT
 ACTGATGAAC TTGCCACATT ATTATAGGAA TATATGTGCA TATCCATGTA CCTTTCACTG
 TCCATTTCAC TGGTCTACTG ATTT

GeneView

GeneView via analysis of contig annotation: FAT FAT tumor suppressor homolog 1 (Drosophila)

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_022792->NM_005245

function

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


reference	NT_022792->NM_005245->NP_005236	19989060	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs327072 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_001838921.1	47806811	183324572	minus	C	alt_assembly_8	HuRef	HuRef	view	634
4	NW_922217.1	67155568	184898089	minus	C	alt_assembly_1	Celera	Celera	view	634
4	NT_022792.17	19989060	187814114	minus	C	ref_assembly	reference	reference	view	634

NCBI Resource Links

Submitter-Referenced
GenBank
NC_000004.9 AC024664 AC040966.2 AC058794 AC058794.1

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
ss2004279	HapMap-CEU	European	116	IG	0.759	0.207	0.034	0.343	0.862	0.138

	HapMap-HCB	Asian	88	IG	0.295	0.545	0.159	0.479	0.568	0.432

	HapMap-JPT	Asian	88	IG	0.227	0.477	0.295	1.000	0.466	0.534

	HapMap-YRI	Sub-Saharan African	120	IG	0.050	0.400	0.550	0.655	0.250	0.750

	CHMJ	Asian	74	IG					0.486	0.514

ss24179948	AFD_EUR_PANEL	European	48	IG	0.708	0.292		0.439	0.854	0.146

	AFD_AFR_PANEL	African American	46	IG	0.174	0.522	0.304	1.000	0.435	0.565

	AFD_CHN_PANEL	Asian	48	IG	0.292	0.458	0.250	0.752	0.521	0.479

ss68922750	HapMap-CEU	European	120	GF	0.750	0.217	0.033		0.858	0.142

	HapMap-HCB	Asian	90	GF	0.356	0.556	0.089		0.633	0.367

	HapMap-JPT	Asian	90	GF	0.356	0.356	0.289		0.533	0.467

	HapMap-YRI	Sub-Saharan African	120	GF	0.083	0.417	0.500		0.292	0.708

Concordant Genotype	Total Sample	G/G	G/T	T/T
ss2004279	255	95	91	63
ss24179948	71
ss68922750	255

RefSNP Genotype Summary	Total Individual	G/G	G/T	T/T
rs327072	332	95	91	63

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
5138	ss2004279	T/T	CSHL-HAPMAP	HapMap-YRI	NA19130	YOR101.03	r23_ch4_YRI_perlegen:genotyping_1.0.0	2673875
5138	ss68922750	A/C	CSHL-HAPMAP	HapMap-YRI	NA19130	YOR101.03	chr4-HapMap-YRI
5156	ss2004279	T/T	CSHL-HAPMAP	HapMap-HCB	NA18603	CH18603	r23_ch4_HCB_perlegen:genotyping_1.0.0	2673875
5156	ss68922750	A/C	CSHL-HAPMAP	HapMap-HCB	NA18603	CH18603	chr4-HapMap-HCB
5157	ss2004279	T/T	CSHL-HAPMAP	HapMap-HCB	NA18540	CH18540	r23_ch4_HCB_perlegen:genotyping_1.0.0	2673875
5157	ss68922750	A/C	CSHL-HAPMAP	HapMap-HCB	NA18540	CH18540	chr4-HapMap-HCB
5159	ss2004279	T/T	CSHL-HAPMAP	HapMap-HCB	NA18542	CH18542	r23_ch4_HCB_perlegen:genotyping_1.0.0	2673875
5159	ss68922750	C/C	CSHL-HAPMAP	HapMap-HCB	NA18542	CH18542	chr4-HapMap-HCB
5190	ss2004279	G/T	CSHL-HAPMAP	HapMap-HCB	NA18636	CH18636	r23_ch4_HCB_perlegen:genotyping_1.0.0	2673875
5190	ss68922750	C/C	CSHL-HAPMAP	HapMap-HCB	NA18636	CH18636	chr4-HapMap-HCB
5192	ss2004279	G/T	CSHL-HAPMAP	HapMap-HCB	NA18637	CH18637	r23_ch4_HCB_perlegen:genotyping_1.0.0	2673875
5192	ss68922750	C/C	CSHL-HAPMAP	HapMap-HCB	NA18637	CH18637	chr4-HapMap-HCB
5201	ss2004279	G/T	CSHL-HAPMAP	HapMap-JPT	NA18948	JA18948	r23_ch4_JPT_perlegen:genotyping_1.0.0	2673875
5201	ss68922750	C/C	CSHL-HAPMAP	HapMap-JPT	NA18948	JA18948	chr4-HapMap-JPT
5204	ss2004279	G/T	CSHL-HAPMAP	HapMap-JPT	NA18964	JA18964	r23_ch4_JPT_perlegen:genotyping_1.0.0	2673875
5204	ss68922750	C/C	CSHL-HAPMAP	HapMap-JPT	NA18964	JA18964	chr4-HapMap-JPT
5210	ss2004279	G/T	CSHL-HAPMAP	HapMap-JPT	NA18961	JA18961	r23_ch4_JPT_perlegen:genotyping_1.0.0	2673875
5210	ss68922750	C/C	CSHL-HAPMAP	HapMap-JPT	NA18961	JA18961	chr4-HapMap-JPT
5235	ss2004279	G/T	CSHL-HAPMAP	HapMap-JPT	NA19007	JA19007	r23_ch4_JPT_perlegen:genotyping_1.0.0	2673875
5235	ss68922750	C/C	CSHL-HAPMAP	HapMap-JPT	NA19007	JA19007	chr4-HapMap-JPT
5236	ss2004279	G/T	CSHL-HAPMAP	HapMap-JPT	NA19003	JA19003	r23_ch4_JPT_perlegen:genotyping_1.0.0	2673875
5236	ss68922750	C/C	CSHL-HAPMAP	HapMap-JPT	NA19003	JA19003	chr4-HapMap-JPT
5243	ss2004279	T/T	CSHL-HAPMAP	HapMap-YRI	NA18507	YOR009.03	r23_ch4_YRI_perlegen:genotyping_1.0.0	2673875
5243	ss68922750	A/C	CSHL-HAPMAP	HapMap-YRI	NA18507	YOR009.03	chr4-HapMap-YRI
5254	ss2004279	G/T	CSHL-HAPMAP	HapMap-YRI	NA18870	YOR017.02	r23_ch4_YRI_perlegen:genotyping_1.0.0	2673875
5254	ss68922750	C/C	CSHL-HAPMAP	HapMap-YRI	NA18870	YOR017.02	chr4-HapMap-YRI
5273	ss2004279	T/T	CSHL-HAPMAP	HapMap-YRI	NA19101	YOR042.03	r23_ch4_YRI_perlegen:genotyping_1.0.0	2673875
5273	ss68922750	A/C	CSHL-HAPMAP	HapMap-YRI	NA19101	YOR042.03	chr4-HapMap-YRI
5305	ss2004279	G/T	CSHL-HAPMAP	HapMap-YRI	NA19152	YOR072.02	r23_ch4_YRI_perlegen:genotyping_1.0.0	2673875
5305	ss68922750	C/C	CSHL-HAPMAP	HapMap-YRI	NA19152	YOR072.02	chr4-HapMap-YRI

Genotype data submitted for	341	samples from	332	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

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Revised: May 25, 2006 1:38 PM .