Reference SNP(refSNP) Cluster Report: rs4351

Reference SNP(refSNP) Cluster Report: rs4351

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	36/130
Map to Genome Build:	36.3
Citation:	PubMed

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	A/G
Ancestral Allele:	G
Clinical Association:	unknown

HGVS Names
NM_000789.2:c.2912+990G>A
NM_152830.1:c.1190+990G>A
NT_010783.14:g.20221743G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss10861846 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs4351 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
ss4740	DEBNICK\|dcp1-18222	fwd/T	A/G	gaaaaaagtccctcccacttgggagaagtg	caaagaccatctgtcacagctgaagaagtg	05/03/99	12/23/03	36	Genomic	unknown
ss5957396	SC_JCM\|NT_035428.1_981132	fwd/T	A/G	gaaaaaagtccctcccacttgggagaagtg	caaagaccatctgtcacagctgaagaagtg	01/10/03	10/10/03	111	Genomic	unknown
ss10861846	BCM_SSAHASNP\|chr17.NT_010783.13_16861664	fwd/T	A/G	gaaaaaagtccctcccacttgggagaagtg	caaagaccatctgtcacagctgaagaagtg	06/30/03	10/25/06	116	Genomic	unknown
ss19358133	CSHL-HAPMAP\|CSHL-HuDD-200402.chr17.NT_010783.14_20221743	fwd/T	A/G	gaaaaaagtccctcccacttgggagaagtg	caaagaccatctgtcacagctgaagaagtg	02/20/04	03/04/04	120	Genomic	unknown
ss23142662	PARC\|ACE-017652	fwd/T	A/G	gaaaaaagtccctcccacttgggagaagtg	caaagaccatctgtcacagctgaagaagtg	05/07/04	05/16/04	126	Genomic	unknown
ss23448585	PERLEGEN\|afd4275312	fwd/T	A/G	gaaaaaagtccctcccacttgggagaagtg	caaagaccatctgtcacagctgaagaagtg	08/10/04	09/13/04	123	Genomic	unknown
ss40774195	ABI\|hCV1247715	fwd/T	A/G	gaaaaaagtccctcccacttgggagaagtg	caaagaccatctgtcacagctgaagaagtg	07/17/05	07/17/05	126	Genomic	unknown
ss66510465	AFFY\|SNP_A-4214465	fwd/T	A/G	ccacttgggagaagtg	caaagaccatctgtca	10/29/06	08/14/07	127	Genomic	unknown
ss69199755	PERLEGEN\|PGP04275312	fwd/T	A/G	gaaaaaagtccctcccacttgggagaagtg	caaagaccatctgtcacagctgaagaagtg	01/30/07	08/14/07	127	Genomic	unknown
ss69365650	PHARMGKB_PARC\|PS205301_PA141144424_17652	fwd/T	A/G	gaaaaaagtccctcccacttgggagaagtg	caaagaccatctgtcacagctgaagaagtg	03/22/07	08/14/07	127	Genomic	unknown
ss76333140	AFFY\|AFFY_6_1M_SNP_A-4214465	fwd/T	A/G	ccacttgggagaagtg	caaagaccatctgtca	08/28/07	08/30/07	129	Genomic	unknown
ss76857478	AFFY\|AFFY_6_1M_AFFX-SNP_3894260	fwd/T	A/G	ccacttgggagaagtg	caaagaccatctgtca	08/28/07	08/30/07	129	Genomic	unknown
ss81404091	KRIBB_YJKIM\|KHS30276	fwd/T	A/G	gaaaaaagtccctcccacttgggagaagtg	caaagaccatctgtcacagctgaagaagtg	11/30/07	11/30/07	130	Genomic	unknown
ss84149609	PHARMGKB_PARC\|PS206642_PA151797798_17652	fwd/T	A/G	gaaaaaagtccctcccacttgggagaagtg	caaagaccatctgtcacagctgaagaagtg	12/06/07	12/10/07	130	Genomic	unknown
ss90634046	BCMHGSC_JDW\|JWB-1038662	fwd/T	A/G	gaaaaaagtccctcccacttgggagaagtg	caaagaccatctgtcacagctgaagaagtg	02/26/08	02/29/08	129	Genomic	unknown
ss109855947	1000GENOMES\|CEU.trio.12.15.2008_3421272_chr17_58923464	fwd/T	A/G	gaaaaaagtccctcccacttgggagaagtg	caaagaccatctgtcacagctgaagaagtg	12/15/08	12/16/08	130	Genomic	unknown
ss113710685	1000GENOMES\|NA19240_2008_12_16_3080158_chr17_58923464	fwd/T	A/G	gaaaaaagtccctcccacttgggagaagtg	caaagaccatctgtcacagctgaagaagtg	12/18/08	12/18/08	130	Genomic	unknown
ss118097390	ILLUMINA-UK\|NA18507_000064313_NCBI36.1_chr17_58923464	fwd/T	A/G	gaaaaaagtccctcccacttgggagaagtg	caaagaccatctgtcacagctgaagaagtg	01/20/09	01/20/09	130	Genomic	99 %

Fasta sequence (Legend)

 TCTCCCTGGG GGCACATGCT GTGACACAGG GAGGCACACG AGGATGTTGG GTGCTCTGTA
 CAGATCCACT CTCACCCCTG ACAGGCTCAG AAGCTGCCTT CCTTGGAGGA TGGCgtttta
 gttacctatt gctgtgcaac caagcacccc agagcttagc cttacgaaac aaccagttga
 ttttgcttat gattttatgt gccaggaatt caggcagtac acagtggaaa tggcctttct
 ctacagggcc ccctctgttg ggggcagctc tcacagccgg gatggctcaa tgggggCCAT
 ACGTCCAGAG CCCCAGTTCT GGCTGTCGGT tgaggtcctc ggtttttccc atgtggcaga
 tgctggggca catgttccca gtggcctctt ggctcacatg ttgggtgctt ggggtgagat
 ggctggaacg gctggaggtg ggtcaggcat ctctccaggc tagctcgggc gccctcccag
 cgtggaatct gaggtgggca gatttacctg gcagccagca tcccccacag caactactga
 cgcagccagt tctcaaggct aggtccaaaa ctggcccaga gtcacttctg ccatgtttta
 ttggctagaa caagtcacaa gttcacccag attcaagaga agagaaaaaa gtccctccca
 cttgggagaa gtg
 R
 caaagACCAT CTGTCACAGC TGAAGAAGTG TCTCTTACAA GGAGAACAGA CACGGGGAGC
 CTGAAACAAA ACCCGATGGG ATTCCCTGGG CTGTGCAGGC CCTTCCAGGC ATGAGGACTC
 AGCCACAGGG CTGAGAGGAG ACAGGATCTG GGGGATGAGA GCCCTTGTGG GGTCTTCCCT
 TTTATGGGGA GTCAGAGGAG AAGCT

GeneView

GeneView via analysis of contig annotation:

View more variation on this gene (click to hide).

Assembly	SNP to Chr	Chr	Chr position	Contig	Contig position	Allele

Function	mRNA				Protein
Function	mRNA to Chr	Accession	Position	Allele change	Accession	Position	Residue change

GeneView via analysis of contig annotation: N/A.

GeneView via direct blast against RefSeq sequences (used when no gene model is available):

Function	Chr	mRNA				Protein
Function	Chr	SNP to mRNA	Accession	Position	Allele change	Accession	Position	Residue change

GeneView via direct blast against RefSeq sequences (used when no gene model is available): N/A

Integrated Maps:

Genome Build	Chr	Chr Pos	Contig	Contig Pos	SNP to Chr	Contig allele	Group term	Group label	Contig label	Neighbor SNP	Map Method

doesn't map to any assembly.

NCBI Resource Links

Resource

Submitter-Referenced
GenBank
NT_035428.1

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss10861846	HapMap-CEU	European	120	IG	0.317	0.417	0.267		0.525	0.475

	HapMap-HCB	Asian	90	IG	0.489	0.467	0.044		0.722	0.278

	HapMap-JPT	Asian	90	IG	0.178	0.667	0.156		0.511	0.489

	HapMap-YRI	Sub-Saharan African	118	IG	0.356	0.508	0.136		0.610	0.390

	CHMJ	Asian	74	IG					0.595	0.405

ss23142662	PARC-EUROPEAN-PANEL	European	46	AF					0.391	0.609

ss23448585	AFD_EUR_PANEL	European	46	IG	0.217	0.391	0.391	0.371	0.413	0.587

	AFD_AFR_PANEL	African American	42	IG	0.190	0.571	0.238	0.527	0.476	0.524

	AFD_CHN_PANEL	Asian	30	IG	0.467	0.333	0.200	0.294	0.633	0.367

ss66510465	HapMap-CEU	European	118	GF	0.322	0.407	0.271		0.525	0.475

	HapMap-HCB	Asian	90	GF	0.489	0.467	0.044		0.722	0.278

	HapMap-JPT	Asian	90	GF	0.156	0.689	0.156		0.500	0.500

	HapMap-YRI	Sub-Saharan African	120	GF	0.333	0.517	0.150		0.592	0.408

ss69199755	HapMap-CEU	European	120	GF	0.300	0.467	0.233		0.533	0.467

	HapMap-HCB	Asian	90	GF	0.489	0.467	0.044		0.722	0.278

	HapMap-JPT	Asian	90	GF	0.178	0.711	0.111		0.533	0.467

	HapMap-YRI	Sub-Saharan African	120	GF	0.333	0.550	0.117		0.608	0.392

ss69365650	PA141144431		946	AF					0.486	0.514

ss76333140	ICMHP		4	IG		0.500	0.500		0.250	0.750

ss84149609	PA151797799		90	AF					0.478	0.522

Concordant Genotype	Total Sample	A/A	A/G	G/G
ss10861846	1188	312	568	279
ss23448585	71	16	26	17
ss66510465	250	81	128	41
ss76333140	6		3	3

RefSNP Genotype Summary	Total Individual	A/A	A/G	G/G
rs4351	1267	334	598	298

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
170	ss10861846	A/A	CSHL-HAPMAP	HapMap-CEU	NA07000	CEPH1340.10	r27_ch17_CEU_affymetrix:genomewidesnp_6.0
170	ss66510465	A/A	CSHL-HAPMAP	HapMap-CEU	NA07000	CEPH1340.10	chr17-HapMap-CEU
263	ss10861846	A/A	CSHL-HAPMAP	HapMap-CEU	NA11830	CEPH1350.11	r27_ch17_CEU_affymetrix:genomewidesnp_6.0
263	ss66510465	A/A	CSHL-HAPMAP	HapMap-CEU	NA11830	CEPH1350.11	chr17-HapMap-CEU
467	ss10861846	G/G	CSHL-HAPMAP	HapMap-CEU	NA12006	CEPH1420.12	r27_ch17_CEU_affymetrix:genomewidesnp_6.0
467	ss66510465	G/G	CSHL-HAPMAP	HapMap-CEU	NA12006	CEPH1420.12	chr17-HapMap-CEU
577	ss10861846	G/G	CSHL-HAPMAP	HapMap-CEU	NA12813	CEPH1454.13	r27_ch17_CEU_affymetrix:genomewidesnp_6.0
577	ss66510465	G/G	CSHL-HAPMAP	HapMap-CEU	NA12813	CEPH1454.13	chr17-HapMap-CEU
5146	ss10861846	A/G	CSHL-HAPMAP	HapMap-YRI	NA19238	YOR117.02	r27_ch17_YRI_affymetrix:genomewidesnp_6.0
5146	ss66510465	A/G	CSHL-HAPMAP	HapMap-YRI	NA19238	YOR117.02	chr17-HapMap-YRI
5206	ss10861846	G/G	CSHL-HAPMAP	HapMap-JPT	NA18968	JA18968	r27_ch17_JPT_affymetrix:genomewidesnp_6.0
5206	ss66510465	G/G	CSHL-HAPMAP	HapMap-JPT	NA18968	JA18968	chr17-HapMap-JPT
5225	ss10861846	G/G	CSHL-HAPMAP	HapMap-JPT	NA18987	JA18987	r27_ch17_JPT_affymetrix:genomewidesnp_6.0
5225	ss66510465	G/G	CSHL-HAPMAP	HapMap-JPT	NA18987	JA18987	chr17-HapMap-JPT
5231	ss10861846	A/A	CSHL-HAPMAP	HapMap-JPT	NA18998	JA18998	r27_ch17_JPT_affymetrix:genomewidesnp_6.0
5231	ss66510465	A/G	CSHL-HAPMAP	HapMap-JPT	NA18998	JA18998	chr17-HapMap-JPT
5247	ss10861846	G/G	CSHL-HAPMAP	HapMap-YRI	NA18515	YOR013.01	r27_ch17_YRI_affymetrix:genomewidesnp_6.0
5247	ss66510465	G/G	CSHL-HAPMAP	HapMap-YRI	NA18515	YOR013.01	chr17-HapMap-YRI
5248	ss10861846	G/G	CSHL-HAPMAP	HapMap-YRI	NA18517	YOR013.02	r27_ch17_YRI_affymetrix:genomewidesnp_6.0
5248	ss66510465	G/G	CSHL-HAPMAP	HapMap-YRI	NA18517	YOR013.02	chr17-HapMap-YRI
5250	ss10861846	N/N	CSHL-HAPMAP	HapMap-YRI	NA18521	YOR016.01	r27_ch17_YRI_affymetrix:genomewidesnp_6.0
5250	ss66510465	A/A	CSHL-HAPMAP	HapMap-YRI	NA18521	YOR016.01	chr17-HapMap-YRI
5259	ss10861846	G/G	CSHL-HAPMAP	HapMap-YRI	NA18857	YOR023.01	r27_ch17_YRI_affymetrix:genomewidesnp_6.0
5259	ss66510465	G/G	CSHL-HAPMAP	HapMap-YRI	NA18857	YOR023.01	chr17-HapMap-YRI
5274	ss10861846	A/A	CSHL-HAPMAP	HapMap-YRI	NA19139	YOR043.01	r27_ch17_YRI_affymetrix:genomewidesnp_6.0
5274	ss66510465	A/A	CSHL-HAPMAP	HapMap-YRI	NA19139	YOR043.01	chr17-HapMap-YRI
5275	ss10861846	A/A	CSHL-HAPMAP	HapMap-YRI	NA19137	YOR043.02	r27_ch17_YRI_affymetrix:genomewidesnp_6.0
5275	ss66510465	A/A	CSHL-HAPMAP	HapMap-YRI	NA19137	YOR043.02	chr17-HapMap-YRI
5277	ss10861846	A/A	CSHL-HAPMAP	HapMap-YRI	NA19202	YOR045.01	r27_ch17_YRI_affymetrix:genomewidesnp_6.0
5277	ss66510465	A/A	CSHL-HAPMAP	HapMap-YRI	NA19202	YOR045.01	chr17-HapMap-YRI
5278	ss10861846	A/G	CSHL-HAPMAP	HapMap-YRI	NA19201	YOR045.02	r27_ch17_YRI_affymetrix:genomewidesnp_6.0
5278	ss66510465	A/G	CSHL-HAPMAP	HapMap-YRI	NA19201	YOR045.02	chr17-HapMap-YRI
5287	ss10861846	N/N	CSHL-HAPMAP	HapMap-YRI	NA19209	YOR050.02	r27_ch17_YRI_affymetrix:genomewidesnp_6.0
5287	ss66510465	G/G	CSHL-HAPMAP	HapMap-YRI	NA19209	YOR050.02	chr17-HapMap-YRI
5303	ss10861846	A/A	CSHL-HAPMAP	HapMap-YRI	NA19141	YOR071.03	r27_ch17_YRI_affymetrix:genomewidesnp_6.0
5303	ss66510465	A/A	CSHL-HAPMAP	HapMap-YRI	NA19141	YOR071.03	chr17-HapMap-YRI
5307	ss10861846	N/N	CSHL-HAPMAP	HapMap-YRI	NA19145	YOR074.01	r27_ch17_YRI_affymetrix:genomewidesnp_6.0
5307	ss66510465	A/A	CSHL-HAPMAP	HapMap-YRI	NA19145	YOR074.01	chr17-HapMap-YRI

Genotype data submitted for	1282	samples from	1267	individuals	Individual with multiple genotypes submission:	275

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

YES

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Revised: May 25, 2006 1:38 PM .