Reference SNP(refSNP) Cluster Report: rs698422

Reference SNP(refSNP) Cluster Report: rs698422

refSNP ID: rs698422
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	86/129
Map to Genome Build:	36.3

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

HGVS Names
NM_007098.2:c.2919+1568T>A
NT_011519.10:g.2357976A>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss1367041 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs698422 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
ss1040999	KWOK\|OVLP-000804-553118	fwd/T	A/T	atgtctgatgtctgggaacctggatgtaga	ccctagtagaatattgtgttgtttaatatt	09/02/00	10/10/03	86	Genomic	97 %
ss1041288	KWOK\|OVLP-000804-556678	fwd/T	A/T	atgtctgatgtctgggaacctggatgtaga	ccctagtagaatattgtgttgtttaatatt	09/02/00	10/10/03	86	Genomic	97 %
ss1367041	TSC-CSHL\|TSC0246012	fwd/T	A/T	atgtctgatgtctgggaacctggatgtaga	ccctagtagaatattgtgttgtttaatatt	09/06/00	04/07/04	86	Genomic	95 %
ss1734580	KWOK\|OVLP-000925-408462	fwd/T	A/T	atgtctgatgtctgggaacctggatgtaga	ccctagtagaatattgtgttgtttaatatt	10/05/00	10/10/03	87	Genomic	97 %
ss1734662	KWOK\|OVLP-000925-411095	fwd/T	A/T	atgtctgatgtctgggaacctggatgtaga	ccctagtagaatattgtgttgtttaatatt	10/05/00	10/10/03	87	Genomic	97 %
ss1735188	KWOK\|OVLP-000925-425262	fwd/T	A/T	atgtctgatgtctgggaacctggatgtaga	ccctagtagaatattgtgttgtttaatatt	10/05/00	10/10/03	87	Genomic	97 %
ss2631140	SC_JCM\|AL359537.3_69812	fwd/T	A/T	atgtctgatgtctgggaacctggatgtaga	ccctagtagaatattgtgttgtttaatatt	11/03/00	10/10/03	89	Genomic	unknown
ss4974664	YUSUKE\|IMS-JST145227	fwd/T	A/T	atgtctgatgtctgggaacctggatgtaga	ccctagtagaatattgtgttgtttaatatt	08/12/02	10/10/03	108	Genomic	unknown
ss6217813	SC_JCM\|NT_011519.9_2353723	fwd/T	A/T	atgtctgatgtctgggaacctggatgtaga	ccctagtagaatattgtgttgtttaatatt	01/10/03	10/10/03	111	Genomic	unknown
ss10997721	BCM_SSAHASNP\|chr22.NT_011519.10_2357976	fwd/T	A/T	atgtctgatgtctgggaacctggatgtaga	ccctagtagaatattgtgttgtttaatatt	06/30/03	10/10/03	116	Genomic	unknown
ss13346375	SC_SNP\|NT_011519.10_2357976	fwd/T	A/T	atgtctgatgtctgggaacctggatgtaga	ccctagtagaatattgtgttgtttaatatt	10/22/03	10/31/03	119	Genomic	unknown
ss16919448	CSHL-HAPMAP\|CSHL-HuAA-200402.chr22.NT_011519.10_2357976	fwd/T	A/T	atgtctgatgtctgggaacctggatgtaga	ccctagtagaatattgtgttgtttaatatt	02/17/04	03/04/04	120	Genomic	unknown
ss17715122	CSHL-HAPMAP\|CSHL-HuCC-200402.chr22.NT_011519.10_2357976	fwd/T	A/T	atgtctgatgtctgggaacctggatgtaga	ccctagtagaatattgtgttgtttaatatt	02/19/04	03/04/04	120	Genomic	unknown
ss20139430	CSHL-HAPMAP\|CSHL-HuFF-200402.chr22.NT_011519.10_2357976	fwd/T	A/T	atgtctgatgtctgggaacctggatgtaga	ccctagtagaatattgtgttgtttaatatt	02/21/04	03/04/04	120	Genomic	unknown
ss23588559	PERLEGEN\|afd4633460	fwd/T	A/T	atgtctgatgtctgggaacctggatgtaga	ccctagtagaatattgtgttgtttaatatt	08/10/04	09/13/04	123	Genomic	unknown
ss44299074	ABI\|hCV3274689	fwd/	A/T	atgtctgatgtctgggaacctggatgtaga	ccctagtagaatattgtgttgtttaatatt	07/18/05	11/03/06	126	Genomic	unknown
ss65825685	KRIBB_YJKIM\|KHS1470	fwd/	A/T	atgtctgatgtctgggaacctggatgtaga	ccctagtagaatattgtgttgtttaatatt	10/17/06	12/16/06	127	Genomic	unknown
ss74837514	AFFY\|SNP_M-595366	fwd/T	A/T	atgtctgatgtctgggaacctggatgtaga	ccctagtagaatattgtgttgtttaatatt	08/09/07	08/09/07	128	Genomic	unknown

Fasta sequence (Legend)

 TGTACCAGGT GGCTGGACTA TACCTGGAGA AATGTCTGAT GTCTGGGAAC CTGGATGTAG
 A
 W
 CCCTAGTAGA ATATTGTGTT GTTTAATATT TTTATTAGAT TTGGATGGGT AAGTCCAAAG
 TTGAAACAGA GATTCAAAAC AACATGACCT TCCATAAATC TCAAAGTATT TCAAAATAAA
 AAGTTTATTT AAAAAAGTAG TGGCACAGGC TTGAGGAAAC AGTGGACAGA AAACGAGAGG
 ATGAAATTCA GTAGAGATAA AGGTCAAATC CAGCCCTCAA GCCTTTCGAA AGCACTGGTC
 CAGCAGGTTG GCAATGTGTA TGAGGGAGGT GGGAGTTTTA ACTGGTCCTA TTCTCAGGGC
 TGAAGCCACT TGTTGGACGA GGGTTTTGTT CCAACATTGG TCTTGCCCCA CCCCTAAACA
 GTCTGCCTAG CACCTAGGGA CAGTGCTGAG GGCAGCAGAG GCACTATCTG CAAATGTCTG
 TGAGGCTATA ACTGGAGAGG AGGCTCTTCC ACAGGGCTGT GGGAAGCCCT CCCAGAGGCC
 GAGGCAGACT CCCACCTGCC AGGCCATACC CAATAATGAC CCCTGGCCCC AGCACTCTGC
 CCAGTCTCCA AGGAGGTGCT GGATAGTCAC AGGGGCATAA AGAGCACCTC AACAAAGGGA
 AGT

GeneView

GeneView via analysis of contig annotation: CLTCL1 clathrin, heavy chain-like 1

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_011519->NM_007098

function

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


reference	NT_011519->NM_007098->NP_009029	2357976	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs698422 maps exactly once on NCBI human chromosome 22

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
22	NW_001838737.2	1118313	2826949	minus	T	alt_assembly_8	HuRef	HuRef	view	61
22	NW_927495.1	327181	3057953	plus	A	alt_assembly_1	Celera	Celera	view	61
22	NT_011519.10	2357976	17585826	plus	A	ref_assembly	reference	reference	view	61

NCBI Resource Links

Submitter-Referenced
GenBank
NT_011519.9 AC000072 AC000081.2 AL359537.2 AL359537.3 AL391096 AL391096.7 L77569.1

dbSNP Blast Analysis
GenBank HTGS Draft:
AL359537.4 AL391096.11

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/T	T/T	HWP	A	N	T
ss1367041	TSC_42_AA		82	AF					0.460		0.540

	TSC_42_C		82	AF					0.430		0.570

	TSC_42_A		82	AF					0.670		0.330

	HapMap-CEU	European	120	IG	0.117	0.517	0.367	0.439	0.375		0.625

	HapMap-HCB	Asian	90	IG	0.289	0.467	0.244	0.752	0.522		0.478

	HapMap-JPT	Asian	88	IG	0.295	0.523	0.182	0.752	0.557		0.443

	HapMap-YRI	Sub-Saharan African	120	IG	0.200	0.550	0.250	0.439	0.475		0.525

	CHMJ	Asian	74	IG					0.419	0.014	0.568

ss23588559	AFD_EUR_PANEL	European	48	IG	0.167	0.417	0.417	0.655	0.375		0.625

	AFD_AFR_PANEL	African American	46	IG	0.304	0.348	0.348	0.150	0.478		0.522

	AFD_CHN_PANEL	Asian	46	IG	0.261	0.609	0.130	0.254	0.565		0.435

ss44299074	AoD_Chinese		90	AF					0.390		0.610

	AoD_Japanese		90	AF					0.570		0.430

ss4974664	JBIC-allele		1460	AF					0.527		0.473

ss65825685	KHP1		180	AF	0.311	0.500	0.189	1.000	0.561		0.439

Concordant Genotype	Total Sample	A/A	A/T	T/T
ss1367041	268	54	138	75
ss23588559	69	15	32	21

RefSNP Genotype Summary	Total Individual	A/A	A/T	T/T
rs698422	332	69	166	93

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
162	ss1367041	A/T	CSHL-HAPMAP	HapMap-CEU	NA07019	CEPH1340.02	r23_ch22_CEU_illumina:golden_gate_1.0.0	965495
162	ss23588559	A/A	PERLEGEN	AFD_EUR_PANEL	NA07019		71_IND_CHR_22
349	ss1367041	A/T	CSHL-HAPMAP	HapMap-CEU	NA10861	CEPH1362.02	r23_ch22_CEU_illumina:golden_gate_1.0.0	965495
349	ss23588559	A/A	PERLEGEN	AFD_EUR_PANEL	NA10861		71_IND_CHR_22

Genotype data submitted for	341	samples from	332	individuals	Individual with multiple genotypes submission:	9

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 .