Reference SNP(refSNP) Cluster Report: rs740422

Reference SNP(refSNP) Cluster Report: rs740422

refSNP ID: rs740422
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:	C/T
Ancestral Allele:	C
Clinical Association:	unknown

HGVS Names
NM_017829.5:c.846-45G>A
NM_033070.2:c.936-45G>A
NT_011519.10:g.771442C>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss88603 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs740422 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
ss88603	TSC-CSHL\|TSC0104021	fwd/B	C/T	cacaccggaaaaggaaaaaggagaaaaaac	ctaaatcaatgttgcaaagcaaagggagca	09/06/00	04/07/04	86	Genomic	95 %
ss3227579	YUSUKE\|IMS-JST037663	fwd/B	C/T	cacaccggaaaaggaaaaaggagaaaaaac	ctaaatcaatgttgcaaagcaaagggagca	09/05/01	10/10/03	100	Genomic	unknown
ss5451119	TSC-CSHL\|TSC0106506	rev/T	A/G	tgctccctttgctttgcaacattgatttag	gttttttctcctttttccttttccggtgtg	09/21/02	10/10/03	108	Genomic	unknown
ss24700265	PERLEGEN\|afd0103912	fwd/B	C/T	cacaccggaaaaggaaaaaggagaaaaaac	ctaaatcaatgttgcaaagcaaagggagca	08/10/04	09/13/04	123	Genomic	unknown
ss44329209	ABI\|hCV2635419	fwd/B	C/T	cacaccggaaaaggaaaaaggagaaaaaac	ctaaatcaatgttgcaaagcaaagggagca	07/18/05	11/03/06	126	Genomic	unknown
ss65826157	KRIBB_YJKIM\|KHS1943	fwd/B	C/T	cacaccggaaaaggaaaaaggagaaaaaac	ctaaatcaatgttgcaaagcaaagggagca	10/17/06	12/16/06	127	Genomic	unknown
ss66723578	ILLUMINA\|HumanHap300v1.1_rs740422	fwd/T	C/T	cacaccggaaaaggaaaaaggagaaaaaac	ctaaatcaatgttgcaaagcaaagggagca	11/09/06	11/09/06	127	Genomic	unknown
ss67576288	ILLUMINA\|HumanHap550v1.1_rs740422	fwd/B	C/T	cacaccggaaaaggaaaaaggagaaaaaac	ctaaatcaatgttgcaaagcaaagggagca	11/14/06	11/14/06	127	Genomic	unknown
ss67957666	ILLUMINA\|HumanHap650Yv1.0_rs740422	fwd/B	C/T	cacaccggaaaaggaaaaaggagaaaaaac	ctaaatcaatgttgcaaagcaaagggagca	11/14/06	11/15/06	127	Genomic	unknown
ss69277660	PERLEGEN\|PGP00103912	fwd/B	C/T	cacaccggaaaaggaaaaaggagaaaaaac	ctaaatcaatgttgcaaagcaaagggagca	01/30/07	08/14/07	127	Genomic	unknown
ss70926749	ILLUMINA\|HumanHap550v3.0__rs740422	rev/T	A/G	tgctccctttgctttgcaacattgatttag	gttttttctcctttttccttttccggtgtg	04/20/07	03/31/08	130	Genomic	unknown
ss71527761	ILLUMINA\|HumanHap650Yv3.0_rs740422	fwd/B	C/T	cacaccggaaaaggaaaaaggagaaaaaac	ctaaatcaatgttgcaaagcaaagggagca	04/23/07	04/23/07	127	Genomic	unknown
ss74847850	AFFY\|SNP_M-606793	fwd/B	C/T	cacaccggaaaaggaaaaaggagaaaaaac	ctaaatcaatgttgcaaagcaaagggagca	08/09/07	08/09/07	128	Genomic	unknown
ss75672098	ILLUMINA\|ILMN_Human_1M_rs740422	fwd/B	C/T	cacaccggaaaaggaaaaaggagaaaaaac	ctaaatcaatgttgcaaagcaaagggagca	08/28/07	08/29/07	129	Genomic	unknown
ss76474287	AFFY\|AFFY_6_1M_SNP_A-8335078	fwd/B	C/T	aaaaaggagaaaaaac	ctaaatcaatgttgca	08/28/07	08/30/07	129	Genomic	unknown
ss78093170	HGSV\|Cor12878_SNV_20070510.chr22_15993846	fwd/B	C/T	cacaccggaaaaggaaaaaggagaaaaaac	ctaaatcaatgttgcaaagcaaagggagca	10/17/07	10/17/07	129	Genomic	unknown
ss79256333	ILLUMINA\|HumanHap300v2.0_rs740422	fwd/B	C/T	cacaccggaaaaggaaaaaggagaaaaaac	ctaaatcaatgttgcaaagcaaagggagca	04/18/07	11/18/07	130	Genomic	unknown
ss83543563	KRIBB_YJKIM\|KHS486138	fwd/B	C/T	cacaccggaaaaggaaaaaggagaaaaaac	ctaaatcaatgttgcaaagcaaagggagca	12/04/07	12/05/07	130	Genomic	unknown

Fasta sequence (Legend)

 TGCACAGCCT CATTCACGTC ATTCACCACG TGGGAGGCCT CCATGAGCCC TGGACTGAAG
 CATAAGTCTC GGTGCCCGTG GAATGGAGGC TCCCCTCCTC CAAGGACAGG CTCCGTGGAC
 TGTGGGTTCC TGGGATTGTA GACGCCTGTA CACACCAGGA TGGAGATGCA GCTCTGGCTT
 GCTGAGGGCT GTTGCTGCCG TGTGCCCCCG GCCCCTAGTT CTGGCGCCCC ATCATGCGTT
 GCCTTCTGCA GGTACTGGTG GAACAGGTTG GCGCCGTATA CGTCAGACAT AGGGTTATCA
 CTGGCAGGGG CAGCCACACC GGAAAAGGAA AAAGGAGAAA AAAC
 Y
 CTAAATCAAT GTTGCAAAGC AAAGGGAGCA GAGAAGAGTT TCGGGGCAGA AGAGTGAATT
 AGATATAGGG AAATGGGGGT GAGAGTAGAG GAGGAGGGAG AGAAGGGGAT GTCATAAAAG
 GGACAAAGGA GGGAGAGCAG AGCCTACCCC ACAGCATAGA GCTTCCGGAT GGGGGCGGCC
 CAGCCCCGCC TCTCCGCCTG TCGCCTGATC AGGTCCTCGG CATACTGGTA AGTGAGGATG
 CTGGGTTTGC CCATCAGGCC CTCGTATCTC AGCTCCTTGC CCGTCACTTT CTGGTAAATG
 GTTCCAGGCA CAGCAGAAAG GTGCCATGTC AAACCTGCCA GAAACGAGCA CGCAGCAGTT
 CAGTCTTCCT GATCTCCAAG CTCTTTTAGA GAACACGACT GGCACTGTCT AAGCAGCAAA
 CGCACAGACC AGCCTTTTCC CCAGGGT

GeneView

GeneView via analysis of contig annotation: CECR5 cat eye syndrome chromosome region, candidate 5

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_017829

function

reference

NT_011519->NM_033070

function

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


reference	NT_011519->NM_017829->NP_060299	771442	reverse	intron

reference	NT_011519->NM_033070->NP_149061	771442	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs740422 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_927406.1	574277	1241277	plus	C	alt_assembly_1	Celera	Celera	view	344
22	NW_001838735.2	1042150	1438184	minus	A	alt_assembly_8	HuRef	HuRef	view	344
22	NT_011519.10	771442	15999292	plus	C	ref_assembly	reference	reference	view	344

NCBI Resource Links

Submitter-Referenced
GenBank
NC_000022.8 AC006946.20

dbSNP Blast Analysis

UniGene Cluster ID
26890

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss24700265	AFD_EUR_PANEL	European	48	IG	0.625	0.292	0.083	0.403	0.771	0.229

	AFD_AFR_PANEL	African American	46	IG	0.826	0.174		0.655	0.913	0.087

	AFD_CHN_PANEL	Asian	48	IG	0.792	0.208		0.584	0.896	0.104

ss44329209	AoD_Chinese		90	AF					0.920	0.080

	AoD_Japanese		90	AF					0.930	0.070

ss65826157	KHP1		180	AF	0.889	0.111		0.584	0.944	0.056

ss69277660	HapMap-CEU	European	120	GF	0.583	0.333	0.083		0.750	0.250

	HapMap-HCB	Asian	90	GF	0.933	0.067			0.967	0.033

	HapMap-JPT	Asian	90	GF	0.800	0.200			0.900	0.100

	HapMap-YRI	Sub-Saharan African	120	GF	0.683	0.283	0.033		0.825	0.175

ss88603	TSC_42_C		78	AF					0.760	0.240

	SC_12_A	Asian	22	IG	0.909	0.091		1.000	0.955	0.045

	SC_12_AA	African American	22	IG	0.727	0.273		0.655	0.864	0.136

	SC_12_C	European	14	IG	0.429	0.571		0.294	0.714	0.286

	SC_95_C	European	92	IG	0.457	0.478	0.065	0.403	0.696	0.304

	HapMap-CEU	European	120	IG	0.583	0.333	0.083	0.403	0.750	0.250

	HapMap-HCB	Asian	90	IG	0.933	0.067		1.000	0.967	0.033

	HapMap-JPT	Asian	88	IG	0.795	0.205		0.479	0.898	0.102

	HapMap-YRI	Sub-Saharan African	120	IG	0.683	0.267	0.050	0.403	0.817	0.183

Concordant Genotype	Total Sample	C/C	C/T	T/T
ss24700265	70	53	16	1
ss69277660	268	192	68	8
ss88603	348	229	103	10

RefSNP Genotype Summary	Total Individual	C/C	C/T	T/T
rs740422	401	271	113	11

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
229	ss88603	C/C	TSC-CSHL	SC_12_C	CEPH1347.02		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE	950608
229	ss88603	C/T	TSC-CSHL	SC_95_C	CEPH1347.02		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE	950608
229	ss88603	C/C	CSHL-HAPMAP	HapMap-CEU	NA10859	CEPH1347.02	r23_ch22_CEU_illumina:golden_gate_1.0.0	950608
229	ss69277660	C/C	CSHL-HAPMAP	HapMap-CEU	NA10859	CEPH1347.02	chr22-HapMap-CEU
483	ss88603	C/T	TSC-CSHL	SC_95_C	CEPH1423.01		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE	950608
483	ss24700265	T/T	PERLEGEN	AFD_EUR_PANEL	NA10842		71_IND_CHR_22
5146	ss88603	T/T	CSHL-HAPMAP	HapMap-YRI	NA19238	YOR117.02	r23_ch22_YRI_illumina:golden_gate_1.1.0	950608
5146	ss69277660	C/T	CSHL-HAPMAP	HapMap-YRI	NA19238	YOR117.02	chr22-HapMap-YRI

Genotype data submitted for	472	samples from	401	individuals	Individual with multiple genotypes submission:	285

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 .