Reference SNP(refSNP) Cluster Report: rs174342

Reference SNP(refSNP) Cluster Report: rs174342

refSNP ID: rs174342
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:	A/G
Ancestral Allele:	G
Clinical Association:	unknown

HGVS Names
NM_031413.2:c.2795-182A>G
NT_011519.10:g.1179806A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44301743 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs174342 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
ss232150	KWOK\|OVLP-000621-87972	fwd/T	A/G	gctaggttttacctttgtgtccgtgaaagg	gtgaaaggaagtgtacagggaccccaatgt	06/30/00	10/10/03	79	Genomic	94 %
ss570207	SC_JCM\|AC004019.20_212679	fwd/T	A/G	gctaggttttacctttgtgtccgtgaaagg	gtgaaaggaagtgtacagggaccccaatgt	07/12/00	10/25/06	80	Genomic	unknown
ss869152	SC\|Em:AC007666_59760	fwd/T	A/G	gctaggttttacctttgtgtccgtgaaagg	gtgaaaggaagtgtacagggaccccaatgt	08/02/00	04/07/04	85	Genomic	unknown
ss1053106	KWOK\|OVLP-000804-86713	fwd/T	A/G	gctaggttttacctttgtgtccgtgaaagg	gtgaaaggaagtgtacagggaccccaatgt	09/02/00	10/10/03	86	Genomic	94 %
ss2066248	KWOK\|OVLP-000925-287777	fwd/T	A/G	gctaggttttacctttgtgtccgtgaaagg	gtgaaaggaagtgtacagggaccccaatgt	10/07/00	10/10/03	87	Genomic	94 %
ss2066378	KWOK\|OVLP-000925-299644	fwd/T	A/G	gctaggttttacctttgtgtccgtgaaagg	gtgaaaggaagtgtacagggaccccaatgt	10/07/00	10/10/03	87	Genomic	94 %
ss3563554	SC_JCM\|AC007666.12_59761	fwd/T	A/G	gctaggttttacctttgtgtccgtgaaagg	gtgaaaggaagtgtacagggaccccaatgt	09/24/01	10/10/03	100	Genomic	unknown
ss11011550	BCM_SSAHASNP\|chr22.NT_011519.10_1179806	fwd/T	A/G	gctaggttttacctttgtgtccgtgaaagg	gtgaaaggaagtgtacagggaccccaatgt	07/01/03	11/10/03	116	Genomic	unknown
ss12533946	WI_SSAHASNP\|chr22.NT_011519.10_1179806	fwd/T	A/G	gctaggttttacctttgtgtccgtgaaagg	gtgaaaggaagtgtacagggaccccaatgt	07/04/03	10/10/03	116	Genomic	unknown
ss13345108	SC_SNP\|NT_011519.10_1179806	fwd/T	A/G	gctaggttttacctttgtgtccgtgaaagg	gtgaaaggaagtgtacagggaccccaatgt	10/22/03	10/31/03	119	Genomic	unknown
ss21863812	SSAHASNP\|WGSA-200403-chr22.chr22.NT_011519.10_1179806	fwd/T	A/G	gctaggttttacctttgtgtccgtgaaagg	gtgaaaggaagtgtacagggaccccaatgt	03/20/04	03/20/04	121	Genomic	unknown
ss24555070	PERLEGEN\|afd4194443	fwd/T	A/G	gctaggttttacctttgtgtccgtgaaagg	gtgaaaggaagtgtacagggaccccaatgt	08/10/04	08/21/04	123	Genomic	unknown
ss44301743	ABI\|hCV2618245	fwd/T	A/G	gctaggttttacctttgtgtccgtgaaagg	gtgaaaggaagtgtacagggaccccaatgt	07/18/05	11/03/06	126	Genomic	unknown
ss65825260	KRIBB_YJKIM\|KHS1044	fwd/T	A/G	gctaggttttacctttgtgtccgtgaaagg	gtgaaaggaagtgtacagggaccccaatgt	10/17/06	11/15/06	127	Genomic	unknown
ss66281742	AFFY\|SNP_A-1799886	rev/B	C/T	gtacacttcctttcac	cctttcacggacacaa	10/29/06	08/14/07	127	Genomic	unknown
ss68408209	CSHL-HAPMAP\|perlegen:assay:25761.4194443:1	fwd/T	A/G	gctaggttttacctttgtgtccgtgaaagg	gtgaaaggaagtgtacagggaccccaatgt	01/11/07	01/11/07	127	NA	unknown
ss75938929	AFFY\|AFFY_6_1M_SNP_A-1799886	rev/B	C/T	gtacacttcctttcac	cctttcacggacacaa	08/28/07	08/29/07	130	Genomic	unknown
ss82688802	HGSV\|Cor18956_SNV_20070510.chr22_16402210	fwd/T	A/G	gctaggttttacctttgtgtccgtgaaagg	gtgaaaggaagtgtacagggaccccaatgt	11/30/07	12/03/07	130	Genomic	unknown
ss82944638	HGSV\|Cor19240_SNV_20070510.chr22_16402210	fwd/T	A/G	gctaggttttacctttgtgtccgtgaaagg	gtgaaaggaagtgtacagggaccccaatgt	11/30/07	12/04/07	130	Genomic	unknown
ss91872035	BCMHGSC_JDW\|JWB-1508650	fwd/T	A/G	gctaggttttacctttgtgtccgtgaaagg	gtgaaaggaagtgtacagggaccccaatgt	02/26/08	03/02/08	129	Genomic	unknown

Fasta sequence (Legend)

 CTGTGGAGCT TTTATTCTCG TGGAGCAGAA ACCAGGCATT TGGCCTTCCT GAGCGCCCGT
 CATGCCCTGT TCTTTCTGGT TGCATCCCAT TTTAGAGCTT CCCAGCATGG CCAGTGATTC
 TGATGACAAC CATCCCCTCC CAGTGTGTTT CACGTGCATC TGCCTAGAGT CCGTGAGCCA
 CAAGCCGTCT CTCAGCCTCT TACGAATCGG GCAACCCACG GTTAAGGACA TTTCCATTCT
 CCGGCCCACT GTAAGAGTGA ATGTAGAGGT GCTAGGTTTT ACCTTTGTGT CCGTGAAAGG
 R
 GTGAAAGGAA GTGTACAGGG ACCCCAATGT CCTGCCCTCT TTCAGGGACT CAAACAATTT
 CCAGGTGGGG CTTGAATCAC CACACATCCA CCTTAATCTG ACTCAGGCAT GTTCTTCACA
 TTAATACTGT CATTTCAGCT ACTGAGTTAT TTTTTCTCCT CTTTTTTTTT TTTTTTTGCA
 GCAGAGCCGT TGCCTGGCCT TGAAGAGAAA CCACCAGGTG TTGGTACTTC AGAGGGGGTC
 TACCTCACAC AACTACCTCA CCCCACACCT CCCCTGCAGA CTGACTGCAC CAGGCAGAGC

GeneView

GeneView via analysis of contig annotation: CECR2 cat eye syndrome chromosome region, candidate 2

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_031413

function

HuRef

NW_001838735->NM_031413

function

Celera

NW_927406->NM_031413

function

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


reference	NT_011519->NM_031413->NP_113601	1179806	forward	intron

HuRef	NW_001838735->NM_031413->NP_113601	634251	reverse	intron

Celera	NW_927406->NM_031413->NP_113601	983076	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs174342 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	983076	1650076	plus	A	alt_assembly_1	Celera	Celera	view	300
22	NW_001838735.2	634251	1846083	minus	T	alt_assembly_8	HuRef	HuRef	view	300
22	NT_011519.10	1179806	16407656	plus	A	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_011519 AC000052 AC004019 AC007666 AC007666.12

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC000052.16 AC004019.20 AC007666.12 NC_000022.9	AC212591.3

Population Diversity

	Sample Ascertainment				Genotype Detail					Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/G	C/C	C/T	G/G	HWP	A	G
ss24555070	AFD_EUR_PANEL	European	48	IG	0.042			0.958	1.000	0.021	0.979

	AFD_AFR_PANEL	African American	46	IG				1.000			1.000

	AFD_CHN_PANEL	Asian	48	IG				1.000			1.000

ss44301743	HapMap-CEU	European	120	IG	0.083			0.917	0.752	0.042	0.958

	HapMap-HCB	Asian	90	IG				1.000			1.000

	HapMap-JPT	Asian	88	IG				1.000			1.000

	HapMap-YRI	Sub-Saharan African	120	IG				1.000			1.000

ss65825260	KHP1		180	AF				1.000			1.000

ss66281742	HapMap-CEU	European	118	GF	0.085			0.915		0.042	0.958

	HapMap-HCB	Asian	90	GF				1.000			1.000

	HapMap-JPT	Asian	90	GF				1.000			1.000

	HapMap-YRI	Sub-Saharan African	120	GF				1.000			1.000

ss869152	SC_12_A	Asian	24	AF		1.000					1.000

	SC_12_AA	African American	24	AF		1.000					1.000

	SC_12_C	European	24	AF		0.857	0.143		0.010	0.040	0.960

	SC_95_C	European	94	IG	0.064			0.936	1.000	0.032	0.968

Concordant Genotype	Total Sample	A/G	C/C	C/T	G/G
ss24555070	65	1			64
ss44301743	268	6			261
ss66281742	267		261	6
ss869152	113	3	24		86

RefSNP Genotype Summary	Total Individual	A/G	C/C	C/T	G/G
rs174342	401	7	285	6	357

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
114	ss869152	C/C	TSC-CSHL	SC_12_C	CEPH1331.12		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE
114	ss869152	G/G	TSC-CSHL	SC_95_C	CEPH1331.12		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE
229	ss869152	C/C	TSC-CSHL	SC_12_C	CEPH1347.02		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE
229	ss869152	G/G	TSC-CSHL	SC_95_C	CEPH1347.02		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE
229	ss44301743	G/G	CSHL-HAPMAP	HapMap-CEU	NA10859	CEPH1347.02	r23_ch22_CEU_illumina:golden_gate_1.0.0
229	ss66281742	C/C	CSHL-HAPMAP	HapMap-CEU	NA10859	CEPH1347.02	chr22-HapMap-CEU
230	ss869152	C/C	TSC-CSHL	SC_12_C	CEPH1347.03		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE
230	ss869152	G/G	TSC-CSHL	SC_95_C	CEPH1347.03		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE
231	ss869152	C/C	TSC-CSHL	SC_12_C	CEPH1347.04		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE
231	ss869152	G/G	TSC-CSHL	SC_95_C	CEPH1347.04		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE
429	ss869152	C/C	TSC-CSHL	SC_12_C	CEPH1416.01		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE
429	ss869152	G/G	TSC-CSHL	SC_95_C	CEPH1416.01		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE
429	ss44301743	G/G	CSHL-HAPMAP	HapMap-CEU	NA10835	CEPH1416.01	r23_ch22_CEU_illumina:golden_gate_1.0.0
429	ss66281742	C/C	CSHL-HAPMAP	HapMap-CEU	NA10835	CEPH1416.01	chr22-HapMap-CEU
430	ss869152	C/T	TSC-CSHL	SC_12_C	CEPH1416.02		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE
430	ss869152	G/G	TSC-CSHL	SC_95_C	CEPH1416.02		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE
840	ss869152	C/C	TSC-CSHL	SC_12_AA	NA17109		TSC-SANGER-SC_12_AA-Sep-18-2003-GENOTYPE
840	ss24555070	G/G	PERLEGEN	AFD_AFR_PANEL	NA17109		71_IND_CHR_22
842	ss869152	C/C	TSC-CSHL	SC_12_AA	NA17111		TSC-SANGER-SC_12_AA-Sep-18-2003-GENOTYPE
842	ss24555070	G/G	PERLEGEN	AFD_AFR_PANEL	NA17111		71_IND_CHR_22
845	ss869152	C/C	TSC-CSHL	SC_12_AA	NA17114		TSC-SANGER-SC_12_AA-Sep-18-2003-GENOTYPE
845	ss24555070	G/G	PERLEGEN	AFD_AFR_PANEL	NA17114		71_IND_CHR_22
846	ss869152	C/C	TSC-CSHL	SC_12_AA	NA17115		TSC-SANGER-SC_12_AA-Sep-18-2003-GENOTYPE
846	ss24555070	G/G	PERLEGEN	AFD_AFR_PANEL	NA17115		71_IND_CHR_22
865	ss869152	C/C	TSC-CSHL	SC_12_AA	NA17134		TSC-SANGER-SC_12_AA-Sep-18-2003-GENOTYPE
865	ss24555070	G/G	PERLEGEN	AFD_AFR_PANEL	NA17134		71_IND_CHR_22
867	ss869152	C/C	TSC-CSHL	SC_12_AA	NA17136		TSC-SANGER-SC_12_AA-Sep-18-2003-GENOTYPE
867	ss24555070	G/G	PERLEGEN	AFD_AFR_PANEL	NA17136		71_IND_CHR_22

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
	UNKNOWN	UNKNOWN	UNKNOWN

Disclaimer Privacy statement

Revised: May 25, 2006 1:38 PM .