Reference SNP(refSNP) Cluster Report: rs293319

Reference SNP(refSNP) Cluster Report: rs293319

refSNP ID: rs293319
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:	C/T
Ancestral Allele:	T
Clinical Association:	unknown

HGVS Names
NM_001098512.1:c.547+15511C>T
NM_006258.2:c.592+15511C>T
NT_008583.16:g.1794262C>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss1671039 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs293319 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
ss379618	KWOK\|OVLP-000621-189789	fwd/B	C/T	agccccctgagccatttctattttggtgcc	ttatgcaggggtttctttccatttaatgcc	06/30/00	10/10/03	79	Genomic	99 %
ss849314	SC_JCM\|AL157399.2_153928	fwd/B	C/T	agccccctgagccatttctattttggtgcc	ttatgcaggggtttctttccatttaatgcc	07/27/00	10/10/03	87	Genomic	unknown
ss943984	KWOK\|OVLP-000804-363420	fwd/B	C/T	agccccctgagccatttctattttggtgcc	ttatgcaggggtttctttccatttaatgcc	09/01/00	10/10/03	86	Genomic	99 %
ss1671039	KWOK\|OVLP-000925-116940	fwd/B	C/T	agccccctgagccatttctattttggtgcc	ttatgcaggggtttctttccatttaatgcc	10/05/00	10/30/04	87	Genomic	99 %
ss12085581	WI_SSAHASNP\|chr10.NT_008583.15_1794262	fwd/B	C/T	agccccctgagccatttctattttggtgcc	ttatgcaggggtttctttccatttaatgcc	07/04/03	10/10/03	116	Genomic	unknown
ss15464706	SC_SNP\|NT_008583.16_1794262	fwd/B	C/T	agccccctgagccatttctattttggtgcc	ttatgcaggggtttctttccatttaatgcc	11/14/03	11/22/03	120	Genomic	unknown
ss17378581	CSHL-HAPMAP\|CSHL-HuCC-200402.chr10.NT_008583.16_1794262	fwd/B	C/T	agccccctgagccatttctattttggtgcc	ttatgcaggggtttctttccatttaatgcc	02/19/04	03/04/04	120	Genomic	unknown
ss20615813	SSAHASNP\|WGSA-200403-chr10.chr10.NT_008583.16_1794262	fwd/B	C/T	agccccctgagccatttctattttggtgcc	ttatgcaggggtttctttccatttaatgcc	03/18/04	03/18/04	121	Genomic	unknown
ss23604377	PERLEGEN\|afd2246749	fwd/B	C/T	agccccctgagccatttctattttggtgcc	ttatgcaggggtttctttccatttaatgcc	08/10/04	09/13/04	123	Genomic	unknown
ss39812236	ABI\|hCV8912851	fwd/B	C/T	agccccctgagccatttctattttggtgcc	ttatgcaggggtttctttccatttaatgcc	07/16/05	07/16/05	126	Genomic	unknown
ss66839295	ILLUMINA\|HumanHap300v1.1_rs293319	fwd/B	C/T	agccccctgagccatttctattttggtgcc	ttatgcaggggtttctttccatttaatgcc	11/09/06	11/09/06	127	Genomic	unknown
ss67283923	ILLUMINA\|HumanHap550v1.1_rs293319	fwd/B	C/T	agccccctgagccatttctattttggtgcc	ttatgcaggggtttctttccatttaatgcc	11/14/06	11/14/06	127	Genomic	unknown
ss67686422	ILLUMINA\|HumanHap650Yv1.0_rs293319	fwd/B	C/T	agccccctgagccatttctattttggtgcc	ttatgcaggggtttctttccatttaatgcc	11/14/06	11/14/06	127	Genomic	unknown
ss69078792	PERLEGEN\|PGP02246749	fwd/B	C/T	agccccctgagccatttctattttggtgcc	ttatgcaggggtttctttccatttaatgcc	01/30/07	08/14/07	127	Genomic	unknown
ss70762451	ILLUMINA\|HumanHap550v3.0__rs293319	fwd/B	C/T	agccccctgagccatttctattttggtgcc	ttatgcaggggtttctttccatttaatgcc	04/20/07	03/30/08	130	Genomic	unknown
ss71336499	ILLUMINA\|HumanHap650Yv3.0_rs293319	fwd/B	C/T	agccccctgagccatttctattttggtgcc	ttatgcaggggtttctttccatttaatgcc	04/23/07	04/23/07	127	Genomic	unknown
ss75868616	ILLUMINA\|ILMN_Human_1M_rs293319	fwd/B	C/T	agccccctgagccatttctattttggtgcc	ttatgcaggggtttctttccatttaatgcc	08/28/07	08/29/07	129	Genomic	unknown
ss79154290	ILLUMINA\|HumanHap300v2.0_rs293319	fwd/B	C/T	agccccctgagccatttctattttggtgcc	ttatgcaggggtttctttccatttaatgcc	04/18/07	11/18/07	130	Genomic	unknown
ss83416421	KRIBB_YJKIM\|KHS456517	fwd/B	C/T	agccccctgagccatttctattttggtgcc	ttatgcaggggtttctttccatttaatgcc	12/04/07	12/05/07	130	Genomic	unknown
ss88205960	BCMHGSC_JDW\|JWB-0276468	fwd/B	C/T	agccccctgagccatttctattttggtgcc	ttatgcaggggtttctttccatttaatgcc	02/26/08	02/27/08	129	Genomic	unknown

Fasta sequence (Legend)

 CCCCAAGCTG TGGTTTTAAC CCCCATGGTT CTCCTAGGCA AGGGAGTATG GTGGCAGAAA
 CATGGTCATC CAGTCTGGGT TGAAAATTGA ATATACTTTG ggccttaaca agcagcttaa
 cttctctaag cttcagtttc atcattcatg aaatagggat aataaggtat atttcacggg
 taaggcttac atcaggtaat atatgtcaaa tgTGGAGTGT CATTCCAGAT AAAATATGTA
 ATCAATAAAT CATGAAATCA TGATTGTTAT AATGTCTTCC TGTTCCAGGA CAACCATTTT
 TAATTACCTC ATAACTTTAG AGATTTCTAA GGTTTCCTGA ATCTTTTCtt ttctttcttt
 tttttttttt tttttttgag atgaagtttc actcttattg cccaggctgg aatgcagtga
 ttcaatggca caatctcagt tcactgcaac ctctgcctcc tggattcaag caattcttcc
 gcgtcagcct cccgagtagc tgggactata ggcgcctgcc accacgactg gctaattttt
 tgtattttta gtagagacag ggttttatta tgttggccag gctagtctca aactcctgac
 ctcagtgatc cacatgcctc ggcctcccaa agtgctggga ttacaggcgt gagccaccgc
 acccagccCC CTGAGCCATT TCTATTTTGG TGCC
 Y
 TTATGCAGGG GTTTCTTTCC ATTTAATGCC TTCCGTGTAA AATTTCTTTT TACTCCATCT
 TTGACTATTA TACTCACACC TACTTTTAGA AATCCCATTC AACTTCCTCC TCCTTTTTTC
 TAGTTCCTTT ATTATTTGTA TCTCAATCTG AATAGTGGAA ATTTCTTCAC TAATTTGTCA
 GGTCTTTATA GGTGTAGACT

GeneView

GeneView via analysis of contig annotation: PRKG1 protein kinase, cGMP-dependent, type I

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_008583->NM_001098512

function

reference

NT_008583->NM_006258

function

HuRef

NW_001837985->NM_001098512

function

HuRef

NW_001837985->NM_006258

function

Celera

NW_924796->NM_001098512

function

Celera

NW_924796->NM_006258

function

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


reference	NT_008583->NM_001098512->NP_001091982	1794262	forward	intron

reference	NT_008583->NM_006258->NP_006249	1794262	forward	intron

HuRef	NW_001837985->NM_001098512->NP_001091982	1337779	forward	intron

HuRef	NW_001837985->NM_006258->NP_006249	1337779	forward	intron

Celera	NW_924796->NM_001098512->NP_001091982	700077	forward	intron

Celera	NW_924796->NM_006258->NP_006249	700077	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs293319 maps exactly once on NCBI human chromosome 10

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
10	NW_924796.1	700077	46505834	plus	C	alt_assembly_1	Celera	Celera	view	694
10	NW_001837985.1	1337779	47221240	plus	T	alt_assembly_8	HuRef	HuRef	view	694
10	NT_008583.16	1794262	52913113	plus	C	ref_assembly	reference	reference	view	694

NCBI Resource Links

Submitter-Referenced
GenBank
NT_008583 AC016206 AL157399.2 AL157399.3

dbSNP Blast Analysis
GenBank HTGS Finished:
AC073584.6 AL157399.14 NC_000010.9

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss1671039	HapMap-CEU	European	120	IG	0.017	0.250	0.733	1.000	0.142	0.858

	HapMap-HCB	Asian	88	IG		0.159	0.841	0.584	0.080	0.920

	HapMap-JPT	Asian	88	IG	0.023	0.227	0.750	1.000	0.136	0.864

	HapMap-YRI	Sub-Saharan African	120	IG	0.083	0.450	0.467	0.752	0.308	0.692

	CHMJ	Asian	74	IG					0.149	0.851

ss23604377	AFD_EUR_PANEL	European	48	IG		0.292	0.708	0.439	0.146	0.854

	AFD_AFR_PANEL	African American	44	IG	0.045	0.318	0.636	1.000	0.205	0.795

	AFD_CHN_PANEL	Asian	48	IG		0.250	0.750	0.527	0.125	0.875

ss69078792	HapMap-CEU	European	120	GF	0.017	0.250	0.733		0.142	0.858

	HapMap-HCB	Asian	90	GF		0.178	0.822		0.089	0.911

	HapMap-JPT	Asian	90	GF	0.022	0.222	0.756		0.133	0.867

	HapMap-YRI	Sub-Saharan African	120	GF	0.117	0.467	0.417		0.350	0.650

Concordant Genotype	Total Sample	C/C	C/T	T/T
ss1671039	260	11	74	171
ss23604377	71	1	20	49
ss69078792	260	11	75	174

RefSNP Genotype Summary	Total Individual	C/C	C/T	T/T
rs293319	332	12	93	216

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
5238	ss1671039	C/T	CSHL-HAPMAP	HapMap-YRI	NA18503	YOR005.01	r23_ch10_YRI_illumina:golden_gate_1.0.0	763659
5238	ss69078792	C/C	CSHL-HAPMAP	HapMap-YRI	NA18503	YOR005.01	chr10-HapMap-YRI
5242	ss1671039	T/T	CSHL-HAPMAP	HapMap-YRI	NA18508	YOR009.02	r23_ch10_YRI_illumina:golden_gate_1.0.0	763659
5242	ss69078792	C/T	CSHL-HAPMAP	HapMap-YRI	NA18508	YOR009.02	chr10-HapMap-YRI
5248	ss1671039	C/T	CSHL-HAPMAP	HapMap-YRI	NA18517	YOR013.02	r23_ch10_YRI_illumina:golden_gate_1.0.0	763659
5248	ss69078792	C/C	CSHL-HAPMAP	HapMap-YRI	NA18517	YOR013.02	chr10-HapMap-YRI
5272	ss1671039	T/T	CSHL-HAPMAP	HapMap-YRI	NA19102	YOR042.02	r23_ch10_YRI_illumina:golden_gate_1.0.0	763659
5272	ss69078792	C/T	CSHL-HAPMAP	HapMap-YRI	NA19102	YOR042.02	chr10-HapMap-YRI
5274	ss1671039	C/T	CSHL-HAPMAP	HapMap-YRI	NA19139	YOR043.01	r23_ch10_YRI_illumina:golden_gate_1.0.0	763659
5274	ss69078792	C/C	CSHL-HAPMAP	HapMap-YRI	NA19139	YOR043.01	chr10-HapMap-YRI
5275	ss1671039	T/T	CSHL-HAPMAP	HapMap-YRI	NA19137	YOR043.02	r23_ch10_YRI_illumina:golden_gate_1.0.0	763659
5275	ss69078792	C/T	CSHL-HAPMAP	HapMap-YRI	NA19137	YOR043.02	chr10-HapMap-YRI
5277	ss1671039	C/T	CSHL-HAPMAP	HapMap-YRI	NA19202	YOR045.01	r23_ch10_YRI_illumina:golden_gate_1.0.0	763659
5277	ss69078792	C/C	CSHL-HAPMAP	HapMap-YRI	NA19202	YOR045.01	chr10-HapMap-YRI
5295	ss1671039	T/T	CSHL-HAPMAP	HapMap-YRI	NA19221	YOR058.01	r23_ch10_YRI_illumina:golden_gate_1.0.0	763659
5295	ss69078792	C/T	CSHL-HAPMAP	HapMap-YRI	NA19221	YOR058.01	chr10-HapMap-YRI
5300	ss1671039	C/T	CSHL-HAPMAP	HapMap-YRI	NA19119	YOR060.03	r23_ch10_YRI_illumina:golden_gate_1.0.0	763659
5300	ss69078792	C/C	CSHL-HAPMAP	HapMap-YRI	NA19119	YOR060.03	chr10-HapMap-YRI
5301	ss1671039	C/T	CSHL-HAPMAP	HapMap-YRI	NA19142	YOR071.01	r23_ch10_YRI_illumina:golden_gate_1.0.0	763659
5301	ss69078792	C/C	CSHL-HAPMAP	HapMap-YRI	NA19142	YOR071.01	chr10-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

Validated by: PERLEGEN

DoubleHit found by: BCM_SSAHASNP

UNKNOWN

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Revised: May 25, 2006 1:38 PM .