Reference SNP(refSNP) Cluster Report: rs1173742

Reference SNP(refSNP) Cluster Report: rs1173742

refSNP ID: rs1173742
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	87/129
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_000908.2:c.1060-1585C>T
NT_006576.15:g.32745986C>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss1611656 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1173742 during BLAST analysis for the current build.

NCBI Assay ID	Handle\|Submitter ID	Validation Status	ss to rs Orientation /Strand	Alleles	5' Near Seq 30 bp	3' Near Seq 30 bp	Entry Date	Update Date	Build Added	Molecule Type	Freq Warning	Ancestral Allele	Success Rate
ss1611656	KWOK\|OVLP-000925-465484		fwd/B	C/T	ttcccacgaggtttccttctagagatgggg	gggtagcaggttttccccactaagccatgc	10/04/00	05/16/04	87	Genomic			99 %
ss2530706	SC_JCM\|AC026751.4_66045		fwd/B	C/T	ttcccacgaggtttccttctagagatgggg	gggtagcaggttttccccactaagccatgc	11/03/00	10/10/03	89	Genomic			unknown

Fasta sequence (Legend)

 TCTCAGCACT AGCTTTTGGC AAACACGAAA TATCTGCTTC CAGGATGCAA ACAGGAGTCC
 CCATCCTAGC TAGGGGTGGG ATAAGGTTAA GTAGATCCAG TCACAGAACC GTATCTTGTG
 AATGTTTGTG TATCTGAACC AGGTGATGCA GAAGGTCAGT TGCAGCTCTC TTCCCACGAG
 GTTTCCTTCT AGAGATGGGG
 Y
 GGGTAGCAGG TTTTCCCCAC TAAGCCATGC CAGGTGGTCA TCTACAGAAT GCCCAGTTCA
 TTCTGCATCA TTGGCATTTC ATCACTGACA CTTTTTTCTG AAATGAGAAG GCTTGGATTT
 TTTGTACTTT TTGTACAGAG TTTTTTTGTA AACCTCTTGG TGTTTCAAGA TTCAATTTGC
 TCATTTCATA TCCAATAAAT

GeneView

GeneView via analysis of contig annotation: NPR3 natriuretic peptide receptor C/guanylate cyclase C (atrionatriuretic peptide receptor C)

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_006576->NM_000908

function

HuRef

NW_001838929->NM_000908

function

Celera

NW_922562->NM_000908

function

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


reference	NT_006576->NM_000908->NP_000899	32745986	forward	intron

HuRef	NW_001838929->NM_000908->NP_000899	11380355	forward	intron

Celera	NW_922562->NM_000908->NP_000899	11217620	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs1173742 maps exactly once on NCBI human chromosome 5

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
5	NW_922562.1	11217620	32654861	plus	C	alt_assembly_1	Celera	Celera	view	200
5	NW_001838929.1	11380355	32741286	plus	C	alt_assembly_8	HuRef	HuRef	view	200
5	NT_006576.15	32745986	32808986	plus	C	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
AC026751 AC008421 AC026703 AC026751.4

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC026703.4 NC_000005.8	AC026751.4

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	HWP	C	T
ss1611656	CEPH		184	AF				0.650	0.350

	HapMap-CEU	European	120	IG	1.000			1.000

	HapMap-HCB	Asian	90	IG	1.000			1.000

	HapMap-JPT	Asian	84	IG	1.000			1.000

	HapMap-YRI	Sub-Saharan African	118	IG	0.983	0.017	1.000	0.992	0.008

ss2530706	SC_12_A	Asian	24	IG	1.000			1.000

	SC_12_AA	African American	24	IG	1.000			1.000

	SC_12_C	European	14	IG	1.000			1.000

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.004+/-0.046	304	235	2	0

Validation Summary:

Validation status	Marker displays Mendelian segregation	PCR results confirmed in multiple reactions	Homozygotes detected in individual genotype data
	UNKNOWN	UNKNOWN	UNKNOWN

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Revised: May 25, 2006 1:38 PM .