Reference SNP(refSNP) Cluster Report: rs620031

Reference SNP(refSNP) Cluster Report: rs620031

refSNP ID: rs620031
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	83/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	G/T
Ancestral Allele:	Not available
Clinical Association:	unknown

HGVS Names
NM_001083539.1:c.35-30T>G
NM_013289.2:c.35-30G>T
NT_011109.15:g.27597149G>T
NT_113949.1:g.71111T>G

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss792405 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs620031 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
ss792405	SC_JCM\|AL133414.3_71110	fwd/B	G/T	ggcagcagggtgccctggtttgcctgcaga	ggatggtccatcatgatctttctttctagg	07/27/00	04/07/04	83	Genomic	unknown
ss4199365	SC_JCM\|AL133414.4_71111	fwd/B	G/T	ggcagcagggtgccctggtttgcctgcaga	ggatggtccatcatgatctttctttctagg	10/15/01	10/10/03	101	Genomic	unknown
ss91012389	BCMHGSC_JDW\|JWB-2970311	fwd/B	G/T	ggcagcagggtgccctggtttgcctgcaga	ggatggtccatcatgatctttctttctagg	02/26/08	03/01/08	129	Genomic	unknown

Fasta sequence (Legend)

 TGGAGATCTG GGCCTGTTGT GTAGATCTAG GCCTGGAGGT AGAGATCTGG GCCTGGAGGC
 TGAGTCTCTG CACAGCCGAG ATCCTTGTTC CTGGGGGCAG GTAGGCAGCG AGGGTGAGTT
 TACCTTCAGC CCAGCAAGGG CCTGGCTGCC AAGACGCACA ACCCAGTGGG GGCAGCAGGG
 TGCCCTGGTT TGCCTGCAGA
 K
 GGATGGTCCA TCATGATCTT TCTTTCTAGG GTTGTTCTTG GTCCAGAGGG CCGGTCCACA
 CATGGGTGAG TCCTTCCCCA AACCTTAGGG TGTCATCTCC CCACATAAGA GGATTTTCCT
 GAAATGGGAG GGAAGTCCTG TCGGGGAGTC TCTCATACAC TAGGAAGAGG GGACCCTCGG
 ATGCTCGGCC CACATTTCTG

GeneView

GeneView via analysis of contig annotation: KIR3DS1 killer cell immunoglobulin-like receptor, three domains, short cytoplasmic tail, 1

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

GeneView via analysis of contig annotation: KIR3DL1 killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 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_113949->NM_001083539

function

reference

NT_011109->NM_013289

function

HuRef

NW_001838498->NM_013289

function

Celera

NW_927284->NM_013289

function

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


reference	NT_113949->NM_001083539->NP_001077008	71111	forward	intron

reference	NT_011109->NM_013289->NP_037421	27597149	forward	intron

HuRef	NW_001838498->NM_013289->NP_037421	614260	reverse	intron

Celera	NW_927284->NM_013289->NP_037421	4676943	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs620031 maps exactly once on NCBI human chromosome 19

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
19	NT_113949.1	71111	unplaced	plus	T	ref_assembly	reference	reference	view	200
19	NW_001838498.2	614260	51651646	minus	A	alt_assembly_8	HuRef	HuRef	view	200
19	NW_927284.1	4676943	52369659	plus	T	alt_assembly_1	Celera	Celera	view	200
19	NT_011109.15	27597149	60020771	plus	G	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
AL133414 AC011501

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC011501.8 AL133414.4 CU459006.1 NC_000019.8	AC145489.1 AC145490.1 AC145829.1 AC145830.1 AC145835.1

Population Diversity

	Sample Ascertainment				Genotype Detail		Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	G/T	HWP	G	T
ss792405	SC_12_A		22	AF			0.500	0.500

	SC_12_CA		18	AF			0.500	0.500

	SC_12_AA		24	AF			0.500	0.500

	SC_12_A	Asian	22	IG	1.000	0.001	0.500	0.500

	SC_12_AA	African American	24	IG	1.000	0.001	0.500	0.500

	SC_12_C	European	12	IG	1.000	0.020	0.500	0.500

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.500+/-0	0	0	0	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 .