Reference SNP(refSNP) Cluster Report: rs687885

Reference SNP(refSNP) Cluster Report: rs687885

refSNP ID: rs687885
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_014218.2:c.331G>T
NM_014512.1:c.331T>G
NP_055033.2:p.V111L
NP_055327.1:p.L111V
NT_011109.15:g.27553234G>T
NT_113949.1:g.118853T>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss91012053 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs687885 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
ss861584	SC_JCM\|AL133414.3_118853	fwd/B	G/T	tacggttctgttactcactccccctatcag	tgtcagctcccagtgaccctctggacatcg	07/27/00	10/10/03	83	Genomic	unknown
ss3251055	YUSUKE\|IMS-JST061140	fwd/B	G/T	tacggttctgttactcactccccctatcag	tgtcagctcccagtgaccctctggacatcg	09/05/01	10/10/03	100	Genomic	unknown
ss4179198	SC_JCM\|AC092275.1_23642	rev/T	A/C	cgatgtccagagggtcactgggagctgaca	ctgatagggggagtgagtaacagaaccgta	10/15/01	10/10/03	110	Genomic	unknown
ss24793675	SEQUENOM\|sqnm112900	fwd/B	G/T	tacggttctgttactcactccccctatcag	tgtcagctcccagtgaccctctggacatcg	06/18/04	11/02/06	124	cDNA	unknown
ss91012053	BCMHGSC_JDW\|JWB-2970252	fwd/B	G/T	tacggttctgttactcactccccctatcag	tgtcagctcccagtgaccctctggacatcg	02/26/08	03/01/08	129	Genomic	unknown

Fasta sequence (Legend)

 AAAACCTTCC CTCCTGGCCC ACCCAGGTCG CCTGGTGAAA TCAGAAGAGA CAGTCATCCT
 GCAGTGTTGG TCAGATGTCA TGTTTGAACA CTTCCTTCTG CACAGAGAGG GGATGTTTAA
 CGACACTTTG CGCCTCATTG GAGAACACCA TGATGGGGTC TCCAAGGCCA ACTTCTCCAT
 CAGTCGCATG ACGCAAGACC TGGCAGGGAC CTACAGATGC TACGGTTCTG TTACTCACTC
 CCCCTATCAG
 K
 TGTCAGCTCC CAGTGACCCT CTGGACATCG TGATCATAGG TGAGAGTGTC CAGACTTTCT
 TCTCATTGTC ATTGGGATGC AGAGTGAATG ATCCAGGAAT TGGAGACCCA GGTGGCTGTA
 AGGAAGATGA GCTTGGTATT CTTATGGAGA GAGACTGACT TGGTGAGGTC TGTGCCAACA
 GAGACAGAGA AACAGGAGAC ACAAGTAGAG ACCAGGTGTC ATAACAGAGA ACAGACACAG
 GGGCCATACC

GeneView

GeneView via analysis of contig annotation: KIR2DS1 killer cell immunoglobulin-like receptor, two 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: KIR2DL1 killer cell immunoglobulin-like receptor, two 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_014512

function

reference

NT_011109->NM_014218

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	mRNA pos	Function	dbSNP allele	Protein residue	Codon pos	Amino acid pos


reference	NT_113949->NM_014512->NP_055327	118854	forward	344	missense	G	Val [V]	1	111
					contig reference	T	Leu [L]	1	111

reference	NT_011109->NM_014218->NP_055033	27553235	forward	369	missense	T	Leu [L]	1	111
					contig reference	G	Val [V]	1	111

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs687885 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	118854	unplaced	plus	T	ref_assembly	reference	reference	view	200
19	NW_001838498.2	658199	51607707	minus	C	alt_assembly_8	HuRef	HuRef	view	200
19	NW_927284.1	4633033	52325749	plus	G	alt_assembly_1	Celera	Celera	view	200
19	NT_011109.15	27553235	59976857	plus	G	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
dbSTS	GenBank
sqnm112900	AL133414 AC011501 AL133414

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank HTGS Finished:	GenBank HTGS Draft:
NM_014218.2 NM_014512.1	AL133414.4 CU041340.3 CU041368.1 CU459006.1 CU459007.1 CU464057.1 CU464058.1 CU464061.5 CU464078.1 CU466259.1 CU468300.1	CU464059.11

UniGene Cluster ID
512574

Population Diversity

	Sample Ascertainment				Genotypes	Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	HWP	G	T
ss24793675	CEPH		184	AF		0.380	0.620

ss3251055	JBIC-allele		1466	AF		0.814	0.186

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.359+/-0.225	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 .