Reference SNP(refSNP) Cluster Report: rs10878247

Reference SNP(refSNP) Cluster Report: rs10878247

refSNP ID: rs10878247
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	120/129
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_198578.2:c.571+195C>T
NT_029419.11:g.2775406C>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss28468573 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs10878247 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
ss16133853	SC_SNP\|NT_029419.10_2775406	fwd/B	C/T	attgcttgttttggtggggtgaatttcatt	gtgggttataaatcatgcccctggagtaga	11/18/03	10/26/06	120	Genomic	unknown
ss16315516	PERLEGEN\|PS02030552	fwd/B	C/T	attgcttgttttggtggggtgaatttcatt	gtgggttataaatcatgcccctggagtaga	11/24/03	11/27/03	120	Genomic	100 %
ss18500126	SC_SNP\|SC-CHR9-12_NA11321-200402.chr12.NT_029419.10_2775406	fwd/B	C/T	attgcttgttttggtggggtgaatttcatt	gtgggttataaatcatgcccctggagtaga	02/20/04	03/04/04	120	Genomic	unknown
ss28468573	BCM-HGSC\|ERO-1938	fwd/B	C/T	attgcttgttttggtggggtgaatttcatt	gtgggttataaatcatgcccctggagtaga	07/13/04	11/02/06	126	Genomic	unknown
ss32471729	BCM-HGSC\|ERJ-2221	fwd/B	C/T	attgcttgttttggtggggtgaatttcatt	gtgggttataaatcatgcccctggagtaga	02/08/05	02/08/05	125	Genomic	unknown
ss66667137	ILLUMINA\|HumanHap300v1.1_rs10878247	fwd/T	C/T	attgcttgttttggtggggtgaatttcatt	gtgggttataaatcatgcccctggagtaga	11/09/06	11/09/06	127	Genomic	unknown
ss66907136	ILLUMINA\|HumanHap550v1.1_rs10878247	fwd/B	C/T	attgcttgttttggtggggtgaatttcatt	gtgggttataaatcatgcccctggagtaga	11/14/06	11/14/06	127	Genomic	unknown
ss67033845	ILLUMINA\|HumanHap650Yv1.0_rs10878247	fwd/B	C/T	attgcttgttttggtggggtgaatttcatt	gtgggttataaatcatgcccctggagtaga	11/14/06	11/14/06	127	Genomic	unknown
ss69106986	PERLEGEN\|PGP02030552	fwd/B	C/T	attgcttgttttggtggggtgaatttcatt	gtgggttataaatcatgcccctggagtaga	01/30/07	03/31/08	127	Genomic	unknown
ss70383272	ILLUMINA\|HumanHap300v2.0_rs10878247	fwd/B	C/T	attgcttgttttggtggggtgaatttcatt	gtgggttataaatcatgcccctggagtaga	04/18/07	11/18/07	127	Genomic	unknown
ss70504661	ILLUMINA\|HumanHap550v3.0__rs10878247	rev/T	A/G	tctactccaggggcatgatttataacccac	aatgaaattcaccccaccaaaacaagcaat	04/20/07	03/30/08	130	Genomic	unknown
ss71031074	ILLUMINA\|HumanHap650Yv3.0_rs10878247	fwd/B	C/T	attgcttgttttggtggggtgaatttcatt	gtgggttataaatcatgcccctggagtaga	04/23/07	04/23/07	127	Genomic	unknown
ss75583280	ILLUMINA\|ILMN_Human_1M_rs10878247	fwd/B	C/T	attgcttgttttggtggggtgaatttcatt	gtgggttataaatcatgcccctggagtaga	08/28/07	08/29/07	129	Genomic	unknown
ss85021780	KRIBB_YJKIM\|KHS877069	fwd/B	C/T	attgcttgttttggtggggtgaatttcatt	gtgggttataaatcatgcccctggagtaga	12/04/07	12/08/07	130	Genomic	unknown

Fasta sequence (Legend)

 GGGTCTACAA ACCATTCACA
 CATCTAGGGC AGTTAAGTAG TTTATCAACA AACAAACAAA CAAACAAACA AGAAAACCAT
 GGGTCTACAA ACCATTCACA GTCTTCATGT AAAAATTAAT TCATGTAAAA ATTAACACAT
 TAAATGTTAA AGCAGCTCTT TACTCAGAGC ATATTATTCT CTTTAAAATA GGTAAAATCA
 CCTTGCTGAT ATTGGATGAA GAAAGTGATA TTTTCATGTT AATTTTTGAT GCCATGCACT
 CATTTCCAGC CAATGATGAA GTCCAGAAAC TTGGATGCAA AGCTTTACAT GTGCTGTTTG
 AGAGAGGTAT TTTAAAATGT CAAATTCCTT AAAGTATATA TAAGAAAAAA AGGCTTATAC
 TGGGAAAAGT AGAACACAGT TATAATAAGA AGAAGGTTTC TAAAATCCTA CTATTTATTA
 AGAAGTGGGA GTTGTCTGTC AAGGGTGAGG AATGGGGTTA ATTCAGAAGT ATTGCTTGTT
 TTGGTGGGGT GAATTTCATT
 Y
 GTGGGTTATA AATCATGCCC CTGGAGTAGA CTTTCTTCAA TTGCTTAACA AGGCATAAGG
 TTTACTTTGA AAACTGGATG TGTGGGTGCT ATGAAAGAAA AAATAAAACT GTGAAGCCAA
 GCATAGGTTA CACTGGGATT ATGATGTTGA GTCATCACCA GAAATCATAG AAATTGCATA
 AAGAGCCTGA AGGTTTACAA AGTGTCCTTC AGGAAAAAGA CTAATATGCA TTTCATAGCC
 TGGCCCTGAG ATTGATAACT GAGATTATTA TGTAATTTTA GAGTTGGTTG GAGTCCTTGT
 TTAGTCTTTC CATTGACCTT AGGAGGAAGT GGGTCACAGC AGTGAAGTGA GCATCCTGCC
 TGAGGACACA GAGCTTGTGA CAGTACAGTT CAATTAGCAA TTATTTTAAG AGCCCCTTTT
 GTATCATTAT GAGAGCCAAC TGTGCTAGGG GTTTAGATAA GAATGATTTA TGTGGGCCCT
 GTGTCAGTTA TCAGTTTACC
 GAATGATTTA TGTGGGCCCT

GeneView

GeneView via analysis of contig annotation: LRRK2 leucine-rich repeat kinase 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_029419->NM_198578

function

HuRef

NW_001838057->NM_198578

function

Celera

NW_925351->NM_198578

function

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


reference	NT_029419->NM_198578->NP_940980	2775406	forward	intron

HuRef	NW_001838057->NM_198578->NP_940980	92184	forward	intron

Celera	NW_925351->NM_198578->NP_940980	2981256	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs10878247 maps exactly once on NCBI human chromosome 12

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
12	NW_001838057.1	92184	37659913	plus	C	alt_assembly_8	HuRef	HuRef	view	520
12	NT_029419.11	2775406	38918367	plus	C	ref_assembly	reference	reference	view	520
12	NW_925351.1	2981256	39435350	plus	C	alt_assembly_1	Celera	Celera	view	520

NCBI Resource Links

Submitter-Referenced
GenBank
NT_029419

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss28468573	HapMap-CEU	European	120	IG	0.500	0.400	0.100	0.752	0.700	0.300

	HapMap-HCB	Asian	90	IG	0.533	0.467			0.767	0.233

	HapMap-JPT	Asian	90	IG	0.378	0.556	0.067		0.656	0.344

	HapMap-YRI	Sub-Saharan African	120	IG	0.883	0.117		0.655	0.942	0.058

ss69106986	HapMap-CEU	European	120	GF	0.500	0.333	0.167		0.667	0.333

	HapMap-HCB	Asian	90	GF	0.533	0.467			0.767	0.233

	HapMap-JPT	Asian	90	GF	0.378	0.556	0.067		0.656	0.344

	HapMap-YRI	Sub-Saharan African	120	GF	0.883	0.117			0.942	0.058

Concordant Genotype	Total Sample	C/C	C/T	T/T
ss28468573	264	164	89	11
ss69106986	264	164	89	11

RefSNP Genotype Summary	Total Individual	C/C	C/T	T/T
rs10878247	270	164	89	11

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
171	ss28468573	C/T	CSHL-HAPMAP	HapMap-CEU	NA07022	CEPH1340.11	r23_ch12_CEU_illumina:golden_gate_1.1.0	799708
171	ss69106986	T/T	CSHL-HAPMAP	HapMap-CEU	NA07022	CEPH1340.11	chr12-HapMap-CEU
252	ss28468573	C/T	CSHL-HAPMAP	HapMap-CEU	NA11839	CEPH1349.13	r23_ch12_CEU_illumina:golden_gate_1.1.0	799708
252	ss69106986	T/T	CSHL-HAPMAP	HapMap-CEU	NA11839	CEPH1349.13	chr12-HapMap-CEU
400	ss28468573	C/T	CSHL-HAPMAP	HapMap-CEU	NA10831	CEPH1408.02	r23_ch12_CEU_illumina:golden_gate_1.1.0	799708
400	ss69106986	T/T	CSHL-HAPMAP	HapMap-CEU	NA10831	CEPH1408.02	chr12-HapMap-CEU
411	ss28468573	C/T	CSHL-HAPMAP	HapMap-CEU	NA12156	CEPH1408.13	r23_ch12_CEU_illumina:golden_gate_1.1.0	799708
411	ss69106986	T/T	CSHL-HAPMAP	HapMap-CEU	NA12156	CEPH1408.13	chr12-HapMap-CEU
566	ss28468573	C/T	CSHL-HAPMAP	HapMap-CEU	NA12802	CEPH1454.02	r23_ch12_CEU_illumina:golden_gate_1.1.0	799708
566	ss69106986	T/T	CSHL-HAPMAP	HapMap-CEU	NA12802	CEPH1454.02	chr12-HapMap-CEU
576	ss28468573	C/T	CSHL-HAPMAP	HapMap-CEU	NA12812	CEPH1454.12	r23_ch12_CEU_illumina:golden_gate_1.1.0	799708
576	ss69106986	T/T	CSHL-HAPMAP	HapMap-CEU	NA12812	CEPH1454.12	chr12-HapMap-CEU

Genotype data submitted for	270	samples from	270	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
	UNKNOWN	UNKNOWN	UNKNOWN

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Revised: May 25, 2006 1:38 PM .