Reference SNP(refSNP) Cluster Report: rs776405

Reference SNP(refSNP) Cluster Report: rs776405

refSNP ID: rs776405
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	86/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	C/G
Ancestral Allele:	C
Clinical Association:	unknown

HGVS Names

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss89229522 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs776405 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
ss901683	KWOK\|OVLP-000804-154835	fwd/T	C/G	gacgcagtcggagcaggattccagacaagt	ccccaagatattctgtaagttaattagatt	09/01/00	10/10/03	86	Genomic	99 %
ss1690013	KWOK\|OVLP-000925-331703	fwd/T	C/G	gacgcagtcggagcaggattccagacaagt	ccccaagatattctgtaagttaattagatt	10/05/00	04/07/04	87	Genomic	99 %
ss3658402	SC_JCM\|AC018921.9_24596	rev/B	C/G	aatctaattaacttacagaatatcttgggg	acttgtctggaatcctgctccgactgcgtc	09/24/01	10/10/03	100	Genomic	unknown
ss4120070	SC_JCM\|AC016153.18_33589	rev/B	C/G	aatctaattaacttacagaatatcttgggg	acttgtctggaatcctgctccgactgcgtc	10/15/01	10/10/03	101	Genomic	unknown
ss16030199	SC_SNP\|NT_029419.10_32156364	fwd/T	C/G	gacgcagtcggagcaggattccagacaagt	ccccaagatattctgtaagttaattagatt	11/18/03	11/22/03	120	Genomic	unknown
ss24137633	PERLEGEN\|afd2054597	fwd/T	C/G	gacgcagtcggagcaggattccagacaagt	ccccaagatattctgtaagttaattagatt	08/10/04	09/13/04	123	Genomic	unknown
ss69112427	PERLEGEN\|PGP02054597	fwd/	C/G	gacgcagtcggagcaggattccagacaagt	ccccaagatattctgtaagttaattagatt	01/30/07	08/14/07	127	Genomic	unknown
ss83710882	HGSV\|Cor19240_SNV_20070510.chr12_68299325	fwd/	C/G	gacgcagtcggagcaggattccagacaagt	ccccaagatattctgtaagttaattagatt	11/30/07	12/05/07	130	Genomic	unknown
ss89229522	BCMHGSC_JDW\|JWB-0576244	fwd/	C/G	gacgcagtcggagcaggattccagacaagt	ccccaagatattctgtaagttaattagatt	02/26/08	02/28/08	129	Genomic	unknown

Fasta sequence (Legend)

 AAAGGAGAGT GGTTCTGAGA AGAACTTGTA AAATTTATCA GAAGAGTTAA TAAGATATAT
 ACAGGGTTGG AAGAACCCAG AAACGAATTC ACATTTGGTT GTTAACTATA AGATAAGCTC
 CAATCTTTGA CTTTACAGAA AACAATGCGA GGGAGGAAGC TAAAGACTTC CCCTGAGACT
 TTAGCCTACC ACTATGAAAA TGTGCTGAGC CTGCTCTATG GACGCAGTCG GAGCAGGATT
 CCAGACAAGT
 S
 CCCCAAGATA TTCTGTAAGT TAATTAGATT CTCTTTCAAT GCTGAACTAC TGGAAACTGT
 TCAACAGCAA CTGCTGTGCT AAGACAATTA TTCTGAGAAA AGTGAGCTTC AATAATCGCC
 GTGAAATGAA ACTTGAATCC TGAAGGAATT CCATCATCAA CTCACAGGGT GAGGAGCTGG
 GGCAAAGTTG AGCCCAAGTG GGAGGGAAGG GTGGGAAGGG TGGCCTTTTT TTTTTTTTTT
 TTTTTTTTTT

GeneView

GeneView: no link established by analysis of contig annotation
GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs776405 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_001838060.2	6504057	67062520	minus	C	alt_assembly_8	HuRef	HuRef	view	200
12	NT_029419.11	32156364	68299325	plus	G	ref_assembly	reference	reference	view	200
12	NW_925395.1	17300560	69676731	plus	G	alt_assembly_1	Celera	Celera	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_029419 AC016153 AC018921 AC018921.8 AC018921.9

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/G	G/G	HWP	C	G
ss1690013	HapMap-CEU	European	120	IG	0.017	0.400	0.583	0.200	0.217	0.783

	HapMap-HCB	Asian	90	IG	0.111	0.467	0.422	1.000	0.344	0.656

	HapMap-JPT	Asian	88	IG	0.250	0.523	0.227	1.000	0.511	0.489

	HapMap-YRI	Sub-Saharan African	120	IG	0.133	0.467	0.400	1.000	0.367	0.633

ss24137633	AFD_EUR_PANEL	European	48	IG		0.333	0.667	0.343	0.167	0.833

	AFD_AFR_PANEL	African American	46	IG	0.043	0.652	0.304	0.100	0.370	0.630

	AFD_CHN_PANEL	Asian	48	IG	0.125	0.542	0.333	0.527	0.396	0.604

ss69112427	HapMap-CEU	European	120	GF	0.017	0.400	0.583		0.217	0.783

	HapMap-HCB	Asian	90	GF	0.111	0.489	0.400		0.356	0.644

	HapMap-JPT	Asian	90	GF	0.244	0.533	0.222		0.511	0.489

	HapMap-YRI	Sub-Saharan African	120	GF	0.150	0.450	0.400		0.375	0.625

Concordant Genotype	Total Sample	C/C	C/G	G/G
ss1690013	266	31	118	115
ss24137633	71	4	36	31
ss69112427	266	31	119	116

RefSNP Genotype Summary	Total Individual	C/C	C/G	G/G
rs776405	332	35	151	142

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
5187	ss1690013	G/G	CSHL-HAPMAP	HapMap-HCB	NA18633	CH18633	r23_ch12_HCB_bcm:genotype_0002
5187	ss69112427	C/G	CSHL-HAPMAP	HapMap-HCB	NA18633	CH18633	chr12-HapMap-HCB
5254	ss1690013	G/G	CSHL-HAPMAP	HapMap-YRI	NA18870	YOR017.02	r23_ch12_YRI_bcm:genotype_0002
5254	ss69112427	C/G	CSHL-HAPMAP	HapMap-YRI	NA18870	YOR017.02	chr12-HapMap-YRI
5258	ss1690013	C/G	CSHL-HAPMAP	HapMap-YRI	NA18853	YOR018.03	r23_ch12_YRI_bcm:genotype_0002
5258	ss69112427	C/C	CSHL-HAPMAP	HapMap-YRI	NA18853	YOR018.03	chr12-HapMap-YRI
5279	ss1690013	C/G	CSHL-HAPMAP	HapMap-YRI	NA19200	YOR045.03	r23_ch12_YRI_bcm:genotype_0002
5279	ss69112427	G/G	CSHL-HAPMAP	HapMap-YRI	NA19200	YOR045.03	chr12-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 .