Reference SNP(refSNP) Cluster Report: rs1260868

Reference SNP(refSNP) Cluster Report: rs1260868

refSNP ID: rs1260868
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:	A/G
Ancestral Allele:	A
Clinical Association:	unknown

HGVS Names
NM_001003398.1:c.213+28386C>T
NM_001714.2:c.213+28386C>T
NT_009714.16:g.25047838C>T

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss1935028 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1260868 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
ss1935028	KWOK\|OVLP-000925-732556	fwd/T	A/G	aagaggcagaactgagaatgcaagtcctgc	ctatcatcctccacacgcctctcctttgtc	10/06/00	08/14/07	87	Genomic	99 %
ss2665892	SC_JCM\|AC026675.12_58382	rev/B	C/T	gacaaaggagaggcgtgtggaggatgatag	gcaggacttgcattctcagttctgcctctt	11/03/00	10/10/03	92	Genomic	unknown
ss11031170	BCM_SSAHASNP\|chr12.NT_009714.15_25047838	rev/B	C/T	gacaaaggagaggcgtgtggaggatgatag	gcaggacttgcattctcagttctgcctctt	07/01/03	10/10/03	116	Genomic	unknown
ss15919511	SC_SNP\|NT_009714.16_25047838	rev/B	C/T	gacaaaggagaggcgtgtggaggatgatag	gcaggacttgcattctcagttctgcctctt	11/17/03	11/22/03	120	Genomic	unknown
ss20972872	SSAHASNP\|WGSA-200403-chr12.chr12.NT_009714.16_25047838	rev/B	C/T	gacaaaggagaggcgtgtggaggatgatag	gcaggacttgcattctcagttctgcctctt	03/19/04	03/19/04	121	Genomic	unknown
ss23328978	PERLEGEN\|afd2026724	rev/B	C/T	gacaaaggagaggcgtgtggaggatgatag	gcaggacttgcattctcagttctgcctctt	08/10/04	09/13/04	123	Genomic	unknown
ss66138114	AFFY\|SNP_A-2094936	fwd/T	A/G	agaatgcaagtcctgc	ctatcatcctccacac	10/27/06	08/14/07	127	Genomic	unknown
ss69106362	PERLEGEN\|PGP02026724	rev/B	C/T	gacaaaggagaggcgtgtggaggatgatag	gcaggacttgcattctcagttctgcctctt	01/30/07	08/14/07	127	Genomic	unknown
ss76152729	AFFY\|AFFY_6_1M_SNP_A-2094936	fwd/T	A/G	agaatgcaagtcctgc	ctatcatcctccacac	08/28/07	08/30/07	130	Genomic	unknown
ss111756036	1000GENOMES\|CEU.trio.12.15.2008_2712384_chr12_32180131	rev/B	C/T	gacaaaggagaggcgtgtggaggatgatag	gcaggacttgcattctcagttctgcctctt	12/15/08	12/17/08	130	Genomic	unknown
ss113381191	1000GENOMES\|NA19240_2008_12_16_2439088_chr12_32180131	rev/B	C/T	gacaaaggagaggcgtgtggaggatgatag	gcaggacttgcattctcagttctgcctctt	12/18/08	12/18/08	130	Genomic	unknown

Fasta sequence (Legend)

 AGTGGAACAT TATAGTTGCC TCAGTCTTTA CAGGGGAACA CAGAGGAGCA CCAGCTAAAG
 AATGTGTACT TTGGACAAAG TTATATGCCA GGTACTCCTA TATATATGAT CTAATACAAA
 AATAAACATC AGTCCTATAC TGTTAGATGA AGAAATAGGT TCCAAGATTT AAGAGGCAGA
 ACTGAGAATG CAAGTCCTGC
 R
 CTATCATCCT CCACACGCCT CTCCTTTGTC CCTCTCCACC TTCCTTCCCC CTTTATTTTC
 CTTTCCTAGA AGGGAAGGAG GGTGTCAGCA TCTCAATCAA AAGTCAAAAC TCACATGTCA
 ACAGGTAAGT GACAGATGAT GTAAATGAGG GAAGAACAGA GATAGTGAGA TAACTCAGAT
 GAGATGGAAT GGTGGGGACT

GeneView

GeneView via analysis of contig annotation: BICD1 bicaudal D homolog 1 (Drosophila)

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_009714->NM_001003398

function

reference

NT_009714->NM_001714

function

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


reference	NT_009714->NM_001003398->NP_001003398	25047838	forward	intron

reference	NT_009714->NM_001714->NP_001705	25047838	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs1260868 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_925295.1	10312804	12109222	minus	C	alt_assembly_1	Celera	Celera	view	200
12	NW_001838055.2	2602500	32040238	plus	A	alt_assembly_8	HuRef	HuRef	view	200
12	NT_009714.16	25047838	32180131	minus	C	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_009714 AC016954 AC021108 AC023766 AC048344 AC068887 AC068887.9

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss1935028	HapMap-CEU	European	120	IG	0.650	0.317	0.033		0.808	0.192

	HapMap-HCB	Asian	90	IG	0.733	0.244	0.022		0.856	0.144

	HapMap-JPT	Asian	90	IG	0.778	0.200	0.022		0.878	0.122

	HapMap-YRI	Sub-Saharan African	120	IG	0.567	0.367	0.067		0.750	0.250

ss23328978	AFD_EUR_PANEL	European	46	IG	0.609	0.304	0.087	0.439	0.761	0.239

	AFD_AFR_PANEL	African American	46	IG	0.609	0.304	0.087	0.439	0.761	0.239

	AFD_CHN_PANEL	Asian	48	IG	0.792	0.167	0.042	0.251	0.875	0.125

ss66138114	HapMap-CEU	European	118	GF	0.644	0.322	0.034		0.805	0.195

	HapMap-HCB	Asian	90	GF	0.733	0.244	0.022		0.856	0.144

	HapMap-JPT	Asian	90	GF	0.778	0.200	0.022		0.878	0.122

	HapMap-YRI	Sub-Saharan African	120	GF	0.567	0.367	0.067		0.750	0.250

ss69106362	HapMap-CEU	European	120	GF	0.650	0.317	0.033		0.808	0.192

	HapMap-HCB	Asian	90	GF	0.733	0.244	0.022		0.856	0.144

	HapMap-JPT	Asian	90	GF	0.778	0.200	0.022		0.878	0.122

	HapMap-YRI	Sub-Saharan African	120	GF	0.567	0.367	0.067		0.750	0.250

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.302+/-0.245	332	260	270	0

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 .