Reference SNP(refSNP) Cluster Report: rs260112

Reference SNP(refSNP) Cluster Report: rs260112

refSNP ID: rs260112
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	79/129
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_001040655.1:c.1144-6910G>A
NM_001040656.1:c.1144-6910G>A
NM_001040657.1:c.1144-6910G>A
NM_001040658.1:c.1144-6910G>A
NM_001040659.1:c.1144-6910G>A
NM_001040660.1:c.1144-6910G>A
NM_022905.4:c.1144-6910G>A
NT_035325.6:g.1136365C>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss1798066 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs260112 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
ss339568	KWOK\|OVLP-000621-85833	fwd/T	A/G	agagaaggcagctcagaaggcccagcttta	gagtctgcatcccttgccttggctggctta	06/30/00	10/10/03	79	Genomic	99 %
ss932092	KWOK\|OVLP-000804-299479	fwd/T	A/G	agagaaggcagctcagaaggcccagcttta	gagtctgcatcccttgccttggctggctta	09/01/00	10/10/03	86	Genomic	99 %
ss1798066	KWOK\|OVLP-000925-610074	fwd/T	A/G	agagaaggcagctcagaaggcccagcttta	gagtctgcatcccttgccttggctggctta	10/05/00	04/07/04	87	Genomic	99 %
ss2537929	SC_JCM\|AC036108.2_96661	fwd/T	A/G	agagaaggcagctcagaaggcccagcttta	gagtctgcatcccttgccttggctggctta	11/03/00	10/10/03	89	Genomic	unknown
ss6872073	WI_SSAHASNP\|NT_035325.2_1126423	rev/B	C/T	taagccagccaaggcaagggatgcagactc	taaagctgggccttctgagctgccttctct	02/12/03	10/10/03	111	Genomic	unknown
ss12337155	WI_SSAHASNP\|chr15.NT_035325.4_1128251	rev/B	C/T	taagccagccaaggcaagggatgcagactc	taaagctgggccttctgagctgccttctct	07/04/03	10/10/03	116	Genomic	unknown
ss23488005	PERLEGEN\|afd4242657	rev/B	C/T	taagccagccaaggcaagggatgcagactc	taaagctgggccttctgagctgccttctct	08/10/04	09/13/04	123	Genomic	unknown
ss43786933	ABI\|hCV1374004	rev/B	C/T	taagccagccaaggcaagggatgcagactc	taaagctgggccttctgagctgccttctct	07/18/05	07/18/05	126	Genomic	unknown
ss66137848	AFFY\|SNP_A-2094145	fwd/T	A/G	agaaggcccagcttta	gagtctgcatcccttg	10/27/06	08/14/07	127	Genomic	unknown
ss76152121	AFFY\|AFFY_6_1M_SNP_A-2094145	fwd/T	A/G	agaaggcccagcttta	gagtctgcatcccttg	08/28/07	08/30/07	129	Genomic	unknown
ss85887206	HGSV\|Cor18517_SNV_20070510.chr15_97504037	rev/B	C/T	taagccagccaaggcaagggatgcagactc	taaagctgggccttctgagctgccttctct	12/06/07	12/10/07	130	Genomic	unknown
ss90273902	BCMHGSC_JDW\|JWB-0902542	rev/B	C/T	taagccagccaaggcaagggatgcagactc	taaagctgggccttctgagctgccttctct	02/26/08	02/29/08	129	Genomic	unknown

Fasta sequence (Legend)

 TGGGTACATG GCCAGGGATG GAGGGAAAAG CAAAAGCTCC TATTACATAA ATCTAGTGTA
 ACTTTAAACA AGTTGAAAGA CCAATGGTCA GGGATGGCTG GTGTGGATAG CACAGACTCG
 GGAAGGACTA AACCAGATCG CTGAGCTGCA TGTAATAGGG AAATTTGCCA AGAGAAGGCA
 GCTCAGAAGG CCCAGCTTTA
 R
 GAGTCTGCAT CCCTTGCCTT GGCTGGCTTA GAAATAGGCA GATCCAGCTT TTATACAAAA
 AGCCGGCTCC ACTTGAAAAA GAAACCATAA TTTCTATGTG GGTACACAGC AGGATTTCTC
 TCAATAGCAA GTCCTGCCAA TGCATTTATT TTCTAAATAT TTGTATTGCA GTCGTTGTGG
 AGAAGGATGG TGGTACCTGC TCCAGTACAG TAGCCAAGGG ATGGAACAAA GTCGTGGGGG
 AGTCAAGGGA TGTCGATAAG GACATTAGAA CCCATGGGAC TTGGCAACCT GGAGGTGAGG
 AGTGAGGGAG ACAGCAAGGA TGACATCCAT GCCCCCAGGG CTGGCACCCA GGAGATACTC
 AGGGCGAGCT TTCTGAAAGA GTCCGCTCTG AGGAGTTGTG CGGGTGGCAG TGGCTGGACC
 TCACCCCCT

GeneView

GeneView via analysis of contig annotation: TTC23 tetratricopeptide repeat domain 23

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_035325->NM_001040655

function

reference

NT_035325->NM_001040656

function

reference

NT_035325->NM_001040657

function

reference

NT_035325->NM_001040658

function

reference

NT_035325->NM_001040659

function

reference

NT_035325->NM_001040660

function

reference

NT_035325->NM_022905

function

HuRef

NW_001838224->NM_001040655

function

HuRef

NW_001838224->NM_001040656

function

HuRef

NW_001838224->NM_001040657

function

HuRef

NW_001838224->NM_001040658

function

HuRef

NW_001838224->NM_001040659

function

HuRef

NW_001838224->NM_001040660

function

HuRef

NW_001838224->NM_022905

function

Celera

NW_925940->NM_001040655

function

Celera

NW_925940->NM_001040656

function

Celera

NW_925940->NM_001040657

function

Celera

NW_925940->NM_001040658

function

Celera

NW_925940->NM_001040659

function

Celera

NW_925940->NM_001040660

function

Celera

NW_925940->NM_022905

function

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


reference	NT_035325->NM_001040655->NP_001035745	1136365	reverse	intron

reference	NT_035325->NM_001040656->NP_001035746	1136365	reverse	intron

reference	NT_035325->NM_001040657->NP_001035747	1136365	reverse	intron

reference	NT_035325->NM_001040658->NP_001035748	1136365	reverse	intron

reference	NT_035325->NM_001040659->NP_001035749	1136365	reverse	intron

reference	NT_035325->NM_001040660->NP_001035750	1136365	reverse	intron

reference	NT_035325->NM_022905->NP_075056	1136365	reverse	intron

HuRef	NW_001838224->NM_001040655->NP_001035745	2702629	forward	intron

HuRef	NW_001838224->NM_001040656->NP_001035746	2702629	forward	intron

HuRef	NW_001838224->NM_001040657->NP_001035747	2702629	forward	intron

HuRef	NW_001838224->NM_001040658->NP_001035748	2702629	forward	intron

HuRef	NW_001838224->NM_001040659->NP_001035749	2702629	forward	intron

HuRef	NW_001838224->NM_001040660->NP_001035750	2702629	forward	intron

HuRef	NW_001838224->NM_022905->NP_075056	2702629	forward	intron

Celera	NW_925940->NM_001040655->NP_001035745	14598283	reverse	intron

Celera	NW_925940->NM_001040656->NP_001035746	14598283	reverse	intron

Celera	NW_925940->NM_001040657->NP_001035747	14598283	reverse	intron

Celera	NW_925940->NM_001040658->NP_001035748	14598283	reverse	intron

Celera	NW_925940->NM_001040659->NP_001035749	14598283	reverse	intron

Celera	NW_925940->NM_001040660->NP_001035750	14598283	reverse	intron

Celera	NW_925940->NM_022905->NP_075056	14598283	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs260112 maps exactly once on NCBI human chromosome 15

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
15	NW_001838224.2	2702629	75816078	plus	G	alt_assembly_8	HuRef	HuRef	view	200
15	NW_925940.1	14598283	76105463	minus	T	alt_assembly_1	Celera	Celera	view	200
15	NT_035325.6	1136365	97504037	minus	C	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_035325 AC018999 AC036108.2

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC022819.8 AC036108.19 NC_000015.8	AC018999.3

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G	N
ss1798066	CEPH		184	AF					0.470	0.530

	HapMap-CEU	European	120	IG	0.100	0.367	0.533	0.479	0.283	0.717

	HapMap-HCB	Asian	88	IG	0.159	0.364	0.477	0.251	0.341	0.659

	HapMap-JPT	Asian	88	IG	0.159	0.523	0.318	0.655	0.420	0.580

	HapMap-YRI	Sub-Saharan African	120	IG	0.433	0.450	0.117	1.000	0.658	0.342

	CHMJ	Asian	74	IG					0.311	0.486	0.203

ss23488005	AFD_EUR_PANEL	European	48	IG		0.500	0.500	0.150	0.250	0.750

	AFD_AFR_PANEL	African American	46	IG	0.304	0.522	0.174	1.000	0.565	0.435

	AFD_CHN_PANEL	Asian	48	IG	0.167	0.500	0.333	1.000	0.417	0.583

ss66137848	HapMap-CEU	European	118	GF	0.102	0.373	0.525		0.288	0.712

	HapMap-HCB	Asian	90	GF	0.156	0.378	0.467		0.344	0.656

	HapMap-JPT	Asian	90	GF	0.156	0.533	0.311		0.422	0.578

	HapMap-YRI	Sub-Saharan African	120	GF	0.433	0.450	0.117		0.658	0.342

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.490+/-0.069	332	260	269	0

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: ILLUMINA

DoubleHit found by: BCM_SSAHASNP

UNKNOWN

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Revised: May 25, 2006 1:38 PM .