Reference SNP(refSNP) Cluster Report: rs26608

Reference SNP(refSNP) Cluster Report: rs26608

refSNP ID: rs26608
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	76/129
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_019087.1:c.253+8813A>G
NT_006713.14:g.4035956T>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44661293 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs26608 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
ss31651	KWOK\|OVLP-18860	fwd/T	A/G	atgacccaagatgcaagagtaatgctagac	cttcacaagcaaaaggttgttttgttattg	04/28/00	10/10/03	76	Genomic	99 %
ss38195	KWOK\|OVLP-47243	fwd/T	A/G	atgacccaagatgcaagagtaatgctagac	cttcacaagcaaaaggttgttttgttattg	04/28/00	10/10/03	76	Genomic	99 %
ss360119	KWOK\|OVLP-000621-137729	fwd/T	A/G	atgacccaagatgcaagagtaatgctagac	cttcacaagcaaaaggttgttttgttattg	06/30/00	10/10/03	79	Genomic	99 %
ss361121	KWOK\|OVLP-000621-140309	fwd/T	A/G	atgacccaagatgcaagagtaatgctagac	cttcacaagcaaaaggttgttttgttattg	06/30/00	10/10/03	79	Genomic	99 %
ss963702	KWOK\|OVLP-000804-475608	fwd/T	A/G	atgacccaagatgcaagagtaatgctagac	cttcacaagcaaaaggttgttttgttattg	09/01/00	10/10/03	86	Genomic	99 %
ss969632	KWOK\|OVLP-000804-509105	fwd/T	A/G	atgacccaagatgcaagagtaatgctagac	cttcacaagcaaaggttgttttgttattgt	09/01/00	10/10/03	94	Genomic	99 %
ss971412	KWOK\|OVLP-000804-519815	fwd/T	A/G	atgacccaagatgcaagagtaatgctagac	cttcacaagcaaaaggttgttttgttattg	09/01/00	10/10/03	86	Genomic	99 %
ss1036574	KWOK\|OVLP-000804-486313	fwd/T	A/G	atgacccaagatgcaagagtaatgctagac	cttcacaagcaaaaggttgttttgttattg	09/02/00	10/10/03	86	Genomic	97 %
ss1038261	KWOK\|OVLP-000804-513604	fwd/T	A/G	atgacccaagatgcaagagtaatgctagac	cttcacaagcaaaaggttgttttgttattg	09/02/00	10/10/03	86	Genomic	97 %
ss1039306	KWOK\|OVLP-000804-526986	fwd/T	A/G	atgacccaagatgcaagagtaatgctagac	cttcacaagcaaaaggttgttttgttattg	09/02/00	10/10/03	86	Genomic	97 %
ss1676970	KWOK\|OVLP-000925-179239	fwd/T	A/G	atgacccaagatgcaagagtaatgctagac	cttcacaagcaaaggttgttttgttattgt	10/05/00	10/10/03	92	Genomic	99 %
ss1677215	KWOK\|OVLP-000925-182220	fwd/T	A/G	atgacccaagatgcaagagtaatgctagac	cttcacaagcaaaaggttgttttgttattg	10/05/00	10/10/03	87	Genomic	99 %
ss1724622	KWOK\|OVLP-000925-193629	fwd/T	A/G	atgacccaagatgcaagagtaatgctagac	cttcacaagcaaaaggttgttttgttattg	10/05/00	10/10/03	87	Genomic	97 %
ss1724772	KWOK\|OVLP-000925-198996	fwd/T	A/G	atgacccaagatgcaagagtaatgctagac	cttcacaagcaaaaggttgttttgttattg	10/05/00	10/10/03	87	Genomic	97 %
ss3373170	TSC-CSHL\|TSC1644605	fwd/T	A/G	atgacccaagatgcaagagtaatgctagac	cttcacaagcaaaaggttgttttgttattg	09/20/01	10/25/06	100	Genomic	unknown
ss3642698	SC_JCM\|AC016580.5_68033	fwd/T	A/G	atgacccaagatgcaagagtaatgctagac	cttcacaagcaaaaggttgttttgttattg	09/24/01	10/10/03	100	Genomic	unknown
ss19630027	CSHL-HAPMAP\|CSHL-HuDD-200402.chr5.NT_006431.13_4006340	rev/B	C/T	caataacaaaacaaccttttgcttgtgaag	gtctagcattactcttgcatcttgggtcat	02/20/04	03/04/04	120	Genomic	unknown
ss24339493	PERLEGEN\|afd0842092	rev/B	C/T	caataacaaaacaaccttttgcttgtgaag	gtctagcattactcttgcatcttgggtcat	08/10/04	09/13/04	123	Genomic	unknown
ss44661293	ABI\|hCV2842177	rev/B	C/T	caataacaaaacaaccttttgcttgtgaag	gtctagcattactcttgcatcttgggtcat	07/19/05	11/03/06	126	Genomic	unknown
ss66557837	ILLUMINA\|HumanHap300v1.1_rs26608	fwd/B	A/G	atgacccaagatgcaagagtaatgctagac	cttcacaagcaaaaggttgttttgttattg	11/09/06	11/09/06	127	Genomic	unknown
ss67266132	ILLUMINA\|HumanHap550v1.1_rs26608	fwd/T	A/G	atgacccaagatgcaagagtaatgctagac	cttcacaagcaaaaggttgttttgttattg	11/14/06	11/14/06	127	Genomic	unknown
ss67666066	ILLUMINA\|HumanHap650Yv1.0_rs26608	fwd/T	A/G	atgacccaagatgcaagagtaatgctagac	cttcacaagcaaaaggttgttttgttattg	11/14/06	11/14/06	127	Genomic	unknown
ss68934681	PERLEGEN\|PGP00842092	rev/B	C/T	caataacaaaacaaccttttgcttgtgaag	gtctagcattactcttgcatcttgggtcat	01/30/07	08/14/07	127	Genomic	unknown
ss70744536	ILLUMINA\|HumanHap550v3.0__rs26608	fwd/T	A/G	atgacccaagatgcaagagtaatgctagac	cttcacaagcaaaaggttgttttgttattg	04/20/07	03/30/08	130	Genomic	unknown
ss71316032	ILLUMINA\|HumanHap650Yv3.0_rs26608	fwd/T	A/G	atgacccaagatgcaagagtaatgctagac	cttcacaagcaaaaggttgttttgttattg	04/23/07	04/23/07	127	Genomic	unknown
ss74929000	ILLUMINA\|ILMN_Human_1M_rs26608	fwd/T	A/G	atgacccaagatgcaagagtaatgctagac	cttcacaagcaaaaggttgttttgttattg	08/28/07	08/29/07	129	Genomic	unknown
ss79142489	ILLUMINA\|HumanHap300v2.0_rs26608	fwd/T	A/G	atgacccaagatgcaagagtaatgctagac	cttcacaagcaaaaggttgttttgttattg	04/18/07	11/18/07	130	Genomic	unknown
ss83352904	KRIBB_YJKIM\|KHS441458	fwd/T	A/G	atgacccaagatgcaagagtaatgctagac	cttcacaagcaaaaggttgttttgttattg	12/04/07	12/04/07	130	Genomic	unknown

Fasta sequence (Legend)

 AGTCTGGTGT GGTAAGTCCT GTAACAAGAC TGAGTATAAG ATGCAGTTAG GATCATATAG
 GAAGGAGAAA GGAGACTTCA CAGAGGAAAA GAGTCTACGA AAAGGGACAG ATGAGACAAA
 AGTCATGGAG ATACACTAAG TTTAGTTTAC AGATGAAACA AGATTGGAGA TTTATGAATC
 ATTGAAAAAC AAACCATAAT CTTAAGGGTT CACTGTACTA TAGTATAAAA TATCTCAGCA
 GTTTCAAGCT GGAGGGAAAT TTGCCAAATT ATGACCCAAG ATGCAAGAGT AATGCTAGAC
 R
 CTTCACAAGC AAAAGGTTGT TTTGTTATTG TTATTTAATT CACTTCAGTG AATATTTAAT
 GAATACCAAC TCCATGCCAG GCCCTGAGGA TGCAATCCCT GCCATGCCCA GGTGTGGGTG
 AACACACACA CACACGCACG CACACACACA CACACACCAT CCTCTGAGAC TGTTTCTTTG
 TATACTTCGG TGGGAGAGTG ATGTTGGCCA TAATGATTAT GGAAGTTCTC AGAAAAACAT
 AAAACTAGAT TCCCATAAAT GGAATGGCAA CTCGACAACT GTTGAAGAGG TAATATGCTT

GeneView

GeneView via analysis of contig annotation: ARL15 ADP-ribosylation factor-like 15

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_006713->NM_019087

function

HuRef

NW_001838934->NM_019087

function

Celera

NW_922607->NM_019087

function

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


reference	NT_006713->NM_019087->NP_061960	4035956	reverse	intron

HuRef	NW_001838934->NM_019087->NP_061960	4022516	reverse	intron

Celera	NW_922607->NM_019087->NP_061960	4010604	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs26608 maps exactly once on NCBI human chromosome 5

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
5	NW_922607.1	4010604	50395218	minus	T	alt_assembly_1	Celera	Celera	view	300
5	NW_001838934.1	4022516	50415196	minus	T	alt_assembly_8	HuRef	HuRef	view	300
5	NT_006713.14	4035956	53477354	minus	T	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_006431 AC008960 AC016580.5 AC022444.3 AC026476 AC026476.3 AC034246 AC034246.3

dbSNP Blast Analysis
GenBank HTGS Finished:
AC008960.6 AC016580.7 AC034246.4 NC_000005.8

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss24339493	AFD_EUR_PANEL	European	48	IG	0.458	0.500	0.042	0.317	0.708	0.292

	AFD_AFR_PANEL	African American	46	IG	0.826	0.174		0.655	0.913	0.087

	AFD_CHN_PANEL	Asian	48	IG	0.042	0.417	0.542	0.655	0.250	0.750

ss44661293	HapMap-CEU	European	120	IG	0.567	0.350	0.083	0.584	0.742	0.258

	HapMap-HCB	Asian	90	IG	0.022	0.356	0.622	0.479	0.200	0.800

	HapMap-JPT	Asian	90	IG	0.133	0.378	0.489	0.294	0.322	0.678

	HapMap-YRI	Sub-Saharan African	120	IG	0.683	0.300	0.017	0.584	0.833	0.167

	AoD_African_American		90	AF					0.830	0.170

	AoD_Caucasian		92	AF					0.700	0.300

	AoD_Chinese		90	AF					0.310	0.690

	AoD_Japanese		90	AF					0.320	0.680

ss68934681	HapMap-CEU	European	120	GF	0.567	0.350	0.083		0.742	0.258

	HapMap-HCB	Asian	90	GF	0.022	0.356	0.622		0.200	0.800

	HapMap-JPT	Asian	90	GF	0.133	0.378	0.489		0.322	0.678

	HapMap-YRI	Sub-Saharan African	120	GF	0.683	0.300	0.017		0.833	0.167

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.490+/-0.070	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, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .