Reference SNP(refSNP) Cluster Report: rs26496

Reference SNP(refSNP) Cluster Report: rs26496

refSNP ID: rs26496
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:	G
Clinical Association:	unknown

HGVS Names
NM_001040458.1:c.525-1179T>C
NM_016442.3:c.525-1179T>C
NT_023148.12:g.4451754A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss1767702 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs26496 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
ss30340	KWOK\|OVLP-11305	fwd/T	A/G	ggcatttattctaaagaaataatttacaaa	atgctcatcaaagtgttgttgatactgaaa	04/28/00	10/10/03	76	Genomic	99 %
ss30372	KWOK\|OVLP-11394	fwd/T	A/G	ggcatttattctaaagaaataatttacaaa	atgctcatcaaagtgttgttgatactgaaa	04/28/00	10/10/03	76	Genomic	99 %
ss31545	KWOK\|OVLP-18690	fwd/T	A/G	ggcatttattctaaagaaataatttacaaa	atgctcatcaaagtgttgttgatactgaaa	04/28/00	10/10/03	76	Genomic	99 %
ss37666	KWOK\|OVLP-44042	fwd/T	A/G	ggcatttattctaaagaaataatttacaaa	atgctcatcaaagtgttgttgatactgaaa	04/28/00	10/10/03	76	Genomic	99 %
ss315997	KWOK\|OVLP-000621-6427	fwd/T	A/G	ggcatttattctaaagaaataatttacaaa	atgctcatcaaagtgttgttgatactgaaa	06/30/00	10/10/03	79	Genomic	99 %
ss317747	KWOK\|OVLP-000621-12350	fwd/T	A/G	ggcatttattctaaagaaataatttacaaa	atgctcatcaaagtgttgttgatactgaaa	06/30/00	10/10/03	79	Genomic	99 %
ss320687	KWOK\|OVLP-000621-21746	fwd/T	A/G	ggcatttattctaaagaaataatttacaaa	atgctcatcaaagtgttgttgatactgaaa	06/30/00	10/10/03	79	Genomic	99 %
ss323516	KWOK\|OVLP-000621-30954	fwd/T	A/G	ggcatttattctaaagaaataatttacaaa	atgctcatcaaagtgttgttgatactgaaa	06/30/00	10/10/03	79	Genomic	99 %
ss329811	KWOK\|OVLP-000621-51225	fwd/T	A/G	ggcatttattctaaagaaataatttacaaa	atgctcatcaaagtgttgttgatactgaaa	06/30/00	10/10/03	79	Genomic	99 %
ss330002	KWOK\|OVLP-000621-52033	fwd/T	A/G	ggcatttattctaaagaaataatttacaaa	atgctcatcaaagtgttgttgatactgaaa	06/30/00	10/10/03	79	Genomic	99 %
ss336597	KWOK\|OVLP-000621-75093	fwd/T	A/G	ggcatttattctaaagaaataatttacaaa	atgctcatcaaagtgttgttgatactgaaa	06/30/00	10/10/03	79	Genomic	99 %
ss639746	SC_JCM\|AC020923.4_127538	fwd/T	A/G	ggcatttattctaaagaaataatttacaaa	atgctcatcaaagtgttgttgatactgaaa	07/12/00	10/10/03	80	Genomic	unknown
ss1069473	KWOK\|OVLP-000804-3530	fwd/T	A/G	ggcatttattctaaagaaataatttacaaa	atgctcatcaaagtgttgttgatactgaaa	09/02/00	10/10/03	92	Genomic	99 %
ss1074504	KWOK\|OVLP-000804-31434	rev/B	C/T	tttcagtatcaacaacactttgatgagcat	tttgtaaattatttctttagaataaatgcc	09/02/00	10/10/03	92	Genomic	99 %
ss1188943	KWOK\|OVLP-000804-625248	fwd/T	A/G	ggcatttattctaaagaaataatttacaaa	atgctcatcaaagtgttgttgatactgaaa	09/02/00	10/10/03	92	Genomic	99 %
ss1191062	KWOK\|OVLP-000804-632516	rev/B	C/T	tttcagtatcaacaacactttgatgagcat	tttgtaaattatttctttagaataaatgcc	09/02/00	10/10/03	92	Genomic	99 %
ss1200291	KWOK\|OVLP-000804-19250	fwd/T	A/G	ggcatttattctaaagaaataatttacaaa	atgctcatcaaagtgttgttgatactgaaa	09/02/00	10/10/03	92	Genomic	97 %
ss1200720	KWOK\|OVLP-000804-23293	rev/B	C/T	tttcagtatcaacaacactttgatgagcat	tttgtaaattatttctttagaataaatgcc	09/02/00	10/10/03	92	Genomic	97 %
ss1202571	KWOK\|OVLP-000804-38921	fwd/T	A/G	ggcatttattctaaagaaataatttacaaa	atgctcatcaaagtgttgttgatactgaaa	09/02/00	10/10/03	92	Genomic	97 %
ss1261365	KWOK\|OVLP-000804-635731	fwd/T	A/G	ggcatttattctaaagaaataatttacaaa	atgctcatcaaagtgttgttgatactgaaa	09/02/00	10/10/03	92	Genomic	97 %
ss1268359	KWOK\|OVLP-000804-30295	fwd/T	A/G	ggcatttattctaaagaaataatttacaaa	atgctcatcaaagtgttgttgatactgaaa	09/02/00	10/10/03	92	Genomic	94 %
ss1767702	KWOK\|OVLP-000925-162914	fwd/T	A/G	ggcatttattctaaagaaataatttacaaa	atgctcatcaaagtgttgttgatactgaaa	10/05/00	05/16/04	92	Genomic	99 %
ss1768223	KWOK\|OVLP-000925-167791	rev/B	C/T	tttcagtatcaacaacactttgatgagcat	tttgtaaattatttctttagaataaatgcc	10/05/00	10/10/03	92	Genomic	99 %
ss1769007	KWOK\|OVLP-000925-182510	fwd/T	A/G	ggcatttattctaaagaaataatttacaaa	atgctcatcaaagtgttgttgatactgaaa	10/05/00	10/10/03	92	Genomic	99 %
ss1769377	KWOK\|OVLP-000925-187133	rev/B	C/T	tttcagtatcaacaacactttgatgagcat	tttgtaaattatttctttagaataaatgcc	10/05/00	10/10/03	92	Genomic	99 %
ss1822939	KWOK\|OVLP-000925-179101	fwd/T	A/G	ggcatttattctaaagaaataatttacaaa	atgctcatcaaagtgttgttgatactgaaa	10/05/00	10/10/03	92	Genomic	97 %
ss1823917	KWOK\|OVLP-000925-198501	fwd/T	A/G	ggcatttattctaaagaaataatttacaaa	atgctcatcaaagtgttgttgatactgaaa	10/05/00	10/10/03	92	Genomic	97 %
ss1824560	KWOK\|OVLP-000925-213428	rev/B	C/T	tttcagtatcaacaacactttgatgagcat	tttgtaaattatttctttagaataaatgcc	10/05/00	10/10/03	92	Genomic	97 %
ss1851068	KWOK\|OVLP-000925-222608	fwd/T	A/G	ggcatttattctaaagaaataatttacaaa	atgctcatcaaagtgttgttgatactgaaa	10/06/00	10/10/03	92	Genomic	94 %
ss14670857	WI_SSAHASNP\|chr5.NT_023148.12_4451754	fwd/T	A/G	ggcatttattctaaagaaataatttacaaa	atgctcatcaaagtgttgttgatactgaaa	11/05/03	11/22/03	119	Genomic	unknown
ss20248051	CSHL-HAPMAP\|CSHL-HuFF-200402.chr5.NT_023148.12_4451754	fwd/T	A/G	ggcatttattctaaagaaataatttacaaa	atgctcatcaaagtgttgttgatactgaaa	02/21/04	03/04/04	120	Genomic	unknown
ss22248280	SSAHASNP\|WGSA-200403-chr5.chr5.NT_023148.12_4451754	fwd/T	A/G	ggcatttattctaaagaaataatttacaaa	atgctcatcaaagtgttgttgatactgaaa	03/21/04	03/21/04	121	Genomic	unknown
ss42582096	ABI\|hCV11471246	fwd/T	A/G	ggcatttattctaaagaaataatttacaaa	atgctcatcaaagtgttgttgatactgaaa	07/18/05	07/18/05	126	Genomic	unknown
ss85809873	HGSV\|Cor18517_SNV_20070510.chr5_96163638	fwd/T	A/G	ggcatttattctaaagaaataatttacaaa	atgctcatcaaagtgttgttgatactgaaa	12/06/07	12/10/07	130	Genomic	unknown
ss93177948	BCMHGSC_JDW\|JWB-2009824	fwd/T	A/G	ggcatttattctaaagaaataatttacaaa	atgctcatcaaagtgttgttgatactgaaa	02/26/08	03/04/08	129	Genomic	unknown

Fasta sequence (Legend)

 CCTAAAGTTA CTATAAGATT GATGGATTTT GCTACTAAAA AATATTTCAT CTGACAAAAG
 CTATCATAAA CTAAGTTAAA AGACGAGTTA CACTGGGCAT ggtcatggtg tctcatgcct
 gtaatcctaa cacatttttg ggaggttgag gtgggaggat tacttgagcc caggagtgtg
 agacctacct gggcaacatg gtaaaacccc atctctacca aaaatacaaa aattagccag
 gcatggtggt gcaggcctgt agtcccagct acttgggagg cagaggtgag acgatggttt
 gagcccagga ggcagaggtt tcagtgacct gagattgcgc cattgcactc cagcctgggc
 gacagaacca gaccctgtct cgggaagaaa aaaaaaaaag ttaaaaagaa aaaGTAAAAA
 ACAGGGAAAA TTCATTTAAG AAGTATGTGA GGAAAACTTA ATAGCCTTAA CAGATAGTGA
 GATCCTAAAA ATATGTAATC CTAAAAAtgg ctcatacctg taatcttggc actttgagag
 gcctaggcgg gcggatcacg aggacaggag ttcgagacca ccctggccaa catggtgaaa
 ccccatctct actaaaaata caaaaattag ctgggtgtgg tggtgcgcgt ctgtaatccc
 agctactcag gaggctgagg caggagaatt gcttgaaccc gggaggcgga ggttgcagtg
 agccgagttc gcgccactgc actccagcct gggtgacaga gcaagactcc gtctcgacaa
 aaaaaaaaaa aaaaaaaaaa aaaaaAAAAT CCCCAACAAC CAAGGGAATC TCAGGCAAAG
 TCAAAGGTCA TTAACAGGCA ATTCATAAAA GAAGAACCTA TAAATCATTA ACAAACATAT
 CAAAAGCTGC TCAACTTCCT TAATCAAAGT TACGTAAATT AAAAAGAGAT CATTTATTTG
 GGGACCTTTT TTGCTCTAAA AAGACTGCCA ATATACACTA TTGGTGAGGG GTAAGAAAAA
 ATGACAAGGT TTATCAAAAA TTTATAGGCT CTTTGGCTTA CCAGTTTTAC TTCTAGGCAT
 TTATTCTAAA GAAATAATTT ACAAA
 R
 ATGCTCATCA AAGTGTTGTT GATACTGAAA AATTGGAAAC AATTTCATTT CCATTCCCGA
 GGGATTAAAG ATATTAATGT ACAACTATGT ATTTTAATAA AATCATTAAA AAGATGTCTA
 GTAATAGTCA TTTATATAAA ACATCTTCCC AACATATTAA GTTAAAAAAT TTCCTTGTAA
 AAGAGaaaat ataagaattc tatttatata aaataatata tatGCATATC CAGAAAGAAG
 TCTGGCAGAA TATTCCAGTG AAATAGAAGT AGTGGTCAGT TCAGGGGGCT ATGAGTGAAA
 TAAATTTTAC TTTCTTACCT TGA

GeneView

GeneView via analysis of contig annotation: ERAP1 endoplasmic reticulum aminopeptidase 1

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_023148->NM_001040458

function

reference

NT_023148->NM_016442

function

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


reference	NT_023148->NM_001040458->NP_001035548	4451754	reverse	intron

reference	NT_023148->NM_016442->NP_057526	4451754	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs26496 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_001838952.2	42648580	91328128	minus	C	alt_assembly_8	HuRef	HuRef	view	1105
5	NW_922729.1	25422133	92022289	plus	G	alt_assembly_1	Celera	Celera	view	1105
5	NT_023148.12	4451754	96163638	plus	A	ref_assembly	reference	reference	view	1105

NCBI Resource Links

Submitter-Referenced
GenBank
NT_023148 AC008906 AC008955 AC008955.3 AC008963 AC008963.5 AC009073.8 AC020923.5 AC026435 AC026435.2

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
ss1767702	CEPH		184	AF					0.070	0.930

	HapMap-CEU	European	116	IG	0.017	0.328	0.655	0.439	0.181	0.819

	HapMap-HCB	Asian	86	IG	0.209	0.465	0.326	0.752	0.442	0.558

	HapMap-JPT	Asian	90	IG	0.311	0.333	0.356	0.050	0.478	0.522

	HapMap-YRI	Sub-Saharan African	118	IG	0.153	0.492	0.356	1.000	0.398	0.602

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.463+/-0.131	270	210	0	0

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

DoubleHit found by: BCM_SSAHASNP

UNKNOWN

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Revised: May 25, 2006 1:38 PM .