Reference SNP(refSNP) Cluster Report: rs153541

Reference SNP(refSNP) Cluster Report: rs153541

refSNP ID: rs153541
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:	G
Clinical Association:	unknown

HGVS Names
NM_001040458.1:c.524+1165C>T
NM_016442.3:c.524+1165C>T
NT_023148.12:g.4451813G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss42600617 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs153541 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
ss315796	KWOK\|OVLP-000621-5671	fwd/T	A/G	aaaattggaaacaatttcatttccattccc	agggattaaagatattaatgtacaactatg	06/30/00	10/10/03	79	Genomic	99 %
ss320688	KWOK\|OVLP-000621-21747	fwd/T	A/G	aaaattggaaacaatttcatttccattccc	agggattaaagatattaatgtacaactatg	06/30/00	10/10/03	85	Genomic	99 %
ss329812	KWOK\|OVLP-000621-51226	fwd/T	A/G	aaaattggaaacaatttcatttccattccc	agggattaaagatattaatgtacaactatg	06/30/00	10/10/03	79	Genomic	99 %
ss336598	KWOK\|OVLP-000621-75094	fwd/T	A/G	aaaattggaaacaatttcatttccattccc	agggattaaagatattaatgtacaactatg	06/30/00	10/10/03	85	Genomic	99 %
ss867782	SC_JCM\|AC008508.4_115564	fwd/T	A/G	aaaattggaaacaatttcatttccattccc	agggattaaagatattaatgtacaactatg	07/28/00	10/10/03	85	Genomic	unknown
ss1074503	KWOK\|OVLP-000804-31433	rev/B	C/T	catagttgtacattaatatctttaatccct	gggaatggaaatgaaattgtttccaatttt	09/02/00	10/10/03	86	Genomic	99 %
ss1191061	KWOK\|OVLP-000804-632515	rev/B	C/T	catagttgtacattaatatctttaatccct	gggaatggaaatgaaattgtttccaatttt	09/02/00	10/10/03	86	Genomic	99 %
ss1198758	KWOK\|OVLP-000804-6071	fwd/T	A/G	aaaattggaaacaatttcatttccattccc	agggattaaagatattaatgtacaactatg	09/02/00	10/10/03	86	Genomic	97 %
ss1200292	KWOK\|OVLP-000804-19251	fwd/T	A/G	aaaattggaaacaatttcatttccattccc	agggattaaagatattaatgtacaactatg	09/02/00	10/10/03	86	Genomic	97 %
ss1200719	KWOK\|OVLP-000804-23292	rev/B	C/T	catagttgtacattaatatctttaatccct	gggaatggaaatgaaattgtttccaatttt	09/02/00	10/10/03	86	Genomic	97 %
ss1202572	KWOK\|OVLP-000804-38922	fwd/T	A/G	aaaattggaaacaatttcatttccattccc	agggattaaagatattaatgtacaactatg	09/02/00	10/10/03	86	Genomic	97 %
ss1261366	KWOK\|OVLP-000804-635732	fwd/T	A/G	aaaattggaaacaatttcatttccattccc	agggattaaagatattaatgtacaactatg	09/02/00	10/10/03	86	Genomic	97 %
ss1268360	KWOK\|OVLP-000804-30296	fwd/T	A/G	aaaattggaaacaatttcatttccattccc	agggattaaagatattaatgtacaactatg	09/02/00	10/10/03	86	Genomic	94 %
ss1768222	KWOK\|OVLP-000925-167790	rev/B	C/T	catagttgtacattaatatctttaatccct	gggaatggaaatgaaattgtttccaatttt	10/05/00	10/10/03	92	Genomic	99 %
ss1769376	KWOK\|OVLP-000925-187132	rev/B	C/T	catagttgtacattaatatctttaatccct	gggaatggaaatgaaattgtttccaatttt	10/05/00	10/10/03	92	Genomic	99 %
ss1822940	KWOK\|OVLP-000925-179102	fwd/T	A/G	aaaattggaaacaatttcatttccattccc	agggattaaagatattaatgtacaactatg	10/05/00	10/10/03	87	Genomic	97 %
ss1823918	KWOK\|OVLP-000925-198502	fwd/T	A/G	aaaattggaaacaatttcatttccattccc	agggattaaagatattaatgtacaactatg	10/05/00	10/10/03	87	Genomic	97 %
ss1824415	KWOK\|OVLP-000925-210039	fwd/T	A/G	aaaattggaaacaatttcatttccattccc	agggattaaagatattaatgtacaactatg	10/05/00	10/10/03	87	Genomic	97 %
ss1824559	KWOK\|OVLP-000925-213427	rev/B	C/T	catagttgtacattaatatctttaatccct	gggaatggaaatgaaattgtttccaatttt	10/05/00	10/10/03	92	Genomic	97 %
ss1851069	KWOK\|OVLP-000925-222609	fwd/T	A/G	aaaattggaaacaatttcatttccattccc	agggattaaagatattaatgtacaactatg	10/06/00	10/10/03	92	Genomic	94 %
ss42600617	ABI\|hCV794813	fwd/T	A/G	aaaattggaaacaatttcatttccattccc	agggattaaagatattaatgtacaactatg	07/18/05	11/03/06	126	Genomic	unknown

Fasta sequence (Legend)

 ATAAAAGAAG AACCTATAAA TCATTAACAA ACATATCAAA AGCTGCTCAA CTTCCTTAAT
 CAAAGTTACG TAAATTAAAA AGAGATCATT TATTTGGGGA CCTTTTTTGC TCTAAAAAGA
 CTGCCAATAT ACACTATTGG TGAGGGGTAA GAAAAAATGA CAAGGTTTAT CAAAAATTTA
 TAGGCTCTTT GGCTTACCAG TTTTACTTCT AGGCATTTAT TCTAAAGAAA TAATTTACAA
 AGATGCTCAT CAAAGTGTTG TTGATACTGA AAAATTGGAA ACAATTTCAT TTCCATTCCC
 R
 AGGGATTAAA GATATTAATG TACAACTATG TATTTTAATA AAATCATTAA AAAGATGTCT
 AGTAATAGTC ATTTATATAA AACATCTTCC CAACATATTA AGTTAAAAAA TTTCCTTGTA
 AAAGAGAAAA TATAAGAATT CTATTTATAT AAAATAATAT ATATGCATAT CCAGAAAGAA
 GTCTGGCAGA ATATTCCAGT GAAATAGAAG TAGTGGTCAG TTCAGGGGGC TATGAGTGAA
 ATAAATTTTA CTTTCTTACC TTGATAAAAT AATATGGAAT TTGAAAAATA AATTAGTATA

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

HuRef

NW_001838952->NM_001040458

function

HuRef

NW_001838952->NM_016442

function

Celera

NW_922729->NM_001040458

function

Celera

NW_922729->NM_016442

function

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


reference	NT_023148->NM_001040458->NP_001035548	4451813	reverse	intron

reference	NT_023148->NM_016442->NP_057526	4451813	reverse	intron

HuRef	NW_001838952->NM_001040458->NP_001035548	42648521	forward	intron

HuRef	NW_001838952->NM_016442->NP_057526	42648521	forward	intron

Celera	NW_922729->NM_001040458->NP_001035548	25422192	reverse	intron

Celera	NW_922729->NM_016442->NP_057526	25422192	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs153541 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	42648521	91328187	minus	C	alt_assembly_8	HuRef	HuRef	view	300
5	NW_922729.1	25422192	92022348	plus	G	alt_assembly_1	Celera	Celera	view	300
5	NT_023148.12	4451813	96163697	plus	G	ref_assembly	reference	reference	view	300

NCBI Resource Links

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

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC008906.5 AC009073.8 AC009126.2 NC_000005.8	AC008963.5 AC026435.2

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss42600617	HapMap-CEU	European	118	IG	0.034	0.356	0.610	0.655	0.212	0.788

	HapMap-HCB	Asian	90	IG		0.044	0.956	1.000	0.022	0.978

	HapMap-JPT	Asian	90	IG		0.089	0.911	1.000	0.044	0.956

	HapMap-YRI	Sub-Saharan African	114	IG		0.193	0.807	0.439	0.096	0.904

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.183+/-0.241	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 .