Reference SNP(refSNP) Cluster Report: rs223390

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Reference SNP(refSNP) Cluster Report: rs223390

refSNP ID: rs223390
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_003340.4:c.-177C>T
NM_181886.1:c.-385C>T
NM_181888.1:c.-129+98C>T
NM_181889.1:c.-129+307C>T
NM_181890.1:c.-128-1004C>T
NM_181893.1:c.31-17809C>T
NT_016354.18:g.28296629G>A

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44524956 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs223390 during BLAST analysis for the current build.

NCBI Assay ID	Handle\|Submitter ID	Validation Status	ss to rs Orientation /Strand	Alleles	5' Near Seq 30 bp	3' Near Seq 30 bp	Entry Date	Update Date	Build Added	Molecule Type	Freq Warning	Ancestral Allele	Success Rate
ss290055	KWOK\|OVLP-000621-268075		rev/B	C/T	aagccgtctggcttcggcctcacatcggtc	tgtgctcgggacggcggcgttggcggactg	06/30/00	10/10/03	79	Genomic			97 %
ss294473	KWOK\|OVLP-000621-289899		fwd/T	A/G	cagtccgccaacgccgccgtcccgagcaca	gaccgatgtgaggccgaagccagacggctt	06/30/00	10/10/03	85	Genomic			97 %
ss512055	SC_JCM\|AF224669.1_202571		fwd/T	A/G	cagtccgccaacgccgccgtcccgagcaca	gaccgatgtgaggccgaagccagacggctt	07/12/00	10/10/03	80	Genomic			unknown
ss1042252	KWOK\|OVLP-000804-566857		rev/B	C/T	aagccgtctggcttcggcctcacatcggtc	tgtgctcgggacggcggcgttggcggactg	09/02/00	10/10/03	86	Genomic			97 %
ss1948602	KWOK\|OVLP-000925-207625		rev/B	C/T	aagccgtctggcttcggcctcacatcggtc	tgtgctcgggacggcggcgttggcggactg	10/06/00	10/10/03	92	Genomic			97 %
ss1972574	KWOK\|OVLP-000925-196512		fwd/T	A/G	cagtccgccaacgccgccgtcccgagcaca	gaccgatgtgaggccgaagccagacggctt	10/06/00	10/10/03	92	Genomic			94 %
ss4961063	YUSUKE\|IMS-JST130501		fwd/T	A/G	cagtccgccaacgccgccgtcccgagcaca	gaccgatgtgaggccgaagccagacggctt	08/07/02	10/10/03	108	Genomic			unknown
ss16264782	CGAP-GAI\|1529880		rev/B	C/T	aagccgtctggcttcggcctcacatcggtc	tgtgctcgggacggcggcgttggcggactg	11/18/03	11/22/03	120	cDNA			unknown
ss17024709	CSHL-HAPMAP\|CSHL-HuAA-200402.chr4.NT_016354.16_28243613		fwd/T	A/G	cagtccgccaacgccgccgtcccgagcaca	gaccgatgtgaggccgaagccagacggctt	02/17/04	03/04/04	120	Genomic			unknown
ss19585723	CSHL-HAPMAP\|CSHL-HuDD-200402.chr4.NT_016354.16_28243613		fwd/T	A/G	cagtccgccaacgccgccgtcccgagcaca	gaccgatgtgaggccgaagccagacggctt	02/20/04	03/04/04	120	Genomic			unknown
ss22066167	SSAHASNP\|WGSA-200403-chr4.chr4.NT_016354.16_28243613		fwd/T	A/G	cagtccgccaacgccgccgtcccgagcaca	gaccgatgtgaggccgaagccagacggctt	03/20/04	03/20/04	121	Genomic			unknown
ss24416917	PERLEGEN\|afd0646148		fwd/T	A/G	cagtccgccaacgccgccgtcccgagcaca	gaccgatgtgaggccgaagccagacggctt	08/10/04	09/13/04	123	Genomic			unknown
ss44524956	ABI\|hCV1346997		fwd/T	A/G	cagtccgccaacgccgccgtcccgagcaca	gaccgatgtgaggccgaagccagacggctt	07/19/05	11/03/06	126	Genomic			unknown
ss92711486	BCMHGSC_JDW\|JWB-1828206		fwd/T	A/G	cagtccgccaacgccgccgtcccgagcaca	gaccgatgtgaggccgaagccagacggctt	02/26/08	03/03/08	129	Genomic			unknown

Fasta sequence (Legend)

>gnl|dbSNP|rs223390|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=129

 CGCCCAGGTC CCGCACTGCC CCTCTTACCC GGCCGGCCAC TGGGCCGGCC TCCCTTCCCT
 GCCCTAGCCG TCCACACCCA CGCGTACAGA GGGGCCGGGG CCTCCCTCAA GCTGCGGCCT
 CGGCCTCCTC CCCGCGCGGC AGCTGGTGCC TCCCCGGCCC TACGGGGCTC ACGCGCACGA
 CACAGCCACA AGATGTCCGC TCTGACGGAA CTACTGCCAG CTGCCACGCT CCGCCCCTCC
 CCCTCCTCCT GCCTCTTCAC CGCCGCGGAT CAGTCCGCCA ACGCCGCCGT CCCGAGCACA
 R
 GACCGATGTG AGGCCGAAGC CAGACGGCTT GCTTCCCACG TCCGGGGCCG AGTGAATACG
 TGTCAAGCCC TTTTCCTTCT TCTCGGAACA GCACCTTCTT ACTAAACAGA TCGGAGATTG
 GACCAGGAGG GCGGGGGAGG GAGGAGGATC ATGAGCTGGG GGGAGGGTGA ACGAGTGGCG
 GAAACCCTTA GGCTCAGAGA AGCATCGAGA ACCGGAAGGA GACCATGGGA GGAAGGTAAA
 GGAAGCAGCC GCTGCGCGAT CCAGCCCCAC GCCCCTCCCC ACAGCGTCCC CCAGTTTCCT

GeneView via analysis of contig annotation: UBE2D3 ubiquitin-conjugating enzyme E2D 3 (UBC4/5 homolog, yeast)

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_016354->NM_003340

reference

NT_016354->NM_181886

reference

NT_016354->NM_181887

reference

NT_016354->NM_181888

reference

NT_016354->NM_181889

reference

NT_016354->NM_181890

reference

NT_016354->NM_181891

reference

NT_016354->NM_181893

HuRef

NW_001838915->NM_003340

HuRef

NW_001838915->NM_181886

HuRef

NW_001838915->NM_181887

HuRef

NW_001838915->NM_181888

HuRef

NW_001838915->NM_181889

HuRef

NW_001838915->NM_181890

HuRef

NW_001838915->NM_181891

HuRef

NW_001838915->NM_181893

Celera

NW_922162->NM_003340

Celera

NW_922162->NM_181886

Celera

NW_922162->NM_181887

Celera

NW_922162->NM_181888

Celera

NW_922162->NM_181889

Celera

NW_922162->NM_181890

Celera

NW_922162->NM_181891

Celera

NW_922162->NM_181893

"

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	mRNA pos	Function	dbSNP allele	Protein residue	Codon pos	Amino acid pos


reference	NT_016354->NM_003340->	28296629	reverse	312	5' UTR

reference	NT_016354->NM_181886->	28296629	reverse	312	5' UTR

reference	NT_016354->NM_181887->NP_871616	28296629	reverse		5' near gene

reference	NT_016354->NM_181888->NP_871617	28296629	reverse		intron

reference	NT_016354->NM_181889->NP_871618	28296629	reverse		intron

reference	NT_016354->NM_181890->NP_871619	28296629	reverse		intron

reference	NT_016354->NM_181891->NP_871620	28296629	reverse		5' near gene

reference	NT_016354->NM_181893->NP_871622	28296629	reverse		intron

HuRef	NW_001838915->NM_003340->	28246492	reverse	312	5' UTR

HuRef	NW_001838915->NM_181886->	28246492	reverse	312	5' UTR

HuRef	NW_001838915->NM_181887->NP_871616	28246492	reverse		5' near gene

HuRef	NW_001838915->NM_181888->NP_871617	28246492	reverse		intron

HuRef	NW_001838915->NM_181889->NP_871618	28246492	reverse		intron

HuRef	NW_001838915->NM_181890->NP_871619	28246492	reverse		intron

HuRef	NW_001838915->NM_181891->NP_871620	28246492	reverse		5' near gene

HuRef	NW_001838915->NM_181893->NP_871622	28246492	reverse		intron

Celera	NW_922162->NM_003340->	50873031	reverse	309	5' UTR

Celera	NW_922162->NM_181886->	50873031	reverse	309	5' UTR

Celera	NW_922162->NM_181887->NP_871616	50873031	reverse		5' near gene

Celera	NW_922162->NM_181888->NP_871617	50873031	reverse		intron

Celera	NW_922162->NM_181889->NP_871618	50873031	reverse		intron

Celera	NW_922162->NM_181890->NP_871619	50873031	reverse		intron

Celera	NW_922162->NM_181891->NP_871620	50873031	reverse		5' near gene

Celera	NW_922162->NM_181893->NP_871622	50873031	reverse		intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs223390 maps exactly once on NCBI human chromosome 4

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
4	NW_001838915.1	28246492	99484942	plus	G	alt_assembly_8	HuRef	HuRef	view	300
4	NW_922162.1	50873031	101048057	plus	A	alt_assembly_1	Celera	Celera	view	300
4	NT_016354.18	28296629	103967932	plus	G	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_016354 AC018797 AF224669.1 BM548587

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC018797.4 NC_000004.10	AC024629.1 AC080124.3

UniGene Cluster ID
518773

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss24416917	AFD_EUR_PANEL	European	48	IG	0.167	0.625	0.208	0.251	0.479	0.521

	AFD_AFR_PANEL	African American	44	IG	0.091	0.500	0.409	0.655	0.341	0.659

	AFD_CHN_PANEL	Asian	48	IG	0.250	0.417	0.333	0.439	0.458	0.542

ss44524956	HapMap-CEU	European	120	IG	0.233	0.483	0.283	1.000	0.475	0.525

	HapMap-HCB	Asian	88	IG	0.318	0.432	0.250	0.403	0.534	0.466

	HapMap-JPT	Asian	90	IG	0.311	0.422	0.267	0.317	0.522	0.478

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.499+/-0.018	242	200	9	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

UNKNOWN

UNKNOWN

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Revised: May 25, 2006 1:38 PM .