Reference SNP(refSNP) Cluster Report: rs738127

Reference SNP(refSNP) Cluster Report: rs738127

refSNP ID: rs738127
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	86/129
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_003347.2:c.310+2889G>A
NM_198157.1:c.311-625G>A
NT_011520.11:g.1358790G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss12530184 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs738127 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
ss85328	TSC-CSHL\|TSC0108294	fwd/T	A/G	ggttccagggtgaaggcatagaactggtac	gtgtcacttctgtggattcttttggtcagg	09/06/00	04/07/04	86	Genomic	95 %
ss3223328	YUSUKE\|IMS-JST033412	fwd/T	A/G	ggttccagggtgaaggcatagaactggtac	gtgtcacttctgtggattcttttggtcagg	09/05/01	10/10/03	100	Genomic	unknown
ss8293845	SC_SNP\|NT_011520.8_1267168	fwd/T	A/G	ggttccagggtgaaggcatagaactggtac	gtgtcacttctgtggattcttttggtcagg	04/17/03	10/10/03	114	Genomic	unknown
ss12530184	WI_SSAHASNP\|chr22.NT_011520.9_1358790	fwd/T	A/G	ggttccagggtgaaggcatagaactggtac	gtgtcacttctgtggattcttttggtcagg	07/04/03	04/07/04	116	Genomic	unknown
ss13384650	SC_SNP\|NT_011520.9_1358790	fwd/T	A/G	ggttccagggtgaaggcatagaactggtac	gtgtcacttctgtggattcttttggtcagg	10/23/03	10/31/03	119	Genomic	unknown
ss19502959	CSHL-HAPMAP\|CSHL-HuDD-200402.chr22.NT_011520.9_1358790	fwd/T	A/G	ggttccagggtgaaggcatagaactggtac	gtgtcacttctgtggattcttttggtcagg	02/20/04	03/04/04	120	Genomic	unknown
ss24094893	PERLEGEN\|afd4577558	fwd/T	A/G	ggttccagggtgaaggcatagaactggtac	gtgtcacttctgtggattcttttggtcagg	08/10/04	09/13/04	123	Genomic	unknown
ss44322918	ABI\|hCV3005057	fwd/T	A/G	ggttccagggtgaaggcatagaactggtac	gtgtcacttctgtggattcttttggtcagg	07/18/05	07/18/05	126	Genomic	unknown
ss65825957	KRIBB_YJKIM\|KHS1743	fwd/T	A/G	ggttccagggtgaaggcatagaactggtac	gtgtcacttctgtggattcttttggtcagg	10/17/06	12/16/06	127	Genomic	unknown
ss75188601	ILLUMINA\|ILMN_Human_1M_rs738127	fwd/T	A/G	ggttccagggtgaaggcatagaactggtac	gtgtcacttctgtggattcttttggtcagg	08/28/07	08/29/07	129	Genomic	unknown

Fasta sequence (Legend)

 GTAAAAATTT TGGTACAGGA GCTATTCTGT GTGCCATGAT GGACAGAACT GGAATTGCTA
 TTTTGTGATT TGGGACAGTT GAGGATTCCT TCCTAGAACA TTATTATGTA GATTGTTTGT
 GGCATGGCCT TGATCCCCAT CCTCACATAC ATCAAGAATG TTGTTCCTTG CACTTGACGG
 CCACATTCCC Atgtttgtta tctattactg cattataacc cctatcaaaa ctttgtggct
 taaagtaata ccagtttatt agtttttact ctggaggttg gctgggctta gctacatggt
 tctacagctg actgttcatt cctggggtca ctcatgcagc tgtattgagg tgggaactca
 acttggctgg gaagagctgg taggcatagt gcacatgtgc ggaaatggta ttagctaagg
 cacttcggtt ctctttgtgt tctcttattt tccacaaggc tacattggac cccttcatag
 catggtggtc tcagggttcc aggGTGAagg catagaactg gtac
 R
 gtgtcacttc tgtggattct tttggtcagg caagtccaga tttaatgaga gggaaaatag
 acttcagctc ttgatgggag gagtatgcaG GATGGGAGAC ATGATGGCAG AGGTGGGACA
 GGCAGGCAAG GTTGCTGAGT CCCCTTGCTG CCTCCTCAGG CCCACTTGGG CCTGCTTTTC
 CCAAATGGCA GCTCCTCTGG ACATGCCATT CCTTCTCCCA CCTGCCTGAT TCTTCATATG
 TTGGGTGTCC CTGTTTTTCT GGTGCTATTT CCTGACTGCT GTTCAGCTG

GeneView

GeneView via analysis of contig annotation: UBE2L3 ubiquitin-conjugating enzyme E2L 3

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_011520->NM_003347

function

reference

NT_011520->NM_198157

function

HuRef

NW_001838745->NM_003347

function

HuRef

NW_001838745->NM_198157

function

Celera

NW_927628->NM_003347

function

Celera

NW_927628->NM_198157

function

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


reference	NT_011520->NM_003347->NP_003338	1358790	forward	intron

reference	NT_011520->NM_198157->NP_937800	1358790	forward	intron

HuRef	NW_001838745->NM_003347->NP_003338	53198	forward	intron

HuRef	NW_001838745->NM_198157->NP_937800	53198	forward	intron

Celera	NW_927628->NM_003347->NP_003338	51955	forward	intron

Celera	NW_927628->NM_198157->NP_937800	51955	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs738127 maps exactly once on NCBI human chromosome 22

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
22	NW_001838745.1	53198	4926065	plus	G	alt_assembly_8	HuRef	HuRef	view	524
22	NW_927628.1	51955	5785761	plus	G	alt_assembly_1	Celera	Celera	view	524
22	NT_011520.11	1358790	20298221	plus	G	ref_assembly	reference	reference	view	524

NCBI Resource Links

Submitter-Referenced
GenBank
NT_011520 AC018751.30 AP000553.1

dbSNP Blast Analysis
GenBank HTGS Finished:
AC009516.19 AC018751.30 NC_000022.9

Population Diversity

	Sample Ascertainment				Genotype Detail							Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	C/C	C/T	G/G	T/T	HWP	A	G
ss12530184	HapMap-CEU	European	120	IG	0.033	0.217			0.750		0.403	0.142	0.858

	HapMap-HCB	Asian	90	IG	0.156	0.600			0.244		0.200	0.456	0.544

	HapMap-JPT	Asian	88	IG	0.205	0.523			0.273		0.752	0.466	0.534

	HapMap-YRI	Sub-Saharan African	120	IG	0.033	0.133			0.833		0.050	0.100	0.900

ss24094893	AFD_EUR_PANEL	European	48	IG		0.375			0.625		0.273	0.188	0.812

	AFD_AFR_PANEL	African American	46	IG	0.043	0.174			0.783		0.273	0.130	0.870

	AFD_CHN_PANEL	Asian	48	IG	0.250	0.708			0.042		0.020	0.604	0.396

ss65825957	KHP1		178	AF	0.213	0.438			0.348		0.317	0.433	0.567

ss85328	SC_12_A	Asian	24	AF			0.167	0.500		0.333	0.001	0.580	0.420

	SC_12_AA	African American	20	AF			0.800	0.200			0.003	0.100	0.900

	SC_12_C	European	24	AF			0.714	0.286			0.010	0.080	0.920

	SC_95_C	European	82	IG	0.073	0.195			0.732		0.050	0.171	0.829

Concordant Genotype	Total Sample	A/A	A/G	C/C	C/T	G/G	T/T
ss12530184	268	20	87			160
ss24094893	65	7	30			28
ss85328	113	3	13	10	8	61	4

RefSNP Genotype Summary	Total Individual	A/A	A/G	C/C	C/T	G/G	T/T
rs738127	401	29	121	10	8	208	4

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
114	ss85328	A/G	TSC-CSHL	SC_95_C	CEPH1331.12		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE
114	ss85328	C/T	TSC-CSHL	SC_12_C	CEPH1331.12		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE
229	ss85328	C/C	TSC-CSHL	SC_12_C	CEPH1347.02		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE
229	ss85328	G/G	TSC-CSHL	SC_95_C	CEPH1347.02		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE
229	ss12530184	G/G	CSHL-HAPMAP	HapMap-CEU	NA10859	CEPH1347.02	r23_ch22_CEU_illumina:golden_gate_1.0.0	958478
230	ss85328	C/C	TSC-CSHL	SC_12_C	CEPH1347.03		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE
230	ss85328	G/G	TSC-CSHL	SC_95_C	CEPH1347.03		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE
231	ss85328	C/C	TSC-CSHL	SC_12_C	CEPH1347.04		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE
231	ss85328	G/G	TSC-CSHL	SC_95_C	CEPH1347.04		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE
429	ss85328	C/T	TSC-CSHL	SC_12_C	CEPH1416.01		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE
429	ss85328	G/G	TSC-CSHL	SC_95_C	CEPH1416.01		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE
429	ss12530184	G/G	CSHL-HAPMAP	HapMap-CEU	NA10835	CEPH1416.01	r23_ch22_CEU_illumina:golden_gate_1.0.0	958478
430	ss85328	C/C	TSC-CSHL	SC_12_C	CEPH1416.02		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE
430	ss85328	G/G	TSC-CSHL	SC_95_C	CEPH1416.02		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE
840	ss85328	C/C	TSC-CSHL	SC_12_AA	NA17109		TSC-SANGER-SC_12_AA-Sep-18-2003-GENOTYPE
840	ss24094893	G/G	PERLEGEN	AFD_AFR_PANEL	NA17109		71_IND_CHR_22
842	ss85328	C/C	TSC-CSHL	SC_12_AA	NA17111		TSC-SANGER-SC_12_AA-Sep-18-2003-GENOTYPE
842	ss24094893	G/G	PERLEGEN	AFD_AFR_PANEL	NA17111		71_IND_CHR_22
845	ss85328	C/C	TSC-CSHL	SC_12_AA	NA17114		TSC-SANGER-SC_12_AA-Sep-18-2003-GENOTYPE
845	ss24094893	G/G	PERLEGEN	AFD_AFR_PANEL	NA17114		71_IND_CHR_22
846	ss85328	C/C	TSC-CSHL	SC_12_AA	NA17115		TSC-SANGER-SC_12_AA-Sep-18-2003-GENOTYPE
846	ss24094893	G/G	PERLEGEN	AFD_AFR_PANEL	NA17115		71_IND_CHR_22
865	ss85328	C/C	TSC-CSHL	SC_12_AA	NA17134		TSC-SANGER-SC_12_AA-Sep-18-2003-GENOTYPE
865	ss24094893	G/G	PERLEGEN	AFD_AFR_PANEL	NA17134		71_IND_CHR_22
867	ss85328	C/C	TSC-CSHL	SC_12_AA	NA17136		TSC-SANGER-SC_12_AA-Sep-18-2003-GENOTYPE
867	ss24094893	G/G	PERLEGEN	AFD_AFR_PANEL	NA17136		71_IND_CHR_22

Genotype data submitted for	472	samples from	401	individuals	Individual with multiple genotypes submission:	63

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, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .