Reference SNP(refSNP) Cluster Report: rs225376

Reference SNP(refSNP) Cluster Report: rs225376

refSNP ID: rs225376
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:	C/G
Ancestral Allele:	G
Clinical Association:	unknown

HGVS Names
NM_004915.3:c.287-17058G>C
NM_016818.2:c.287-17058G>C
NM_207174.1:c.320-17058G>C
NM_207627.1:c.293-17058G>C
NM_207628.1:c.221-17058G>C
NM_207629.1:c.278-17058G>C
NT_030188.4:g.668563G>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44282815 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs225376 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
ss292204	KWOK\|OVLP-000621-277059	rev/B	C/G	tctaagcaggcaggaaggagacagctgctg	tgctgcttagagttaggcgcagggatgaaa	06/30/00	10/10/03	79	Genomic	97 %
ss519256	SC_JCM\|AC015555.4_173207	fwd/T	C/G	tttcatccctgcgcctaactctaagcagca	cagcagctgtctccttcctgcctgcttaga	07/12/00	05/16/04	80	Genomic	unknown
ss686096	SC_JCM\|AP001746.1_87870	rev/B	C/G	tctaagcaggcaggaaggagacagctgctg	tgctgcttagagttaggcgcagggatgaaa	07/27/00	10/10/03	85	Genomic	unknown
ss1837899	KWOK\|OVLP-000925-594300	fwd/T	C/G	tttcatccctgcgcctaactctaagcagca	cagcagctgtctccttcctgcctgcttaga	10/05/00	10/10/03	87	Genomic	97 %
ss4974353	YUSUKE\|IMS-JST144888	rev/B	C/G	tctaagcaggcaggaaggagacagctgctg	tgctgcttagagttaggcgcagggatgaaa	08/12/02	10/10/03	108	Genomic	unknown
ss5601803	RIKENSNPRC\|ssj0001858	rev/B	C/G	tctaagcaggcaggaaggagacagctgctg	tgctgcttagagttaggcgcagggatgaaa	10/18/02	10/10/03	110	Genomic	unknown
ss10976672	BCM_SSAHASNP\|chr21.NT_030188.2_423448	rev/B	C/G	tctaagcaggcaggaaggagacagctgctg	tgctgcttagagttaggcgcagggatgaaa	06/30/03	10/10/03	116	Genomic	unknown
ss21809424	SSAHASNP\|WGSA-200403-chr21.chr21.NT_030188.3_423448	rev/B	C/G	tctaagcaggcaggaaggagacagctgctg	tgctgcttagagttaggcgcagggatgaaa	03/20/04	03/20/04	121	Genomic	unknown
ss44282815	ABI\|hCV1723807	rev/	C/G	tctaagcaggcaggaaggagacagctgctg	tgctgcttagagttaggcgcagggatgaaa	07/18/05	11/03/06	126	Genomic	unknown
ss65790903	ILLUMINA\|Human1-rs225376	fwd/T	C/G	tttcatccctgcgcctaactctaagcagca	cagcagctgtctccttcctgcctgcttaga	10/10/06	10/10/06	127	Genomic	unknown
ss91850484	BCMHGSC_JDW\|JWB-1501047	rev/	C/G	tctaagcaggcaggaaggagacagctgctg	tgctgcttagagttaggcgcagggatgaaa	02/26/08	03/02/08	129	Genomic	unknown

Fasta sequence (Legend)

 ATGAAAATCT GCCGCTGGAT TTCGAACGGA TGCTGTGCTC TGAAGTCCAC TGGATGACAG
 GCAAAGCTGC AAGCATCTAT GTGGTTTCTC CAAGCATGAC TTTAATGGCC TTAACATGGT
 CACCCGGCCA CAGCCAAGGA TTGTTTTCTT GTGTCATCCG GTTCTGGGGT CTCCCTCACA
 TTCAGCATTC CCCATCCATA CTTCTGTCCA TTTCTCCATC CCTCCACTGC CCCCAGTCCC
 TTTCCTCCAC CAGCCTCCTC ATCTCATGGG TTTCATCCCT GCGCCTAACT CTAAGCAGCA
 S
 CAGCAGCTGT CTCCTTCCTG CCTGCTTAGA TCAGATATTT TGAACTGTGC TATGCACAGC
 TCAGCATCCC ACAAGTGATG GGGAATAGTC ACATCAATAA ATATCGTGCA AAGGGAGTAG
 TTACATCAAT AAATATCACC AAAATGATGT TCAGTCTCCC TTAGGCACCC CAAGGAGGCA
 CTCAGACCCC AAGGAGGCAC ACACGACCTC CTCACTTCCC TATAATCCCA ACAATAACAG
 CTGGCAGGTC CATCGATCTC ACCCCCAGTC CTACAGAGGG TCCCCTGATG CTCCTTCAAA

GeneView

GeneView via analysis of contig annotation: ABCG1 ATP-binding cassette, sub-family G (WHITE), member 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_030188->NM_004915

function

reference

NT_030188->NM_016818

function

reference

NT_030188->NM_207174

function

reference

NT_030188->NM_207627

function

reference

NT_030188->NM_207628

function

reference

NT_030188->NM_207629

function

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


reference	NT_030188->NM_004915->NP_004906	668563	forward	intron

reference	NT_030188->NM_016818->NP_058198	668563	forward	intron

reference	NT_030188->NM_207174->NP_997057	668563	forward	intron

reference	NT_030188->NM_207627->NP_997510	668563	forward	intron

reference	NT_030188->NM_207628->NP_997511	668563	forward	intron

reference	NT_030188->NM_207629->NP_997512	668563	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs225376 maps exactly once on NCBI human chromosome 21

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
21	NW_927384.1	28306787	28821664	minus	C	alt_assembly_1	Celera	Celera	view	300
21	NW_001838714.2	156257	29092614	plus	G	alt_assembly_8	HuRef	HuRef	view	300
21	NT_030188.4	668563	42547191	minus	G	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_030188 AC015555 AP001622 AP001622.1

dbSNP Blast Analysis
GenBank HTGS Finished:
AP001622.1

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/G	G/G	HWP	C	G
ss44282815	HapMap-CEU	European	116	IG	0.052	0.414	0.534		0.259	0.741

	HapMap-HCB	Asian	90	IG	0.311	0.444	0.244	0.752	0.533	0.467

	HapMap-JPT	Asian	88	IG	0.341	0.432	0.227	0.655	0.557	0.443

	HapMap-YRI	Sub-Saharan African	118	IG		0.169	0.831		0.085	0.915

ss4974353	JBIC-allele		1476	AF					0.564	0.436

ss519256	CEPH		184	AF					0.520	0.480

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.444+/-0.158	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 .