Reference SNP(refSNP) Cluster Report: rs3900

Reference SNP(refSNP) Cluster Report: rs3900

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	36/130
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	C/G
Ancestral Allele:	C
Clinical Association:	unknown

HGVS Names
NM_001005852.2:c.-16+889G>C
NT_011875.11:g.7881067G>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss115582285 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3900 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
ss3937	OEFNER\|M9	fwd/T	C/G	ctgcaaagaaacggcctaagatggttgaat	ctctttatttttctttaatttagacatgtt	01/23/99	04/07/04	36	Genomic	unknown
ss14424468	WI_SSAHASNP\|chrY.NT_011875.10_7817592	fwd/T	C/G	ctgcaaagaaacggcctaagatggttgaat	ctctttatttttctttaatttagacatgtt	11/05/03	03/31/08	119	Genomic	unknown
ss24726393	PERLEGEN\|afd4205532	fwd/T	C/G	ctgcaaagaaacggcctaagatggttgaat	ctctttatttttctttaatttagacatgtt	08/10/04	09/13/04	123	Genomic	unknown
ss76487895	AFFY\|AFFY_6_1M_SNP_A-8348747	rev/	C/G	aaagaaaaataaagag	attcaaccatcttagg	08/28/07	08/30/07	129	Genomic	unknown
ss104807777	KRIBB_YJKIM\|KHS1200113	fwd/	C/G	ctgcaaagaaacggcctaagatggttgaat	ctctttatttttctttaatttagacatgtt	07/10/08	07/10/08	130	Genomic	unknown
ss115582285	ILLUMINA-UK\|NA18507_000001437_NCBI36.1_chrY_20189645	fwd/	C/G	ctgcaaagaaacggcctaagatggttgaat	ctctttatttttctttaatttagacatgtt	01/15/09	01/15/09	130	Genomic	99 %

Fasta sequence (Legend)

 CGGAAGCTGA AGTGCGGCGT CTTTGATCTC TCAATCCTGG AGACACAGGA ACATTTTCCT
 TACTTTACTC AACTCGTTCC TTTGAATACC GCAAAATTAA GACGGCGTTT AAAACAATCG
 AAATCCCTTT TCTTCTGGGG TTTGGTGCCT AAAGATTAGA AAAGTTTGCG CAAGGAATTC
 GCTGCAGCAT ATAAAACTTT CAGGACCCTG AAATACAGAA CTGCAAAGAA ACGGCCTAAG
 ATGGTTGAAT
 S
 CTCTTTATTT TTCTTTAATT TAGACATGTT CAAACGTTCA ATGTCTTACA TACTTAGTTA
 TGTAAGTAAG GTAGCGCTTA CTTCATTATG CATTTCAATA CTCAAAAAAA ATTCCTTTGT
 GAAATGTTGA AATATTTTTC TAATCTGTTT CACGAGCTTC AAAAATGAGG AAAAAAGATT
 CAGTTTACAT TTCAGCAAAA TGCCTCTTTT TAATCGGATT TATGTTTACT TAACATTTAC
 AGTACATTTA

GeneView

GeneView via analysis of contig annotation:

View more variation on this gene (click to hide).

Assembly	SNP to Chr	Chr	Chr position	Contig	Contig position	Allele

Function	mRNA				Protein
Function	mRNA to Chr	Accession	Position	Allele change	Accession	Position	Residue change

GeneView via analysis of contig annotation: N/A.

GeneView via direct blast against RefSeq sequences (used when no gene model is available):

Function	Chr	mRNA				Protein
Function	Chr	SNP to mRNA	Accession	Position	Allele change	Accession	Position	Residue change

GeneView via direct blast against RefSeq sequences (used when no gene model is available): N/A

Integrated Maps:

Genome Build	Chr	Chr Pos	Contig	Contig Pos	SNP to Chr	Contig allele	Group term	Group label	Contig label	Neighbor SNP	Map Method

doesn't map to any assembly.

NCBI Resource Links

Resource

Submitter-Referenced
dbSTS	GenBank
G42825	NT_011875

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	G/G	HWP	C	G
ss14424468	HapMap-CEU	European	60	IG	0.700	0.300		0.700	0.300

	HapMap-HCB	Asian	46	IG	0.826	0.174		0.826	0.174

	HapMap-JPT	Asian	46	IG	0.435	0.565		0.435	0.565

	HapMap-YRI	Sub-Saharan African	60	IG		1.000			1.000

ss24726393	AFD_EUR_PANEL	European	26	IG	0.538	0.462	0.001	0.538	0.462

	AFD_AFR_PANEL	African American	22	IG	0.818	0.182	0.001	0.818	0.182

	AFD_CHN_PANEL	Asian	18	IG		1.000			1.000

ss3937	Global		718	AF				0.405	0.595

Concordant Genotype	Total Sample	C/C	G/G
ss115582285	521	83	57
ss24726393	29	15	14

RefSNP Genotype Summary	Total Individual	C/C	G/G
rs3900	551	98	71

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
188	ss24726393	G/G	PERLEGEN	AFD_EUR_PANEL	NA10851		71_IND_CHR_Y
188	ss115582285	G/G	CSHL-HAPMAP	HapMap-CEU	NA10851	CEPH1344.01	r27_chY_CEU_affymetrix:genomewidesnp_6.0
215	ss24726393	G/G	PERLEGEN	AFD_EUR_PANEL	NA10857		71_IND_CHR_Y
215	ss115582285	G/G	CSHL-HAPMAP	HapMap-CEU	NA10857	CEPH1346.01	r27_chY_CEU_affymetrix:genomewidesnp_6.0
348	ss24726393	C/C	PERLEGEN	AFD_EUR_PANEL	NA10860		71_IND_CHR_Y
348	ss115582285	C/C	CSHL-HAPMAP	HapMap-CEU	NA10860	CEPH1362.01	r27_chY_CEU_affymetrix:genomewidesnp_6.0
399	ss24726393	G/G	PERLEGEN	AFD_EUR_PANEL	NA10830		71_IND_CHR_Y
399	ss115582285	G/G	CSHL-HAPMAP	HapMap-CEU	NA10830	CEPH1408.01	r27_chY_CEU_affymetrix:genomewidesnp_6.0

Genotype data submitted for	558	samples from	551	individuals	Individual with multiple genotypes submission:	7

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

YES

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Revised: May 25, 2006 1:38 PM .