Reference SNP(refSNP) Cluster Report: rs2515196

Reference SNP(refSNP) Cluster Report: rs2515196

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	100/137
Map to Genome Build:	37.4
Validation Status:

Allele
Variation Class:	SNV: single nucleotide variation
RefSNP Alleles:	A/T
Allele Origin:
Ancestral Allele:	A
Clinical Channel:	unknown
Clinical Significance:	NA
MAF/MinorAlleleCount:	T=0.033/71
MAF Source:	1000 Genomes

HGVS Names
NC_000008.10:g.104048988A>T
NM_001695.4:c.-39-4038A>T
NT_008046.16:g.17322537A>T

Links

SNP Details are organized in the following sections:

Integrated Maps (Hint: click on 'Chr Pos' or 'Contig Pos' column value to see variation in NCBI sequence viewer)

GeneView

GeneView via analysis of contig annotation:

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

Primary Assembly Mapping
Assembly	SNP to Chr	Chr	Chr position	Contig	Contig position	Allele

RefSeqGene Mapping
RefSeqGene	Gene (ID)	SNP to RefSeqGene	Position	Allele

Gene Model(s)
Function	mRNA				Protein
Function	SNP to mRNA	Accession	Position	Allele change	Accession	Position	Residue change

Submitter records for this RefSNP Cluster

The submission ss44844881 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2515196 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
ss3525545	SC_JCM\|AP003550.1_30765	fwd/B	A/T	ttttctggaactctaagtagtatgatagtg	catctactgtaatagcttgtattattacaa	09/24/01	10/10/03	100	Genomic	unknown
ss44844881	ABI\|hCV27253404	fwd/	A/T	ttttctggaactctaagtagtatgatagtg	catctactgtaatagcttgtattattacaa	07/19/05	07/19/05	126	Genomic	unknown
ss223885046	1000GENOMES\|pilot_1_YRI_5694729_chr8_104118164	fwd/	A/T	ttttctggaactctaagtagtatgatagtg	catctactgtaatagcttgtattattacaa	04/22/10	04/22/10	132	Genomic	unknown
ss234563519	1000GENOMES\|pilot_1_CEU_4168148_chr8_104118164	fwd/	A/T	ttttctggaactctaagtagtatgatagtg	catctactgtaatagcttgtattattacaa	05/01/10	05/01/10	132	Genomic	unknown
ss241391098	1000GENOMES\|pilot_1_CHB+JPT_3276175_chr8_104118164	fwd/	A/T	ttttctggaactctaagtagtatgatagtg	catctactgtaatagcttgtattattacaa	05/01/10	05/01/10	132	Genomic	unknown
ss254543922	BL\|SNP114385_8_104118164	fwd/	A/T	ttttctggaactctaagtagtatgatagtg	catctactgtaatagcttgtattattacaa	08/19/10	08/19/10	134	Genomic	unknown

Fasta sequence (Legend)

 GAGGATTGCT TGAGGCTGGG AGTTTGAGAC CAACCTGAAC AACATATCAA GACTCCATCT
 CTACAAAAAA TAAATTTTTT AAAAGCTAAA TTAGAGAACT TCTATCATAT TTTTAGACTG
 TAGTTTTGAT CAGAATTTAT CATGACATTA TTTCCTTTGA TCCTAATAAA AGCTCAGTGA
 AGTAGATAGG GCAGGTATTA TTTATAGATG AGAAATGGGG TCCTCTTTCC TATTCCTTGA
 AATCCTTTGG AAGCCTGTTA GAAGAAAAGA TTTTCTGGAA CTCTAAGTAG TATGATAGTG
 W
 CATCTACTGT AATAGCTTGT ATTATTACAA TCTTTGAGGA AGCTGCAGTT TAGATAATTT
 AGCACAATCA TCAGGAAGAA TTTAACAGTT GATTTTATTA CCTGCCATTT TGGGGGGAGA
 GGAGGTATAA AAATGTATCC TTTGATATAC TAACAGAAAA CCACTTGCAT AAAATTATTA
 TAATAAAATC TCAATTTTTC CAGAAACCAC GATCGCTTAG ATCTGGATTA CAAAAAGAGG
 TTTAAAGATG CTATTAGATT TTCTAATAAC TGAAAATGTT AAAGTTCGAG ACAGTTTGTG

NCBI Resource Links

Submitter-Referenced
GenBank
NC_000008 AC025936 AC051654

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotypes	Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	HWP	A	T
ss223885046	pilot_1_YRI_low_coverage_panel		118	AF		0.924	0.076

ss234563519	pilot_1_CEU_low_coverage_panel		120	AF		0.958	0.042

ss241391098	pilot_1_CHB+JPT_low_coverage_panel		120	AF		0.967	0.033

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.096+/-0.197	0	0	0	0

Validation Summary:

Validation status	Marker displays Mendelian segregation	PCR results confirmed in multiple reactions	Homozygotes detected in individual genotype data
	UNKNOWN	UNKNOWN	UNKNOWN

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GeneView via analysis of contig annotation:

GeneView via analysis of contig annotation: N/A.

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

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