Reference SNP(refSNP) Cluster Report: rs2642208

Reference SNP(refSNP) Cluster Report: rs2642208

refSNP ID: rs2642208
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	100/129
Map to Genome Build:	36.3

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

HGVS Names
NM_000064.2:c.2440+400C>T
NT_011255.14:g.6641738G>A

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss16801906 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2642208 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
ss3722768	SC_JCM\|AC025343.2_62933	fwd/B	C/T	aggtcaggagttcaagaccagcctggtcaa	gtggtgaaaccccgtctctactgaaagtac	09/25/01	10/10/03	100	Genomic	unknown
ss16340923	PGA-UW-FHCRC\|C3-020924	fwd/B	C/T	aggtcaggagttcaagaccagcctggtcaa	gtggtgaaaccccgtctctactgaaagtac	01/02/04	04/07/04	121	Genomic	unknown
ss16801906	CSHL-HAPMAP\|CSHL-HuAA-200402.chr19.NT_011255.14_6641738	rev/T	A/G	gtactttcagtagagacggggtttcaccac	ttgaccaggctggtcttgaactcctgacct	02/17/04	03/04/04	120	Genomic	unknown
ss19404614	CSHL-HAPMAP\|CSHL-HuDD-200402.chr19.NT_011255.14_6641738	rev/T	A/G	gtactttcagtagagacggggtttcaccac	ttgaccaggctggtcttgaactcctgacct	02/20/04	03/04/04	120	Genomic	unknown
ss21540145	SSAHASNP\|WGSA-200403-chr19.chr19.NT_011255.14_6641738	rev/T	A/G	gtactttcagtagagacggggtttcaccac	ttgaccaggctggtcttgaactcctgacct	03/20/04	03/20/04	121	Genomic	unknown
ss40997364	ABI\|hCV26330598	rev/T	A/G	gtactttcagtagagacggggtttcaccac	ttgaccaggctggtcttgaactcctgacct	07/17/05	07/17/05	126	Genomic	unknown

Fasta sequence (Legend)

 TTATTCTCTG CCCTGGTTAC CACAGAGGTG TTGTTACCAG GAACTGTGGG AATCCTTAGT
 TCCTGTCTAA CTTGGAAGAA AGAATTCAGC CAAGAGTCAC ATAGCAAGGG TTAAGTAGCA
 GAGTTTATTG AAGGAAGAAA CAGCTCTGGG CTGGTCCCCC TGGAAAAATA GTAGTAGCAA
 TGCTTATTTA AAGAGACAGg gccagcctcg atggctcaca cctataatcc cagcactttg
 ggaggctgag gcaggggaat cacttcaggt caggagttca agaccagcct ggtcaa
 Y
 gtggtgaaac cccgtctcta ctgaaagtac aaaacaatta gccaggcagg gggtggcggg
 cgcctataat cccagctact cgggaggctg aggcaggaga tttggttgaa cccgggaggt
 ggaggttgcg gtgagctgag attgtgccac tgcactccag cctgggcaac aagagcaaaa
 ctccttctct aaataaataa aaaGTGACCg tatgctctga aagacgacac agacatggct
 gctcaacaga acgagccagc agcagatact gctggtagac tctttttatg agactcttac
 atgatttttc gtgaaggggc gtgagtgggt gtcacttgta agcatgtttt gggaggtctc
 tttgggcgag caggctctgt ggctgtaggt actagcatgc acgtggcatg tctcattagc
 atcgaaaatc tccacccaga ggtgtgtttt ttactatgat aatgagcaAA ACACAACTCT
 AGGGTGTTTT CGGAGCAGTG

GeneView

GeneView via analysis of contig annotation: C3 complement component 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_011255->NM_000064

function

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


reference	NT_011255->NM_000064->NP_000055	6641738	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs2642208 maps exactly once on NCBI human chromosome 19

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
19	NW_001838478.1	239582	6463923	minus	A	alt_assembly_8	HuRef	HuRef	view	296
19	NW_927173.1	5902015	6643291	minus	A	alt_assembly_1	Celera	Celera	view	296
19	NT_011255.14	6641738	6652738	minus	G	ref_assembly	reference	reference	view	296

NCBI Resource Links

Submitter-Referenced
GenBank
NT_011255 AC008760

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss16340923	PGA-AFRICAN-PANEL	African American	48	IG	0.083	0.333	0.583	0.655	0.250	0.750

	PGA-EUROPEAN-PANEL	European	46	IG	0.130	0.478	0.391	1.000	0.370	0.630

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.427+/-0.177	47	26	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

YES

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Revised: May 25, 2006 1:38 PM .