Reference SNP(refSNP) Cluster Report: rs10240521

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Reference SNP(refSNP) Cluster Report: rs10240521

refSNP ID: rs10240521
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	119/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	A/C
Ancestral Allele:	Not available
Clinical Association:	unknown

HGVS Names
NM_000492.3:c.3469-6205C>A
NT_007933.14:g.42444947C>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss14110304 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs10240521 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
ss14110304	WUGSC_SSAHASNP\|chr7.NT_007933.13_42438061	fwd/T	A/C	attttagctctgattttctgtgagtcatag	agagggctcagcaaactttttctataaatg	11/05/03	10/25/06	119	Genomic	unknown
ss50394308	UWGC\|CFTR-807976	fwd/T	A/C	attttagctctgattttctgtgagtcatag	agagggctcagcaaactttttctataaatg	01/30/06	11/03/06	126	Genomic	unknown
ss76666925	AFFY\|AFFY_6_1M_SNP_A-8528335	fwd/T	A/C	tttctgtgagtcatag	agagggctcagcaaac	08/28/07	08/30/07	129	Genomic	unknown
ss82084167	HGSV\|Cor19240_SNV_20070510.chr7_116855322	fwd/T	A/C	attttagctctgattttctgtgagtcatag	agagggctcagcaaactttttctataaatg	11/30/07	12/02/07	130	Genomic	unknown

Fasta sequence (Legend)

 CACAGAGTag ccaggtgcgg tggctcatgc ctgtaatccc agcactttga gagcctgggg
 caggtggatc acttgagaat aggagttgaa gaccaagctg gtcaacatgg caaaaccctg
 tatctactaa aaattcaaaa attagccagg catgatggca catgcctccc agctactggg
 gaggctgagg caggagaatc gattgaaccc gggagatgga ggttgcaggg agctgagata
 gctccactgc actccagcct ggtgacaggg tgagactcca tcacaaacaa aacaaaacaa
 aagaaagcaa aaaCACAGAT tactcagggt ccactaagac cagtgaagtc agttctcttg
 gtagggggca gggtgactga gcatgatgtt tgtaatttta aaagtgctcc aggtgattct
 agcgtgtatc aagcaagact tgtgaaccac tgAACTACAT GCTAAGACTC ATTTTAGCTC
 TGATTTTCTG TGAGTCATAG
 M
 AGagggctca gcaaactttt tctataaatg ctaagatagt aaatattttc agctttgtgg
 gctgtatcgt ctttatgaca actcaactca gtctttgtag agaaaagcag ctgtacataa
 tatgtaaact aatgggagta gctAGATGTG TCCTGTGGGC CATAGTTTTG CTGACTCCTG
 GTCTATGTCA TAGAATTTCC TTTTGAATTG ATGGACCACC AGCAAATGAT TTTTGTCCTG
 TATCAATCAA TGATACATAC ATAAATCTCT ACAAGACATG TAAAGGATGA GGCTTAATGA
 CAGAGTACTT TGGGGAAGAC ATAATATTGC AAAATTAAGA TGCTTAGAGA AAAATCATAT
 TAAAATAGTG AAAACTGT

GeneView

GeneView via analysis of contig annotation: CFTR cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

GeneView via analysis of contig annotation: LOC100133436 hypothetical protein LOC100133436

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

GeneView via analysis of contig annotation: LOC100134538 hypothetical protein LOC100134538

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_007933->NM_000492

function

HuRef

NW_001839071->XM_001715600

function

Celera

NW_923640->XM_001715335

function

CRA_TCAGchr7v2

NT_079596->XM_001718352

function

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


reference	NT_007933->NM_000492->NP_000483	42444947	forward	intron

HuRef	NW_001839071->XM_001715600->XP_001715652	14027669	forward	intron

Celera	NW_923640->XM_001715335->XP_001715387	14828301	reverse	intron

CRA_TCAGchr7v2	NT_079596->XM_001718352->XP_001718404	16692377	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs10240521 maps exactly once on NCBI human chromosome 7

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
7	NW_001839071.2	14027669	111626845	minus	G	alt_assembly_8	HuRef	HuRef	view	500
7	NW_923640.1	14828301	112069550	plus	C	alt_assembly_1	Celera	Celera	view	500
7	NT_079596.2	16692377	116656809	plus	C	alt_assembly_2	CRA_TCAGchr7v2	CRA_TCAGchr7v2	view	500
7	NT_007933.14	42444947	117048607	plus	C	ref_assembly	reference	reference	view	500

NCBI Resource Links

Submitter-Referenced
GenBank
NT_007933

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/C	C/C	HWP	A	C
ss14110304	HapMap-CEU	European	120	IG			1.000			1.000

	HapMap-HCB	Asian	90	IG			1.000			1.000

	HapMap-JPT	Asian	90	IG			1.000			1.000

	HapMap-YRI	Sub-Saharan African	120	IG		0.150	0.850	0.584	0.075	0.925

ss50394308	CFTR_PANEL	multiple	30	IG	0.067	0.067	0.867	0.020	0.100	0.900

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.052+/-0.153	285	225	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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Revised: May 25, 2006 1:38 PM .