Reference SNP(refSNP) Cluster Report: rs469532

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Reference SNP(refSNP) Cluster Report: rs469532

refSNP ID: rs469532
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	80/129
Map to Genome Build:	36.3

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

HGVS Names
NM_001042440.1:c.211-6353T>G
NM_001042441.1:c.211-6353T>G
NM_001042442.1:c.211-6353T>G
NM_001042443.1:c.-39-6353T>G
NM_001042444.1:c.-39-6353T>G
NM_001042445.1:c.-39-6353T>G
NM_001042446.1:c.-39-6353T>G
NM_001750.5:c.211-6353T>G
NM_173060.2:c.-39-6353T>G
NM_173063.1:c.211-6353T>G
NT_023148.12:g.4365862T>G

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss1767072 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs469532 during BLAST analysis for the current build.

NCBI Assay ID	Handle\|Submitter ID	Validation Status	ss to rs Orientation /Strand	Alleles	5' Near Seq 30 bp	3' Near Seq 30 bp	Entry Date	Update Date	Build Added	Molecule Type	Freq Warning	Ancestral Allele	Success Rate
ss639151	SC_JCM\|AC008906.3_36058		fwd/T	A/C	gactgtcatcaaccaggagttgtacaactt	aaaataaaacacatatacgcaaaaccctga	07/12/00	10/10/03	80	Genomic			unknown
ss1069422	KWOK\|OVLP-000804-3431		rev/B	G/T	tcagggttttgcgtatatgtgttttatttt	aagttgtacaactcctggttgatgacagtc	09/02/00	10/10/03	86	Genomic			99 %
ss1183411	KWOK\|OVLP-000804-600741		rev/B	G/T	tcagggttttgcgtatatgtgttttatttt	aagttgtacaactcctggttgatgacagtc	09/02/00	10/10/03	86	Genomic			99 %
ss1192869	KWOK\|OVLP-000804-638402		fwd/T	A/C	gactgtcatcaaccaggagttgtacaactt	aaaataaaacacatatacgcaaaaccctga	09/02/00	10/10/03	86	Genomic			99 %
ss1261962	KWOK\|OVLP-000804-637885		rev/B	G/T	tcagggttttgcgtatatgtgttttatttt	aagttgtacaactcctggttgatgacagtc	09/02/00	10/10/03	86	Genomic			97 %
ss1282930	KWOK\|OVLP-000804-614958		fwd/T	A/C	gactgtcatcaaccaggagttgtacaactt	aaaataaaacacatatacgcaaaaccctga	09/02/00	10/10/03	86	Genomic			89 %
ss1767072	KWOK\|OVLP-000925-149252		rev/B	G/T	tcagggttttgcgtatatgtgttttatttt	aagttgtacaactcctggttgatgacagtc	10/05/00	04/07/04	87	Genomic			99 %
ss1768956	KWOK\|OVLP-000925-182411		rev/B	G/T	tcagggttttgcgtatatgtgttttatttt	aagttgtacaactcctggttgatgacagtc	10/05/00	10/10/03	87	Genomic			99 %
ss1770649	KWOK\|OVLP-000925-201751		fwd/T	A/C	gactgtcatcaaccaggagttgtacaactt	aaaataaaacacatatacgcaaaaccctga	10/05/00	10/10/03	87	Genomic			99 %
ss1824106	KWOK\|OVLP-000925-204929		rev/B	G/T	tcagggttttgcgtatatgtgttttatttt	aagttgtacaactcctggttgatgacagtc	10/05/00	10/10/03	87	Genomic			97 %
ss1857508	KWOK\|OVLP-000925-208963		fwd/T	A/C	gactgtcatcaaccaggagttgtacaactt	aaaataaaacacatatacgcaaaaccctga	10/06/00	10/10/03	87	Genomic			89 %
ss10191822	BCM_SSAHASNP\|chr5.NT_023148.11_4365861		rev/B	G/T	tcagggttttgcgtatatgtgttttatttt	aagttgtacaactcctggttgatgacagtc	06/27/03	10/10/03	116	Genomic			unknown
ss66619266	ILLUMINA\|HumanHap300v1.1_rs469532		fwd/B	A/C	gactgtcatcaaccaggagttgtacaactt	aaaataaaacacatatacgcaaaaccctga	11/09/06	11/09/06	127	Genomic			unknown
ss67360539	ILLUMINA\|HumanHap550v1.1_rs469532		fwd/T	A/C	gactgtcatcaaccaggagttgtacaactt	aaaataaaacacatatacgcaaaaccctga	11/14/06	11/14/06	127	Genomic			unknown
ss67747641	ILLUMINA\|HumanHap650Yv1.0_rs469532		fwd/T	A/C	gactgtcatcaaccaggagttgtacaactt	aaaataaaacacatatacgcaaaaccctga	11/14/06	11/14/06	127	Genomic			unknown
ss70816852	ILLUMINA\|HumanHap550v3.0__rs469532		rev/B	G/T	tcagggttttgcgtatatgtgttttatttt	aagttgtacaactcctggttgatgacagtc	04/20/07	03/30/08	130	Genomic			unknown
ss71397838	ILLUMINA\|HumanHap650Yv3.0_rs469532		fwd/T	A/C	gactgtcatcaaccaggagttgtacaactt	aaaataaaacacatatacgcaaaaccctga	04/23/07	04/23/07	127	Genomic			unknown
ss75440593	ILLUMINA\|ILMN_Human_1M_rs469532		fwd/T	A/C	gactgtcatcaaccaggagttgtacaactt	aaaataaaacacatatacgcaaaaccctga	08/28/07	08/29/07	129	Genomic			unknown
ss79190185	ILLUMINA\|HumanHap300v2.0_rs469532		fwd/T	A/C	gactgtcatcaaccaggagttgtacaactt	aaaataaaacacatatacgcaaaaccctga	04/18/07	11/18/07	130	Genomic			unknown
ss83459741	KRIBB_YJKIM\|KHS466595		fwd/T	A/C	gactgtcatcaaccaggagttgtacaactt	aaaataaaacacatatacgcaaaaccctga	12/04/07	12/05/07	130	Genomic			unknown

Fasta sequence (Legend)

>gnl|dbSNP|rs469532|allelePos=401|totalLen=601|taxid=9606|snpclass=1|alleles='A/C'|mol=Genomic|build=130

 CATGATCAGA TTCTTATTTA ATAACACATC TCAAATATTG AAATAAAGGC AATCATGGGT
 GAAAAAAAAT CCTTTCCTCA CAACATTTAT AAAACAGCCA aatgtgaact ccatgaaggc
 aggggccagg cctgtttgag ttgccaccca tccccatccc catccccgga gccttaacat
 agtagttgct taacaagtat ctgagataaa tgcatgaatT TGTACATGAA TAAACACAAG
 AGTATTATTT TATGGCACAA AACCAATATT GTCTGAGTTT TATTATTTGA TCGTCAGAAA
 TTCTGTTGAC AGCAGAGGTC AGAAAACTGA TTAGAATAAC GCAATTTAAA CTTTAGGTCA
 TTTACGTTAT GACTGTCATC AACCAGGAGT TGTACAACTT
 M
 AAAATAAAAC ACATATACGC AAAACCCTGA GCTGCTTCCT GTAAGACAAC CGCAACAAAA
 CAAGGCTGCT CACAAGGGGC TTTTCTAAGA AAGACATGGA CATTCTTTAA ACACCTTTTA
 TAGGTCTATT GAATACAGGC TTCCATTTTT CTTTCTGTAA TGATGGATTA TTCACTTCAG
 GAAATGAATA TTCAGATGTC

GeneView via analysis of contig annotation: CAST calpastatin

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_023148->NM_001042440

reference

NT_023148->NM_001042441

reference

NT_023148->NM_001042442

reference

NT_023148->NM_001042443

reference

NT_023148->NM_001042444

reference

NT_023148->NM_001042445

reference

NT_023148->NM_001042446

reference

NT_023148->NM_001750

reference

NT_023148->NM_173060

reference

NT_023148->NM_173063

HuRef

NW_001838952->NM_001042440

HuRef

NW_001838952->NM_001042441

HuRef

NW_001838952->NM_001042442

HuRef

NW_001838952->NM_001042443

HuRef

NW_001838952->NM_001042444

HuRef

NW_001838952->NM_001042445

HuRef

NW_001838952->NM_001042446

HuRef

NW_001838952->NM_001750

HuRef

NW_001838952->NM_173060

HuRef

NW_001838952->NM_173063

Celera

NW_922729->NM_001042440

Celera

NW_922729->NM_001042441

Celera

NW_922729->NM_001042442

Celera

NW_922729->NM_001042443

Celera

NW_922729->NM_001042444

Celera

NW_922729->NM_001042445

Celera

NW_922729->NM_001042446

Celera

NW_922729->NM_001750

Celera

NW_922729->NM_173060

Celera

NW_922729->NM_173063

"

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	mRNA pos	Function	dbSNP allele	Protein residue	Codon pos	Amino acid pos


reference	NT_023148->NM_001042440->NP_001035905	4365862	forward		intron

reference	NT_023148->NM_001042441->NP_001035906	4365862	forward		intron

reference	NT_023148->NM_001042442->NP_001035907	4365862	forward		intron

reference	NT_023148->NM_001042443->NP_001035908	4365862	forward		intron

reference	NT_023148->NM_001042444->NP_001035909	4365862	forward		intron

reference	NT_023148->NM_001042445->NP_001035910	4365862	forward		intron

reference	NT_023148->NM_001042446->NP_001035911	4365862	forward		intron

reference	NT_023148->NM_001750->NP_001741	4365862	forward		intron

reference	NT_023148->NM_173060->NP_775083	4365862	forward		intron

reference	NT_023148->NM_173063->NP_775086	4365862	forward		intron

HuRef	NW_001838952->NM_001042440->NP_001035905	42734469	reverse		intron

HuRef	NW_001838952->NM_001042441->NP_001035906	42734469	reverse		intron

HuRef	NW_001838952->NM_001042442->NP_001035907	42734469	reverse		intron

HuRef	NW_001838952->NM_001042443->NP_001035908	42734469	reverse		intron

HuRef	NW_001838952->NM_001042444->NP_001035909	42734469	reverse		intron

HuRef	NW_001838952->NM_001042445->NP_001035910	42734469	reverse		intron

HuRef	NW_001838952->NM_001042446->NP_001035911	42734469	reverse		intron

HuRef	NW_001838952->NM_001750->NP_001741	42734469	reverse		intron

HuRef	NW_001838952->NM_173060->NP_775083	42734469	reverse		intron

HuRef	NW_001838952->NM_173063->NP_775086	42734469	reverse		intron

Celera	NW_922729->NM_001042440->NP_001035905	25336273	forward		intron

Celera	NW_922729->NM_001042441->NP_001035906	25336273	forward		intron

Celera	NW_922729->NM_001042442->NP_001035907	25336273	forward		intron

Celera	NW_922729->NM_001042443->NP_001035908	25336273	forward		intron

Celera	NW_922729->NM_001042444->NP_001035909	25336273	forward		intron

Celera	NW_922729->NM_001042445->NP_001035910	25336273	forward		intron

Celera	NW_922729->NM_001042446->NP_001035911	25336273	forward		intron

Celera	NW_922729->NM_001750->NP_001741	25336273	forward		intron

Celera	NW_922729->NM_173060->NP_775083	25336273	forward		intron

Celera	NW_922729->NM_173063->NP_775086	25336273	forward		intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs469532 maps exactly once on NCBI human chromosome 5

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
5	NW_001838952.2	42734469	91242239	plus	A	alt_assembly_8	HuRef	HuRef	view	400
5	NW_922729.1	25336273	91936429	minus	T	alt_assembly_1	Celera	Celera	view	400
5	NT_023148.12	4365862	96077746	minus	T	ref_assembly	reference	reference	view	400

NCBI Resource Links

Submitter-Referenced
GenBank
NT_023148 AC008963 AC008963.5 AC020900.4 AC020923 AC020923.5 AC026435 AC026435.2

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC008906.5 AC020900.5 NC_000005.8	AC008452.5 AC008508.5 AC008963.5 AC026435.2

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/C	C/C	HWP	A	C
ss1767072	HapMap-CEU	European	120	IG	0.550	0.400	0.050	0.655	0.750	0.250

	HapMap-HCB	Asian	90	IG	0.511	0.400	0.089	1.000	0.711	0.289

	HapMap-JPT	Asian	90	IG	0.622	0.289	0.089	0.251	0.767	0.233

	HapMap-YRI	Sub-Saharan African	120	IG	0.783	0.217		0.371	0.892	0.108

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.337+/-0.234	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, NCBI

UNKNOWN

UNKNOWN

UNKNOWN

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Revised: May 25, 2006 1:38 PM .