Reference SNP(refSNP) Cluster Report: rs897416

Reference SNP(refSNP) Cluster Report: rs897416

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	86/130
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_006771.3:c.1267T>C
NP_006762.3:p.Ser423Pro
NT_010755.15:g.3318064A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss1328204 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs897416 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
ss1328204	TSC-CSHL\|TSC0171531	fwd/B	C/T	tgcagactcccctgcaatccgtgctccacg	ctccctcctgcgtgactgccccctgtgctc	09/06/00	05/16/04	86	Genomic	95 %
ss5787028	SC_JCM\|NT_024901.10_1279501	rev/T	A/G	gagcacagggggcagtcacgcaggagggag	cgtggagcacggattgcaggggagtctgca	01/10/03	10/10/03	111	Genomic	unknown
ss6619856	WI_SSAHASNP\|NT_010840.9_95657	fwd/B	C/T	tgcagactcccctgcaatccgtgctccacg	ctccctcctgcgtgactgccccctgtgctc	02/12/03	10/10/03	111	Genomic	unknown
ss12412248	WI_SSAHASNP\|chr17.NT_010755.13_3316490	rev/T	A/G	gagcacagggggcagtcacgcaggagggag	cgtggagcacggattgcaggggagtctgca	07/04/03	10/10/03	116	Genomic	unknown
ss14302910	BCM_SSAHASNP\|chr17.NT_010755.14_3316266	rev/T	A/G	gagcacagggggcagtcacgcaggagggag	cgtggagcacggattgcaggggagtctgca	11/05/03	11/22/03	119	Genomic	unknown
ss20037608	CSHL-HAPMAP\|CSHL-HuFF-200402.chr17.NT_010755.14_3316266	rev/T	A/G	gagcacagggggcagtcacgcaggagggag	cgtggagcacggattgcaggggagtctgca	02/21/04	03/04/04	120	Genomic	unknown
ss44044016	ABI\|hCV1838297	rev/T	A/G	gagcacagggggcagtcacgcaggagggag	cgtggagcacggattgcaggggagtctgca	07/18/05	07/18/05	126	Genomic	unknown
ss66044479	AFFY\|SNP_A-1804265	rev/T	A/G	gtcacgcaggagggag	cgtggagcacggattg	10/27/06	08/14/07	127	Genomic	unknown
ss69196290	PERLEGEN\|PGP02484596	rev/T	A/G	gagcacagggggcagtcacgcaggagggag	cgtggagcacggattgcaggggagtctgca	01/30/07	08/14/07	127	Genomic	unknown
ss74907534	ILLUMINA\|ILMN_Human_1M_rs897416	fwd/B	C/T	tgcagactcccctgcaatccgtgctccacg	ctccctcctgcgtgactgccccctgtgctc	08/28/07	08/29/07	129	Genomic	unknown
ss75942118	AFFY\|AFFY_6_1M_SNP_A-1804265	rev/T	A/G	gtcacgcaggagggag	cgtggagcacggattg	08/28/07	08/29/07	129	Genomic	unknown
ss78237466	HGSV\|Cor12878_SNV_20070510.chr17_36847294	rev/T	A/G	gagcacagggggcagtcacgcaggagggag	cgtggagcacggattgcaggggagtctgca	10/17/07	10/18/07	129	Genomic	unknown
ss81443504	KRIBB_YJKIM\|KHS69689	fwd/B	C/T	tgcagactcccctgcaatccgtgctccacg	ctccctcctgcgtgactgccccctgtgctc	11/30/07	11/30/07	130	Genomic	unknown
ss82698300	HGSV\|Cor18956_SNV_20070510.chr17_36847294	rev/T	A/G	gagcacagggggcagtcacgcaggagggag	cgtggagcacggattgcaggggagtctgca	11/30/07	12/03/07	130	Genomic	unknown
ss90587558	BCMHGSC_JDW\|JWB-1021154	rev/T	A/G	gagcacagggggcagtcacgcaggagggag	cgtggagcacggattgcaggggagtctgca	02/26/08	02/29/08	129	Genomic	unknown
ss106506733	BGI\|BGI_rs897416	rev/T	A/G	gagcacagggggcagtcacgcaggagggag	cgtggagcacggattgcaggggagtctgca	09/15/08	06/18/09	130	Genomic	unknown
ss109762605	1000GENOMES\|CEU.trio.12.15.2008_3398404_chr17_36847294	rev/T	A/G	gagcacagggggcagtcacgcaggagggag	cgtggagcacggattgcaggggagtctgca	12/15/08	12/16/08	130	Genomic	unknown
ss113530646	1000GENOMES\|NA19240_2008_12_16_3057595_chr17_36847294	rev/T	A/G	gagcacagggggcagtcacgcaggagggag	cgtggagcacggattgcaggggagtctgca	12/18/08	12/18/08	130	Genomic	unknown
ss118053821	ILLUMINA-UK\|NA18507_000042972_NCBI36.1_chr17_36847294	rev/T	A/G	gagcacagggggcagtcacgcaggagggag	cgtggagcacggattgcaggggagtctgca	01/20/09	01/20/09	130	Genomic	99 %

Fasta sequence (Legend)

 TCCATGTTCT GTTGTTTTGC AGTGGGGACT CCTTCCTCAT GCCCCCACAT GGCACTGAGA
 CCCCATTCAT TTCTTGCCTC TCACTTCCCT CACCTTGTCT CTCTGCAGAC TCCCCTGCAA
 TCCGTGCTCC ACG
 Y
 CTCCCTCCTG CGTGACTGCC CCCTGTGCTC CTCGCCCAAG CTGTGGCCCC TGCACCACCT
 GTGGGCCCAC CTGTGGAGCC AGCACCACCG GAAGCCGATT CTGAATTCCT GTGGACCCAC
 AGGGGCTGGC TAAGGCGAGG GATACCCAAA GAGAGATGCT TGTTATACCT TTAGAAAATC
 TGGCTTCTAA CTTTCTGTAT GTATAGGCCT GTCCAAAGGC TATGAGATAC CAGGGACAGT
 GGAATCTTGA TGGAAATCCT TCCTTTCCTG CTCTTGGTTT TCCCAGGTGA GCTCTATGCC
 CTCAGTGGCT GGATTGCAGC CACCCATGGT GGCTCAGAAT ATCTGGATTG GAGAGGCATA
 AGGTTGAAAA GCATTTTGGA GTAGGAACAC GGCATGATTT AAAATTGCAC TTGCACTTCA
 AGAACACCAA CTTTAACTTG AAATTTTTAT AGTTTATGAC AAAGGAAGTG AAGAACAGAC
 TTCACTGTCT GAGATTTCCC ACATTTC

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
GenBank
NT_024901.10

dbSNP Blast Analysis

UniGene Cluster ID
248188

Population Diversity

	Sample Ascertainment				Genotype Detail							Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	C/C	C/T	G/G	T/T	HWP	A	C	G	T
ss1328204	CEPH		184	AF									0.960		0.040

	HapMap-CEU	European	120	IG			0.883	0.117			0.655		0.942		0.058

	HapMap-HCB	Asian	90	IG			0.978	0.022			1.000		0.989		0.011

	HapMap-JPT	Asian	88	IG			1.000						1.000

	HapMap-YRI	Sub-Saharan African	120	IG			0.900	0.100			0.752		0.950		0.050

	EURAME		32	GF	0.688	0.312					0.479	0.844		0.156

	AFRAME		30	GF	0.800	0.200					0.752	0.900		0.100

ss66044479	HapMap-CEU	European	118	GF			0.881	0.085		0.034			0.924		0.076

	HapMap-HCB	Asian	90	GF			0.978	0.022					0.989		0.011

	HapMap-JPT	Asian	90	GF			0.933	0.067					0.967		0.033

	HapMap-YRI	Sub-Saharan African	120	GF			0.900	0.083		0.017			0.942		0.058

ss69196290	HapMap-CEU	European	120	GF			0.883	0.117					0.942		0.058

	HapMap-HCB	Asian	90	GF			0.956	0.044					0.978		0.022

	HapMap-JPT	Asian	90	GF			1.000						1.000

	HapMap-YRI	Sub-Saharan African	120	GF			0.900	0.100					0.950		0.050

ss75942118	ICMHP		8	IG			0.750	0.250					0.875		0.125

Concordant Genotype	Total Sample	A/G	C/C	C/T	G/G	T/T
ss1328204	1113		930	149		9
ss66044479	260	16			244
ss75942118	6	2			4

RefSNP Genotype Summary	Total Individual	A/A	A/G	C/C	C/T	G/G	T/T
rs897416	1127		18	930	149	248	9

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
348	ss1328204	N/N	CSHL-HAPMAP	HapMap-CEU	NA10860	CEPH1362.01	r27_ch17_CEU_illumina:human_1m_beadchip
348	ss66044479	A/A	CSHL-HAPMAP	HapMap-CEU	NA10860	CEPH1362.01	chr17-HapMap-CEU
439	ss1328204	C/T	CSHL-HAPMAP	HapMap-CEU	NA12249	CEPH1416.12	r27_ch17_CEU_illumina:human_1m_beadchip
439	ss66044479	A/A	CSHL-HAPMAP	HapMap-CEU	NA12249	CEPH1416.12	chr17-HapMap-CEU
547	ss1328204	C/T	CSHL-HAPMAP	HapMap-CEU	NA12762	CEPH1447.11	r27_ch17_CEU_illumina:human_1m_beadchip
547	ss66044479	A/A	CSHL-HAPMAP	HapMap-CEU	NA12762	CEPH1447.11	chr17-HapMap-CEU
5137	ss1328204	C/T	CSHL-HAPMAP	HapMap-YRI	NA19131	YOR101.02	r27_ch17_YRI_illumina:human_1m_beadchip
5137	ss66044479	A/A	CSHL-HAPMAP	HapMap-YRI	NA19131	YOR101.02	chr17-HapMap-YRI
5178	ss1328204	C/C	CSHL-HAPMAP	HapMap-HCB	NA18622	CH18622	r27_ch17_CHB_illumina:human_1m_beadchip
5178	ss66044479	G/G	CSHL-HAPMAP	HapMap-HCB	NA18622	CH18622	chr17-HapMap-HCB
5198	ss1328204	C/C	CSHL-HAPMAP	HapMap-JPT	NA18944	JA18944	r27_ch17_JPT_illumina:human_1m_beadchip
5198	ss66044479	A/G	CSHL-HAPMAP	HapMap-JPT	NA18944	JA18944	chr17-HapMap-JPT
5224	ss1328204	C/C	CSHL-HAPMAP	HapMap-JPT	NA18974	JA18974	r27_ch17_JPT_illumina:human_1m_beadchip
5224	ss66044479	A/G	CSHL-HAPMAP	HapMap-JPT	NA18974	JA18974	chr17-HapMap-JPT
5227	ss1328204	C/C	CSHL-HAPMAP	HapMap-JPT	NA18991	JA18991	r27_ch17_JPT_illumina:human_1m_beadchip
5227	ss66044479	A/G	CSHL-HAPMAP	HapMap-JPT	NA18991	JA18991	chr17-HapMap-JPT
5250	ss1328204	N/N	CSHL-HAPMAP	HapMap-YRI	NA18521	YOR016.01	r27_ch17_YRI_illumina:human_1m_beadchip
5250	ss66044479	A/G	CSHL-HAPMAP	HapMap-YRI	NA18521	YOR016.01	chr17-HapMap-YRI

Genotype data submitted for	1127	samples from	1127	individuals	Individual with multiple genotypes submission:	269

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

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Revised: May 25, 2006 1:38 PM .