Reference SNP(refSNP) Cluster Report: rs801630

Reference SNP(refSNP) Cluster Report: rs801630

refSNP ID: rs801630
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	86/129
Map to Genome Build:	36.3

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

HGVS Names
NM_014346.1:c.62+6672C>A
NT_011523.11:g.2436123C>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss8305908 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs801630 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
ss1012331	KWOK\|OVLP-000804-204254	fwd/B	G/T	ggaagcgggacctgtgtaaggaggacatga	cattccacccagtgagggccttgctactct	09/02/00	10/10/03	86	Genomic	97 %
ss2052193	KWOK\|OVLP-000925-527319	fwd/B	G/T	ggaagcgggacctgtgtaaggaggacatga	cattccacccagtgagggccttgctactct	10/06/00	10/10/03	87	Genomic	97 %
ss3882651	SC_JCM\|AL118516.10_50602	rev/T	A/C	agagtagcaaggccctcactgggtggaatg	tcatgtcctccttacacaggtcccgcttcc	09/25/01	10/10/03	100	Genomic	unknown
ss8305908	SC_SNP\|NT_011523.8_677568	rev/T	A/C	agagtagcaaggccctcactgggtggaatg	tcatgtcctccttacacaggtcccgcttcc	04/17/03	08/05/04	114	Genomic	unknown
ss13392707	SC_SNP\|NT_011523.9_745301	rev/T	A/C	agagtagcaaggccctcactgggtggaatg	tcatgtcctccttacacaggtcccgcttcc	10/23/03	10/31/03	119	Genomic	unknown
ss23791360	PERLEGEN\|afd0142752	rev/T	A/C	agagtagcaaggccctcactgggtggaatg	tcatgtcctccttacacaggtcccgcttcc	08/10/04	09/13/04	123	Genomic	unknown
ss44322572	ABI\|hCV8824333	rev/T	A/C	agagtagcaaggccctcactgggtggaatg	tcatgtcctccttacacaggtcccgcttcc	07/18/05	11/03/06	126	Genomic	unknown
ss66325124	AFFY\|SNP_A-1907769	fwd/B	G/T	tgtaaggaggacatga	cattccacccagtgag	10/29/06	08/14/07	127	Genomic	unknown
ss76017200	AFFY\|AFFY_6_1M_SNP_A-1907769	fwd/B	G/T	tgtaaggaggacatga	cattccacccagtgag	08/28/07	08/29/07	129	Genomic	unknown

Fasta sequence (Legend)

 ACCCCCAGCA CCCCGCCCAT CAGTGAATCC TGAGTGTGCC ATGTGTACCC TGAACATGCC
 CGATCCTCTC CAACCCCACA GCATCTGGCC TCGGCCTCCT CAGAAGCCCA CCAGTTTCCT
 CTCTCGCCCT CTCTTCAAGG ATGACAAACA GTGTCACAGT ATCACACCCC TCCCTGTTTA
 AAACCCTTCA ACACTCTCTC ATGGCTCTTA GGACCACAGC TCAGATCTTC ACCATGGCCT
 TGGAAGCAGC TCCAGTGCCT GCTCACCACC CTCCATGCCC CTCCTCCCCA GTCAAGCGCT
 CCCCACTCCT ATACACCCTC CCCTGACCTC AGCAGCCAGA TCGGTTCCTG CTGTACAGCC
 AGGTCTCGGC GGAAGCGGGA CCTGTGTAAG GAGGACATGA
 K
 CATTCCACCC AGTGAGGGCC TTGCTACTCT GCCAGGGTCC CGGGACTGCC ACCTGCCCAG
 CACTGCAGTC TGTGCGCATG TGTTCACAGG GCAGGCGTCC AGCCGTGAAG AGCCACATGG
 CTTGctcagc acgcaccaca gcacctggca caggagagga gctcgtaaac gttttccaaa
 tgaatTCATT ATCCCCAACA GTGCCTCTCC TTCGGCTGAG GACGGACTGT GGCCTATTCA
 GCCGACCGTC TGATTTGCTC ACAGACATCT CGTGGCTCTG GCAATGTAAG CTGAAGGCTG
 TCAGAGCCAC ATCACTAAGA ACCCTCTTGT GCTCCAGCTT TATCCCAGCA CTCACATCCT
 TGCCATGCTC AATTTGGGCC TTTCTTGCTA CCATAACACT

GeneView

GeneView via analysis of contig annotation: TBC1D22A TBC1 domain family, member 22A

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_011523->NM_014346

function

HuRef

NW_001838753->NM_014346

function

Celera

NW_927650->NM_014346

function

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


reference	NT_011523->NM_014346->NP_055161	2436123	forward	intron

HuRef	NW_001838753->NM_014346->NP_055161	785855	forward	intron

Celera	NW_927650->NM_014346->NP_055161	4260739	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs801630 maps exactly once on NCBI human chromosome 22

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
22	NW_001838753.1	785855	30110388	minus	C	alt_assembly_8	HuRef	HuRef	view	400
22	NW_927650.1	4260739	31081106	minus	C	alt_assembly_1	Celera	Celera	view	400
22	NT_011523.11	2436123	45544081	minus	C	ref_assembly	reference	reference	view	400

NCBI Resource Links

Submitter-Referenced
GenBank
NT_011523 AC007689 AL118516.10

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AL118516.10 NC_000022.9	AC007689.13

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	G/G	G/T	T/T	HWP	G	T
ss23791360	AFD_EUR_PANEL	European	46	IG	0.826	0.174		0.655	0.913	0.087

	AFD_AFR_PANEL	African American	44	IG	0.682	0.318		0.403	0.841	0.159

	AFD_CHN_PANEL	Asian	48	IG	1.000				1.000

ss44322572	AoD_African_American		90	AF					0.800	0.200

	AoD_Caucasian		92	AF					0.920	0.080

ss66325124	HapMap-CEU	European	118	GF	0.746	0.254			0.873	0.127

	HapMap-HCB	Asian	90	GF	0.933	0.067			0.967	0.033

	HapMap-JPT	Asian	90	GF	0.956	0.044			0.978	0.022

	HapMap-YRI	Sub-Saharan African	120	GF	0.483	0.500	0.017		0.733	0.267

ss8305908	HapMap-CEU	European	120	IG	0.733	0.250	0.017	1.000	0.858	0.142

	HapMap-HCB	Asian	90	IG	0.933	0.067		1.000	0.967	0.033

	HapMap-JPT	Asian	88	IG	0.955	0.045		1.000	0.977	0.023

	HapMap-YRI	Sub-Saharan African	120	IG	0.467	0.483	0.050	0.200	0.708	0.292

Concordant Genotype	Total Sample	G/G	G/T	T/T
ss23791360	70
ss66325124	263	191	70	2
ss8305908	264

RefSNP Genotype Summary	Total Individual	G/G	G/T	T/T
rs801630	332	191	70	2

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
399	ss8305908	A/A	CSHL-HAPMAP	HapMap-CEU	NA10830	CEPH1408.01	r23_ch22_CEU_illumina:golden_gate_1.0.0	961586
399	ss23791360	N/N	PERLEGEN	AFD_EUR_PANEL	NA10830		71_IND_CHR_22
399	ss66325124	G/T	CSHL-HAPMAP	HapMap-CEU	NA10830	CEPH1408.01	chr22-HapMap-CEU
5142	ss8305908	A/A	CSHL-HAPMAP	HapMap-YRI	NA19194	YOR112.01	r23_ch22_YRI_illumina:golden_gate_1.1.0	961586
5142	ss66325124	G/T	CSHL-HAPMAP	HapMap-YRI	NA19194	YOR112.01	chr22-HapMap-YRI
5146	ss8305908	A/A	CSHL-HAPMAP	HapMap-YRI	NA19238	YOR117.02	r23_ch22_YRI_illumina:golden_gate_1.1.0	961586
5146	ss66325124	G/T	CSHL-HAPMAP	HapMap-YRI	NA19238	YOR117.02	chr22-HapMap-YRI
5267	ss8305908	A/C	CSHL-HAPMAP	HapMap-YRI	NA18913	YOR028.03	r23_ch22_YRI_illumina:golden_gate_1.1.0	961586
5267	ss66325124	G/G	CSHL-HAPMAP	HapMap-YRI	NA18913	YOR028.03	chr22-HapMap-YRI
5279	ss8305908	A/A	CSHL-HAPMAP	HapMap-YRI	NA19200	YOR045.03	r23_ch22_YRI_illumina:golden_gate_1.1.0	961586
5279	ss66325124	G/T	CSHL-HAPMAP	HapMap-YRI	NA19200	YOR045.03	chr22-HapMap-YRI
5295	ss8305908	A/A	CSHL-HAPMAP	HapMap-YRI	NA19221	YOR058.01	r23_ch22_YRI_illumina:golden_gate_1.1.0	961586
5295	ss66325124	G/T	CSHL-HAPMAP	HapMap-YRI	NA19221	YOR058.01	chr22-HapMap-YRI

Genotype data submitted for	341	samples from	332	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

Validated by: PERLEGEN

DoubleHit found by: BCM_SSAHASNP

UNKNOWN

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Revised: May 25, 2006 1:38 PM .