Reference SNP(refSNP) Cluster Report: rs2506101

Reference SNP(refSNP) Cluster Report: rs2506101

refSNP ID: rs2506101
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:	T
Clinical Association:	unknown

HGVS Names
NT_033985.6:g.629119T>C
XM_001724175.1:c.126-4329T>C

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss77725674 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2506101 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
ss3513819	SC_JCM\|AL591181.1_177773	fwd/B	C/T	tggcacaaatagtaaaaccacagttaatag	tcggactatccaaagtggcttgtcatgagg	09/24/01	10/10/03	100	Genomic	unknown
ss12985488	SC_SNP\|NT_033985.5_348120	fwd/B	C/T	tggcacaaatagtaaaaccacagttaatag	tcggactatccaaagtggcttgtcatgagg	10/22/03	10/31/03	119	Genomic	unknown
ss14276606	BCM_SSAHASNP\|chr10.NT_033985.6_629119	fwd/B	C/T	tggcacaaatagtaaaaccacagttaatag	tcggactatccaaagtggcttgtcatgagg	11/05/03	10/25/06	119	Genomic	unknown
ss15591106	SC_SNP\|NT_033985.6_629119	fwd/B	C/T	tggcacaaatagtaaaaccacagttaatag	tcggactatccaaagtggcttgtcatgagg	11/17/03	11/22/03	120	Genomic	unknown
ss24080445	PERLEGEN\|afd2238173	fwd/B	C/T	tggcacaaatagtaaaaccacagttaatag	tcggactatccaaagtggcttgtcatgagg	08/10/04	09/13/04	123	Genomic	unknown
ss66400982	AFFY\|SNP_A-2091121	rev/T	A/G	actttggatagtccga	ctattaactgtggttt	10/29/06	08/14/07	127	Genomic	unknown
ss69077306	PERLEGEN\|PGP02238173	fwd/B	C/T	tggcacaaatagtaaaaccacagttaatag	tcggactatccaaagtggcttgtcatgagg	01/30/07	08/14/07	127	Genomic	unknown
ss75056748	ILLUMINA\|ILMN_Human_1M_rs2506101	fwd/B	C/T	tggcacaaatagtaaaaccacagttaatag	tcggactatccaaagtggcttgtcatgagg	08/28/07	08/29/07	129	Genomic	unknown
ss76150025	AFFY\|AFFY_6_1M_SNP_A-2091121	rev/T	A/G	actttggatagtccga	ctattaactgtggttt	08/28/07	08/30/07	129	Genomic	unknown
ss77725674	HGSV\|Cor12156_SNV_20070510.chr10_42545812	fwd/B	C/T	tggcacaaatagtaaaaccacagttaatag	tcggactatccaaagtggcttgtcatgagg	10/09/07	10/14/07	129	Genomic	unknown
ss80891958	HGSV\|Cor18507_SNV_20070510.chr10_42545812	fwd/B	C/T	tggcacaaatagtaaaaccacagttaatag	tcggactatccaaagtggcttgtcatgagg	11/26/07	11/27/07	130	Genomic	unknown
ss88181935	BCMHGSC_JDW\|JWB-0267533	fwd/B	C/T	tggcacaaatagtaaaaccacagttaatag	tcggactatccaaagtggcttgtcatgagg	02/26/08	02/27/08	129	Genomic	unknown

Fasta sequence (Legend)

 TAGACCCCCT GGTTTTATAA ATTTCTCCAT CATATGCAGA CATTTGCCCA CTTCCAACAT
 GCATTTGAAA AATCTTCCCA TGCAAACAAA GAATTGATAG CACTTGGCAT AGCTGAGACC
 TGCAAAGCTT TATGTTTCAA CACCTGAAGT CACCTGAGAT TAAGCAAGTG TGGCACAAAT
 AGTAAAACCA CAGTTAATAG
 Y
 TCGGACTATC CAAAGTGGCT TGTCATGAGG TGAGCTTGCT CGCTTAGGGC TGATTCAAAA
 TTTTCTCTCA AACCTTTTGA AAAATAATTC TAGCAACAGC TCTCATTTCC TGAGAAGTCA
 CATCTGAGCC ATGGATCAGG TGTTGGGTGC TTCACATATT TTCTCTCTCA TCCTCCCAGT
 GATCCTGCCC TGAAGATGTT GTCAGCCTTA TTTTATAGTC GAGGAAATTC AGTCTCAGAG
 AAGCTGAGTA ACTTGGTCAA GGTCACGCAG CTAGCAAGTG CTGGAGCCAG ATTCCTCACC
 TAGCTGTCTC CTATCTTAAA GCTCCATTCT TTTCCTACTC CCACTGTAAC CTCTCATGGA
 AACCTTGATT GCTAGCAGTG TCAGAGTGGG GCCCTAAGCA TGGAATTCCT ACAAGTGGAA
 ATGTGGATGG ATGGAGATGG ATGTTAGCAC CTGCTGGG

GeneView

GeneView via analysis of contig annotation: AL022344.6 Ras suppressor protein 1 pseudogene

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_033985->XM_001724175

function

HuRef

NW_001837940->XM_001715686

function

Celera

NW_924606->XM_001714876

function

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


reference	NT_033985->XM_001724175->XP_001724227	629119	forward	intron

HuRef	NW_001837940->XM_001715686->XP_001715738	654244	forward	intron

Celera	NW_924606->XM_001714876->XP_001714928	640321	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs2506101 maps exactly once on NCBI human chromosome 10

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
10	NW_924606.1	640321	39229173	plus	T	alt_assembly_1	Celera	Celera	view	200
10	NW_001837940.1	654244	39752525	plus	T	alt_assembly_8	HuRef	HuRef	view	200
10	NT_033985.6	629119	42545812	plus	T	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_033985 AL023808 AL355583 AL590986 AL591132

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AL022344.3	AL023808.4 AL355583.8 AL590986.4 AL591132.1

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	N	T
ss14276606	HapMap-CEU	European	120	IG	0.467	0.450	0.083	0.752	0.692		0.308

	HapMap-HCB	Asian	90	IG	0.267	0.600	0.133	0.150	0.567		0.433

	HapMap-JPT	Asian	88	IG	0.318	0.591	0.091	0.150	0.614		0.386

	HapMap-YRI	Sub-Saharan African	120	IG	0.250	0.617	0.133	0.100	0.558		0.442

	CHMJ	Asian	74	IG					0.554	0.014	0.432

ss24080445	AFD_EUR_PANEL	European	48	IG	0.333	0.583	0.083	0.251	0.625		0.375

	AFD_AFR_PANEL	African American	44	IG	0.455	0.364	0.182	0.317	0.636		0.364

	AFD_CHN_PANEL	Asian	48	IG	0.250	0.583	0.167	0.403	0.542		0.458

ss66400982	HapMap-CEU	European	118	GF	0.475	0.441	0.085		0.695		0.305

	HapMap-HCB	Asian	90	GF	0.267	0.600	0.133		0.567		0.433

	HapMap-JPT	Asian	90	GF	0.311	0.600	0.089		0.611		0.389

	HapMap-YRI	Sub-Saharan African	120	GF	0.250	0.617	0.133		0.558		0.442

ss69077306	HapMap-CEU	European	120	GF	0.433	0.483	0.083		0.675		0.325

	HapMap-HCB	Asian	90	GF	0.200	0.667	0.133		0.533		0.467

	HapMap-JPT	Asian	90	GF	0.289	0.622	0.089		0.600		0.400

	HapMap-YRI	Sub-Saharan African	120	GF	0.233	0.650	0.117		0.558		0.442

Concordant Genotype	Total Sample	C/C	C/T	T/T
ss14276606	255	83	141	30
ss24080445	71	24	36	10
ss66400982	254
ss69077306	255	83	142	30

RefSNP Genotype Summary	Total Individual	C/C	C/T	T/T
rs2506101	332	105	173	38

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
467	ss14276606	C/C	CSHL-HAPMAP	HapMap-CEU	NA12006	CEPH1420.12	r23_ch10_CEU_illumina:golden_gate_1.0.0	787949
467	ss66400982	G/G	CSHL-HAPMAP	HapMap-CEU	NA12006	CEPH1420.12	chr10-HapMap-CEU
467	ss69077306	C/T	CSHL-HAPMAP	HapMap-CEU	NA12006	CEPH1420.12	chr10-HapMap-CEU
545	ss14276606	C/C	CSHL-HAPMAP	HapMap-CEU	NA12760	CEPH1447.09	r23_ch10_CEU_illumina:golden_gate_1.0.0	787949
545	ss66400982	G/G	CSHL-HAPMAP	HapMap-CEU	NA12760	CEPH1447.09	chr10-HapMap-CEU
545	ss69077306	C/T	CSHL-HAPMAP	HapMap-CEU	NA12760	CEPH1447.09	chr10-HapMap-CEU
5145	ss14276606	T/T	CSHL-HAPMAP	HapMap-YRI	NA19240	YOR117.01	r23_ch10_YRI_illumina:golden_gate_1.0.0	787949
5145	ss66400982	A/A	CSHL-HAPMAP	HapMap-YRI	NA19240	YOR117.01	chr10-HapMap-YRI
5145	ss69077306	C/T	CSHL-HAPMAP	HapMap-YRI	NA19240	YOR117.01	chr10-HapMap-YRI
5152	ss14276606	C/C	CSHL-HAPMAP	HapMap-HCB	NA18532	CH18532	r23_ch10_HCB_illumina:golden_gate_1.0.0	787949
5152	ss66400982	G/G	CSHL-HAPMAP	HapMap-HCB	NA18532	CH18532	chr10-HapMap-HCB
5152	ss69077306	C/T	CSHL-HAPMAP	HapMap-HCB	NA18532	CH18532	chr10-HapMap-HCB
5153	ss14276606	C/C	CSHL-HAPMAP	HapMap-HCB	NA18561	CH18561	r23_ch10_HCB_illumina:golden_gate_1.0.0	787949
5153	ss66400982	G/G	CSHL-HAPMAP	HapMap-HCB	NA18561	CH18561	chr10-HapMap-HCB
5153	ss69077306	C/T	CSHL-HAPMAP	HapMap-HCB	NA18561	CH18561	chr10-HapMap-HCB
5164	ss14276606	C/C	CSHL-HAPMAP	HapMap-HCB	NA18550	CH18550	r23_ch10_HCB_illumina:golden_gate_1.0.0	787949
5164	ss66400982	G/G	CSHL-HAPMAP	HapMap-HCB	NA18550	CH18550	chr10-HapMap-HCB
5164	ss69077306	C/T	CSHL-HAPMAP	HapMap-HCB	NA18550	CH18550	chr10-HapMap-HCB
5224	ss14276606	C/C	CSHL-HAPMAP	HapMap-JPT	NA18974	JA18974	r23_ch10_JPT_illumina:golden_gate_1.0.0	787949
5224	ss66400982	G/G	CSHL-HAPMAP	HapMap-JPT	NA18974	JA18974	chr10-HapMap-JPT
5224	ss69077306	C/T	CSHL-HAPMAP	HapMap-JPT	NA18974	JA18974	chr10-HapMap-JPT
5251	ss14276606	C/T	CSHL-HAPMAP	HapMap-YRI	NA18523	YOR016.02	r23_ch10_YRI_illumina:golden_gate_1.0.0	787949
5251	ss66400982	A/G	CSHL-HAPMAP	HapMap-YRI	NA18523	YOR016.02	chr10-HapMap-YRI
5251	ss69077306	T/T	CSHL-HAPMAP	HapMap-YRI	NA18523	YOR016.02	chr10-HapMap-YRI
5252	ss14276606	C/C	CSHL-HAPMAP	HapMap-YRI	NA18522	YOR016.03	r23_ch10_YRI_illumina:golden_gate_1.0.0	787949
5252	ss66400982	G/G	CSHL-HAPMAP	HapMap-YRI	NA18522	YOR016.03	chr10-HapMap-YRI
5252	ss69077306	C/T	CSHL-HAPMAP	HapMap-YRI	NA18522	YOR016.03	chr10-HapMap-YRI
5256	ss14276606	T/T	CSHL-HAPMAP	HapMap-YRI	NA18854	YOR018.01	r23_ch10_YRI_illumina:golden_gate_1.0.0	787949
5256	ss66400982	A/A	CSHL-HAPMAP	HapMap-YRI	NA18854	YOR018.01	chr10-HapMap-YRI
5256	ss69077306	C/T	CSHL-HAPMAP	HapMap-YRI	NA18854	YOR018.01	chr10-HapMap-YRI
5274	ss14276606	C/C	CSHL-HAPMAP	HapMap-YRI	NA19139	YOR043.01	r23_ch10_YRI_illumina:golden_gate_1.0.0	787949
5274	ss66400982	G/G	CSHL-HAPMAP	HapMap-YRI	NA19139	YOR043.01	chr10-HapMap-YRI
5274	ss69077306	C/T	CSHL-HAPMAP	HapMap-YRI	NA19139	YOR043.01	chr10-HapMap-YRI
5290	ss14276606	T/T	CSHL-HAPMAP	HapMap-YRI	NA19206	YOR051.02	r23_ch10_YRI_illumina:golden_gate_1.0.0	787949
5290	ss66400982	A/A	CSHL-HAPMAP	HapMap-YRI	NA19206	YOR051.02	chr10-HapMap-YRI
5290	ss69077306	C/T	CSHL-HAPMAP	HapMap-YRI	NA19206	YOR051.02	chr10-HapMap-YRI
5301	ss14276606	C/C	CSHL-HAPMAP	HapMap-YRI	NA19142	YOR071.01	r23_ch10_YRI_illumina:golden_gate_1.0.0	787949
5301	ss66400982	G/G	CSHL-HAPMAP	HapMap-YRI	NA19142	YOR071.01	chr10-HapMap-YRI
5301	ss69077306	C/T	CSHL-HAPMAP	HapMap-YRI	NA19142	YOR071.01	chr10-HapMap-YRI
5304	ss14276606	C/C	CSHL-HAPMAP	HapMap-YRI	NA19154	YOR072.01	r23_ch10_YRI_illumina:golden_gate_1.0.0	787949
5304	ss66400982	G/G	CSHL-HAPMAP	HapMap-YRI	NA19154	YOR072.01	chr10-HapMap-YRI
5304	ss69077306	C/T	CSHL-HAPMAP	HapMap-YRI	NA19154	YOR072.01	chr10-HapMap-YRI
5309	ss14276606	T/T	CSHL-HAPMAP	HapMap-YRI	NA19144	YOR074.03	r23_ch10_YRI_illumina:golden_gate_1.0.0	787949
5309	ss66400982	A/A	CSHL-HAPMAP	HapMap-YRI	NA19144	YOR074.03	chr10-HapMap-YRI
5309	ss69077306	C/T	CSHL-HAPMAP	HapMap-YRI	NA19144	YOR074.03	chr10-HapMap-YRI

Genotype data submitted for	341	samples from	332	individuals	Individual with multiple genotypes submission:	270

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 .