Reference SNP(refSNP) Cluster Report: rs6940875

Reference SNP(refSNP) Cluster Report: rs6940875

refSNP ID: rs6940875
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	116/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	G/T
Ancestral Allele:	T
Clinical Association:	unknown

HGVS Names
NM_017651.3:c.3053A>C
NP_060121.3:p.Q1018P
NT_025741.14:g.39820398T>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss10346905 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs6940875 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
ss10346905	BCM_SSAHASNP\|chr6.NT_025741.12_39820399	fwd/B	G/T	agaatctcttgagcggtcagcatgtttgac	gctttaacttagactgttgtgaggaaactg	06/29/03	10/25/06	116	Genomic	unknown
ss66112097	AFFY\|SNP_A-2012104	fwd/B	G/T	ggtcagcatgtttgac	gctttaacttagactg	10/27/06	03/31/08	127	Genomic	unknown
ss68992473	PERLEGEN\|PGP04446985	fwd/B	G/T	agaatctcttgagcggtcagcatgtttgac	gctttaacttagactgttgtgaggaaactg	01/30/07	03/31/08	127	Genomic	unknown
ss74907474	ILLUMINA\|ILMN_Human_1M_rs6940875	fwd/B	G/T	agaatctcttgagcggtcagcatgtttgac	gctttaacttagactgttgtgaggaaactg	08/28/07	08/29/07	129	Genomic	unknown
ss76093593	AFFY\|AFFY_6_1M_SNP_A-2012104	fwd/B	G/T	ggtcagcatgtttgac	gctttaacttagactg	08/28/07	08/30/07	130	Genomic	unknown
ss86345714	CANCER-GENOME\|16316	fwd/B	G/T	agaatctcttgagcggtcagcatgtttgac	gctttaacttagactgttgtgaggaaactg	01/25/08	01/25/08	129	Genomic	unknown

Fasta sequence (Legend)

 GGACAAAAGA GATGCTAGAA TATAATTTGT CAAGTGTAAA AACCGACCAT TATGAGCTTT
 ATTTCTAAAG AAATAAGTGA TATTCATCAA CACAACAAGC ATCTGAACAT TTAAAAGAAT
 TGTCAAAGTA AGAAAGGGGC TCACCGGTCT GAGTGAAACC AAACTGATGT AGAATCTCTT
 GAGCGGTCAG CATGTTTGAC
 K
 GCTTTAACTT AGACTGTTGT GAGGAAACTG CTGGTGGTGA AGTAAATGAG AGATTTTTGT
 TGACCTGTAT TAGGAAAACA AATCAGAAAC TACAGTGTAA TTTCCTGGAT TACTAATGCA
 AAAACTGGAT GAGAAATATT TGCTTATTAT ACAAACCAGG ACACATGATA GGTCAAAAGG
 AGTGGTAATG ATGTACATGG

GeneView

GeneView via analysis of contig annotation: AHI1 Abelson helper integration site 1

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_025741->NM_017651

function

HuRef

NW_001838990->NM_017651

function

Celera

NW_923184->NM_017651

function

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


reference	NT_025741->NM_017651->NP_060121	39820399	reverse	3332	missense	C	Pro [P]	2	1018
					contig reference	A	Gln [Q]	2	1018

HuRef	NW_001838990->NM_017651->NP_060121	21842862	forward	3332	missense	C	Pro [P]	2	1018
					contig reference	A	Gln [Q]	2	1018

Celera	NW_923184->NM_017651->NP_060121	68524924	reverse	3332	missense	C	Pro [P]	2	1018
					contig reference	A	Gln [Q]	2	1018

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs6940875 maps exactly once on NCBI human chromosome 6

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
6	NW_001838990.2	21842862	133280036	minus	A	alt_assembly_8	HuRef	HuRef	view	200
6	NT_025741.14	39820399	135757663	plus	T	ref_assembly	reference	reference	view	200
6	NW_923184.1	68524924	136456320	plus	T	alt_assembly_1	Celera	Celera	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_025741

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AL049552.20 NC_000006.10	AC021707.3

UniGene Cluster ID
386684

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	G/G	G/T	T/T	HWP	G	T
ss10346905	HapMap-CEU	European	120	IG			1.000			1.000

	HapMap-HCB	Asian	90	IG			1.000			1.000

	HapMap-JPT	Asian	88	IG			1.000			1.000

	HapMap-YRI	Sub-Saharan African	120	IG	0.017	0.183	0.800	0.752	0.108	0.892

ss66112097	HapMap-CEU	European	118	GF			1.000			1.000

	HapMap-HCB	Asian	90	GF			1.000			1.000

	HapMap-JPT	Asian	90	GF			1.000			1.000

	HapMap-YRI	Sub-Saharan African	120	GF		0.200	0.800		0.100	0.900

ss68992473	HapMap-CEU	European	120	GF			1.000			1.000

	HapMap-HCB	Asian	90	GF			1.000			1.000

	HapMap-JPT	Asian	90	GF			1.000			1.000

	HapMap-YRI	Sub-Saharan African	120	GF	0.017	0.183	0.800		0.108	0.892

Concordant Genotype	Total Sample	G/T	T/T
ss10346905	268	15	252
ss66112097	267	15	252
ss68992473	268	15	253

RefSNP Genotype Summary	Total Individual	G/G	G/T	T/T
rs6940875	270		15	253

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
5240	ss10346905	G/G	CSHL-HAPMAP	HapMap-YRI	NA18504	YOR005.03	r23_ch6_YRI_illumina:golden_gate_1.0.0	525558
5240	ss66112097	G/T	CSHL-HAPMAP	HapMap-YRI	NA18504	YOR005.03	chr6-HapMap-YRI
5240	ss68992473	G/G	CSHL-HAPMAP	HapMap-YRI	NA18504	YOR005.03	chr6-HapMap-YRI
5244	ss10346905	G/G	CSHL-HAPMAP	HapMap-YRI	NA18860	YOR012.01	r23_ch6_YRI_illumina:golden_gate_1.0.0	525558
5244	ss66112097	G/T	CSHL-HAPMAP	HapMap-YRI	NA18860	YOR012.01	chr6-HapMap-YRI
5244	ss68992473	G/G	CSHL-HAPMAP	HapMap-YRI	NA18860	YOR012.01	chr6-HapMap-YRI

Genotype data submitted for	270	samples from	270	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

DoubleHit found by: BCM_SSAHASNP

UNKNOWN

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Revised: May 25, 2006 1:38 PM .