Reference SNP(refSNP) Cluster Report: rs6830958

Reference SNP(refSNP) Cluster Report: rs6830958

refSNP ID: rs6830958
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:	A/G
Ancestral Allele:	A
Clinical Association:	unknown

HGVS Names
NM_001564.2:c.173-1776G>A
NT_022792.17:g.16841599G>A

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss92923174 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs6830958 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
ss10138295	BCM_SSAHASNP\|chr4.NT_022792.15_16841180	fwd/T	A/G	gaactttgttcgaaaatatgctatgcaggt	taagtactctgaactgtgtggtggcacttt	06/27/03	10/25/06	116	Genomic	unknown
ss14628112	WI_SSAHASNP\|chr4.NT_022792.16_16841180	fwd/T	A/G	gaactttgttcgaaaatatgctatgcaggt	taagtactctgaactgtgtggtggcacttt	11/05/03	11/22/03	119	Genomic	unknown
ss20224781	CSHL-HAPMAP\|CSHL-HuFF-200402.chr4.NT_022792.16_16841180	fwd/T	A/G	gaactttgttcgaaaatatgctatgcaggt	taagtactctgaactgtgtggtggcacttt	02/21/04	03/04/04	120	Genomic	unknown
ss22189063	SSAHASNP\|WGSA-200403-chr4.chr4.NT_022792.16_16841180	fwd/T	A/G	gaactttgttcgaaaatatgctatgcaggt	taagtactctgaactgtgtggtggcacttt	03/20/04	03/21/04	121	Genomic	unknown
ss68921720	PERLEGEN\|PGP05197688	fwd/T	A/G	gaactttgttcgaaaatatgctatgcaggt	taagtactctgaactgtgtggtggcacttt	01/30/07	03/31/08	127	Genomic	unknown
ss75207648	ILLUMINA\|ILMN_Human_1M_rs6830958	fwd/T	A/G	gaactttgttcgaaaatatgctatgcaggt	taagtactctgaactgtgtggtggcacttt	08/28/07	08/29/07	129	Genomic	unknown
ss81284495	HGSV\|Cor18507_SNV_20070510.chr4_184804808	fwd/T	A/G	gaactttgttcgaaaatatgctatgcaggt	taagtactctgaactgtgtggtggcacttt	11/26/07	11/29/07	130	Genomic	unknown
ss92923174	BCMHGSC_JDW\|JWB-1909710	fwd/T	A/G	gaactttgttcgaaaatatgctatgcaggt	taagtactctgaactgtgtggtggcacttt	02/26/08	03/03/08	129	Genomic	unknown
ss108671503	1000GENOMES\|CEU.trio.12.15.2008_1170607_chr4_184666653	fwd/T	A/G	gaactttgttcgaaaatatgctatgcaggt	taagtactctgaactgtgtggtggcacttt	12/15/08	12/16/08	130	Genomic	unknown

Fasta sequence (Legend)

 TTTATCTCAT CTATCAATGT GCTGGTATGA TATATACTGT ACTTAGCCTC TAACACCTGA
 TTATTAGGTA CAAAATATTT GAAAAGAGGT TTGCCTCTTT TTTTTTTAAT CCTCAATTTT
 TTATGTGTCT GAGGGAACCA GTTTCCTTAT TTTTCCTGTA GGGAAATGAG GTTCTTAAGA
 AATCTGCTTA GATGCCGAGC TAAGCAAATG GAATAGACAT GAACTTTGTT CGAAAATATG
 CTATGCAGGT
 R
 TAAGTACTCT GAACTGTGTG GTGGCACTTT GTTATATATT CCAAGTTAGA CAGTTGTACA
 TCAAGTACGA GTACCTGCGA TTTCCAGGGA GAAGCTGATT AATGAGTTCT GTTGAATATT
 TGCTTTTGTG TGCCTTACTT GCAGACAGCC CCAATGTATA TATCTACTTG CCTAACATTT
 CTGTTTTTAA TAATTATAAT ATTGGAATAT AAAACTAGTA TGCCATGTGG TATGAAAAAT
 ACCATGCGGA

GeneView

GeneView via analysis of contig annotation: ING2 inhibitor of growth family, member 2

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_022792->NM_001564

function

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


reference	NT_022792->NM_001564->NP_001555	16841599	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs6830958 maps exactly once on NCBI human chromosome 4

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
4	NW_001838921.1	44671257	180189018	plus	A	alt_assembly_8	HuRef	HuRef	view	200
4	NW_922217.1	64020024	181762545	plus	A	alt_assembly_1	Celera	Celera	view	200
4	NT_022792.17	16841599	184666653	plus	G	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_022792

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss10138295	HapMap-CEU	European	120	IG	0.483	0.467	0.050	0.251	0.717	0.283

	HapMap-HCB	Asian	90	IG	0.244	0.556	0.200	0.479	0.522	0.478

	HapMap-JPT	Asian	88	IG	0.409	0.477	0.114	1.000	0.648	0.352

	HapMap-YRI	Sub-Saharan African	120	IG	0.433	0.400	0.167	0.294	0.633	0.367

ss68921720	HapMap-CEU	European	120	GF	0.433	0.483	0.083		0.675	0.325

	HapMap-HCB	Asian	90	GF	0.222	0.556	0.222		0.500	0.500

	HapMap-JPT	Asian	88	GF	0.341	0.545	0.114		0.614	0.386

	HapMap-YRI	Sub-Saharan African	120	GF	0.317	0.500	0.183		0.567	0.433

Concordant Genotype	Total Sample	A/A	A/G	G/G
ss10138295	226	89	109	27
ss68921720	226	90	108	27

RefSNP Genotype Summary	Total Individual	A/A	A/G	G/G
rs6830958	270	90	109	27

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
151	ss10138295	A/A	CSHL-HAPMAP	HapMap-CEU	NA10847	CEPH1334.02	r23_ch4_CEU_illumina:golden_gate_1.1.0	441622
151	ss68921720	A/G	CSHL-HAPMAP	HapMap-CEU	NA10847	CEPH1334.02	chr4-HapMap-CEU
174	ss10138295	A/A	CSHL-HAPMAP	HapMap-CEU	NA07048	CEPH1341.01	r23_ch4_CEU_illumina:golden_gate_1.1.0	441622
174	ss68921720	A/G	CSHL-HAPMAP	HapMap-CEU	NA07048	CEPH1341.01	chr4-HapMap-CEU
188	ss10138295	A/A	CSHL-HAPMAP	HapMap-CEU	NA10851	CEPH1344.01	r23_ch4_CEU_illumina:golden_gate_1.1.0	441622
188	ss68921720	A/G	CSHL-HAPMAP	HapMap-CEU	NA10851	CEPH1344.01	chr4-HapMap-CEU
199	ss10138295	A/A	CSHL-HAPMAP	HapMap-CEU	NA12056	CEPH1344.12	r23_ch4_CEU_illumina:golden_gate_1.1.0	441622
199	ss68921720	A/G	CSHL-HAPMAP	HapMap-CEU	NA12056	CEPH1344.12	chr4-HapMap-CEU
200	ss10138295	A/A	CSHL-HAPMAP	HapMap-CEU	NA12057	CEPH1344.13	r23_ch4_CEU_illumina:golden_gate_1.1.0	441622
200	ss68921720	A/G	CSHL-HAPMAP	HapMap-CEU	NA12057	CEPH1344.13	chr4-HapMap-CEU
215	ss10138295	A/A	CSHL-HAPMAP	HapMap-CEU	NA10857	CEPH1346.01	r23_ch4_CEU_illumina:golden_gate_1.1.0	441622
215	ss68921720	A/G	CSHL-HAPMAP	HapMap-CEU	NA10857	CEPH1346.01	chr4-HapMap-CEU
225	ss10138295	A/G	CSHL-HAPMAP	HapMap-CEU	NA12043	CEPH1346.11	r23_ch4_CEU_illumina:golden_gate_1.1.0	441622
225	ss68921720	G/G	CSHL-HAPMAP	HapMap-CEU	NA12043	CEPH1346.11	chr4-HapMap-CEU
255	ss10138295	A/G	CSHL-HAPMAP	HapMap-CEU	NA10855	CEPH1350.02	r23_ch4_CEU_illumina:golden_gate_1.1.0	441622
255	ss68921720	G/G	CSHL-HAPMAP	HapMap-CEU	NA10855	CEPH1350.02	chr4-HapMap-CEU
344	ss10138295	A/A	CSHL-HAPMAP	HapMap-CEU	NA12716	CEPH1358.11	r23_ch4_CEU_illumina:golden_gate_1.1.0	441622
344	ss68921720	A/G	CSHL-HAPMAP	HapMap-CEU	NA12716	CEPH1358.11	chr4-HapMap-CEU
456	ss10138295	G/G	CSHL-HAPMAP	HapMap-CEU	NA10838	CEPH1420.01	r23_ch4_CEU_illumina:golden_gate_1.1.0	441622
456	ss68921720	A/G	CSHL-HAPMAP	HapMap-CEU	NA10838	CEPH1420.01	chr4-HapMap-CEU
548	ss10138295	A/G	CSHL-HAPMAP	HapMap-CEU	NA12763	CEPH1447.12	r23_ch4_CEU_illumina:golden_gate_1.1.0	441622
548	ss68921720	G/G	CSHL-HAPMAP	HapMap-CEU	NA12763	CEPH1447.12	chr4-HapMap-CEU
565	ss10138295	A/G	CSHL-HAPMAP	HapMap-CEU	NA12801	CEPH1454.01	r23_ch4_CEU_illumina:golden_gate_1.1.0	441622
565	ss68921720	A/A	CSHL-HAPMAP	HapMap-CEU	NA12801	CEPH1454.01	chr4-HapMap-CEU
5137	ss10138295	A/G	CSHL-HAPMAP	HapMap-YRI	NA19131	YOR101.02	r23_ch4_YRI_illumina:golden_gate_1.1.0	441622
5137	ss68921720	G/G	CSHL-HAPMAP	HapMap-YRI	NA19131	YOR101.02	chr4-HapMap-YRI
5139	ss10138295	A/A	CSHL-HAPMAP	HapMap-YRI	NA19100	YOR105.01	r23_ch4_YRI_illumina:golden_gate_1.1.0	441622
5139	ss68921720	G/G	CSHL-HAPMAP	HapMap-YRI	NA19100	YOR105.01	chr4-HapMap-YRI
5144	ss10138295	A/A	CSHL-HAPMAP	HapMap-YRI	NA19192	YOR112.03	r23_ch4_YRI_illumina:golden_gate_1.1.0	441622
5144	ss68921720	A/G	CSHL-HAPMAP	HapMap-YRI	NA19192	YOR112.03	chr4-HapMap-YRI
5146	ss10138295	G/G	CSHL-HAPMAP	HapMap-YRI	NA19238	YOR117.02	r23_ch4_YRI_illumina:golden_gate_1.1.0	441622
5146	ss68921720	A/G	CSHL-HAPMAP	HapMap-YRI	NA19238	YOR117.02	chr4-HapMap-YRI
5174	ss10138295	G/G	CSHL-HAPMAP	HapMap-HCB	NA18571	CH18571	r23_ch4_HCB_illumina:golden_gate_1.1.0	441622
5174	ss68921720	A/G	CSHL-HAPMAP	HapMap-HCB	NA18571	CH18571	chr4-HapMap-HCB
5177	ss10138295	G/G	CSHL-HAPMAP	HapMap-HCB	NA18594	CH18594	r23_ch4_HCB_illumina:golden_gate_1.1.0	441622
5177	ss68921720	A/G	CSHL-HAPMAP	HapMap-HCB	NA18594	CH18594	chr4-HapMap-HCB
5185	ss10138295	A/A	CSHL-HAPMAP	HapMap-HCB	NA18632	CH18632	r23_ch4_HCB_illumina:golden_gate_1.1.0	441622
5185	ss68921720	A/G	CSHL-HAPMAP	HapMap-HCB	NA18632	CH18632	chr4-HapMap-HCB
5188	ss10138295	A/G	CSHL-HAPMAP	HapMap-HCB	NA18635	CH18635	r23_ch4_HCB_illumina:golden_gate_1.1.0	441622
5188	ss68921720	G/G	CSHL-HAPMAP	HapMap-HCB	NA18635	CH18635	chr4-HapMap-HCB
5189	ss10138295	A/G	CSHL-HAPMAP	HapMap-HCB	NA18592	CH18592	r23_ch4_HCB_illumina:golden_gate_1.1.0	441622
5189	ss68921720	G/G	CSHL-HAPMAP	HapMap-HCB	NA18592	CH18592	chr4-HapMap-HCB
5191	ss10138295	A/G	CSHL-HAPMAP	HapMap-HCB	NA18593	CH18593	r23_ch4_HCB_illumina:golden_gate_1.1.0	441622
5191	ss68921720	G/G	CSHL-HAPMAP	HapMap-HCB	NA18593	CH18593	chr4-HapMap-HCB
5194	ss10138295	A/A	CSHL-HAPMAP	HapMap-JPT	NA18940	JA18940	r23_ch4_JPT_illumina:golden_gate_1.1.0	441622
5194	ss68921720	A/G	CSHL-HAPMAP	HapMap-JPT	NA18940	JA18940	chr4-HapMap-JPT
5205	ss10138295	A/A	CSHL-HAPMAP	HapMap-JPT	NA18953	JA18953	r23_ch4_JPT_illumina:golden_gate_1.1.0	441622
5205	ss68921720	A/G	CSHL-HAPMAP	HapMap-JPT	NA18953	JA18953	chr4-HapMap-JPT
5212	ss10138295	A/A	CSHL-HAPMAP	HapMap-JPT	NA18965	JA18965	r23_ch4_JPT_illumina:golden_gate_1.1.0	441622
5212	ss68921720	A/G	CSHL-HAPMAP	HapMap-JPT	NA18965	JA18965	chr4-HapMap-JPT
5215	ss10138295	A/G	CSHL-HAPMAP	HapMap-JPT	NA18975	JA18975	r23_ch4_JPT_illumina:golden_gate_1.1.0	441622
5215	ss68921720	G/G	CSHL-HAPMAP	HapMap-JPT	NA18975	JA18975	chr4-HapMap-JPT
5235	ss10138295	A/A	CSHL-HAPMAP	HapMap-JPT	NA19007	JA19007	r23_ch4_JPT_illumina:golden_gate_1.1.0	441622
5235	ss68921720	A/G	CSHL-HAPMAP	HapMap-JPT	NA19007	JA19007	chr4-HapMap-JPT
5236	ss10138295	G/G	CSHL-HAPMAP	HapMap-JPT	NA19003	JA19003	r23_ch4_JPT_illumina:golden_gate_1.1.0	441622
5236	ss68921720	A/G	CSHL-HAPMAP	HapMap-JPT	NA19003	JA19003	chr4-HapMap-JPT
5237	ss10138295	A/A	CSHL-HAPMAP	HapMap-YRI	NA18501	YOR004.03	r23_ch4_YRI_illumina:golden_gate_1.1.0	441622
5237	ss68921720	A/G	CSHL-HAPMAP	HapMap-YRI	NA18501	YOR004.03	chr4-HapMap-YRI
5238	ss10138295	G/G	CSHL-HAPMAP	HapMap-YRI	NA18503	YOR005.01	r23_ch4_YRI_illumina:golden_gate_1.1.0	441622
5238	ss68921720	A/G	CSHL-HAPMAP	HapMap-YRI	NA18503	YOR005.01	chr4-HapMap-YRI
5240	ss10138295	G/G	CSHL-HAPMAP	HapMap-YRI	NA18504	YOR005.03	r23_ch4_YRI_illumina:golden_gate_1.1.0	441622
5240	ss68921720	A/G	CSHL-HAPMAP	HapMap-YRI	NA18504	YOR005.03	chr4-HapMap-YRI
5249	ss10138295	A/G	CSHL-HAPMAP	HapMap-YRI	NA18516	YOR013.03	r23_ch4_YRI_illumina:golden_gate_1.1.0	441622
5249	ss68921720	G/G	CSHL-HAPMAP	HapMap-YRI	NA18516	YOR013.03	chr4-HapMap-YRI
5251	ss10138295	A/A	CSHL-HAPMAP	HapMap-YRI	NA18523	YOR016.02	r23_ch4_YRI_illumina:golden_gate_1.1.0	441622
5251	ss68921720	A/G	CSHL-HAPMAP	HapMap-YRI	NA18523	YOR016.02	chr4-HapMap-YRI
5253	ss10138295	G/G	CSHL-HAPMAP	HapMap-YRI	NA18872	YOR017.01	r23_ch4_YRI_illumina:golden_gate_1.1.0	441622
5253	ss68921720	A/G	CSHL-HAPMAP	HapMap-YRI	NA18872	YOR017.01	chr4-HapMap-YRI
5255	ss10138295	A/G	CSHL-HAPMAP	HapMap-YRI	NA18871	YOR017.03	r23_ch4_YRI_illumina:golden_gate_1.1.0	441622
5255	ss68921720	G/G	CSHL-HAPMAP	HapMap-YRI	NA18871	YOR017.03	chr4-HapMap-YRI
5265	ss10138295	A/G	CSHL-HAPMAP	HapMap-YRI	NA18914	YOR028.01	r23_ch4_YRI_illumina:golden_gate_1.1.0	441622
5265	ss68921720	G/G	CSHL-HAPMAP	HapMap-YRI	NA18914	YOR028.01	chr4-HapMap-YRI
5270	ss10138295	A/A	CSHL-HAPMAP	HapMap-YRI	NA19092	YOR040.03	r23_ch4_YRI_illumina:golden_gate_1.1.0	441622
5270	ss68921720	A/G	CSHL-HAPMAP	HapMap-YRI	NA19092	YOR040.03	chr4-HapMap-YRI
5287	ss10138295	A/G	CSHL-HAPMAP	HapMap-YRI	NA19209	YOR050.02	r23_ch4_YRI_illumina:golden_gate_1.1.0	441622
5287	ss68921720	G/G	CSHL-HAPMAP	HapMap-YRI	NA19209	YOR050.02	chr4-HapMap-YRI
5290	ss10138295	A/A	CSHL-HAPMAP	HapMap-YRI	NA19206	YOR051.02	r23_ch4_YRI_illumina:golden_gate_1.1.0	441622
5290	ss68921720	A/G	CSHL-HAPMAP	HapMap-YRI	NA19206	YOR051.02	chr4-HapMap-YRI
5293	ss10138295	A/A	CSHL-HAPMAP	HapMap-YRI	NA19159	YOR056.02	r23_ch4_YRI_illumina:golden_gate_1.1.0	441622
5293	ss68921720	A/G	CSHL-HAPMAP	HapMap-YRI	NA19159	YOR056.02	chr4-HapMap-YRI
5295	ss10138295	A/G	CSHL-HAPMAP	HapMap-YRI	NA19221	YOR058.01	r23_ch4_YRI_illumina:golden_gate_1.1.0	441622
5295	ss68921720	G/G	CSHL-HAPMAP	HapMap-YRI	NA19221	YOR058.01	chr4-HapMap-YRI
5297	ss10138295	A/A	CSHL-HAPMAP	HapMap-YRI	NA19223	YOR058.03	r23_ch4_YRI_illumina:golden_gate_1.1.0	441622
5297	ss68921720	A/G	CSHL-HAPMAP	HapMap-YRI	NA19223	YOR058.03	chr4-HapMap-YRI
5303	ss10138295	G/G	CSHL-HAPMAP	HapMap-YRI	NA19141	YOR071.03	r23_ch4_YRI_illumina:golden_gate_1.1.0	441622
5303	ss68921720	A/G	CSHL-HAPMAP	HapMap-YRI	NA19141	YOR071.03	chr4-HapMap-YRI
5310	ss10138295	A/A	CSHL-HAPMAP	HapMap-YRI	NA19129	YOR077.01	r23_ch4_YRI_illumina:golden_gate_1.1.0	441622
5310	ss68921720	A/G	CSHL-HAPMAP	HapMap-YRI	NA19129	YOR077.01	chr4-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
	UNKNOWN	UNKNOWN	UNKNOWN

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Revised: May 25, 2006 1:38 PM .