Reference SNP(refSNP) Cluster Report: rs1738023

Reference SNP(refSNP) Cluster Report: rs1738023

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	89/130
Map to Genome Build:	36.3

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

HGVS Names
NM_012067.2:c.643A>G
NP_036199.2:p.Asn215Asp
NT_004610.18:g.2435583T>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss48402884 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1738023 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
ss2580166	SC_JCM\|AL035413.19_85531	fwd/T	A/G	ctgaccggcaagtacaagtatgaggacaag	atgggaaacagcccgtgggccgcttctttg	11/03/00	10/10/03	89	Genomic	unknown
ss2871801	TSC-CSHL\|TSC0398037	fwd/T	A/G	ctgaccggcaagtacaagtatgaggacaag	atgggaaacagcccgtgggccgcttctttg	01/03/01	04/07/04	92	Genomic	unknown
ss3208348	YUSUKE\|IMS-JST068432	fwd/T	A/G	ctgaccggcaagtacaagtatgaggacaag	atgggaaacagcccgtgggccgcttctttg	09/05/01	10/10/03	100	Genomic	unknown
ss6788947	WI_SSAHASNP\|NT_029218.8_400569	rev/B	C/T	caaagaagcggcccacgggctgtttcccat	cttgtcctcatacttgtacttgccggtcag	02/12/03	10/10/03	111	Genomic	unknown
ss15382963	SC_SNP\|NT_004610.16_414491	rev/B	C/T	caaagaagcggcccacgggctgtttcccat	cttgtcctcatacttgtacttgccggtcag	11/14/03	11/22/03	120	Genomic	unknown
ss16226778	CGAP-GAI\|1461319	fwd/T	A/G	ctgaccggcaagtacaagtatgaggacaag	atgggaaacagcccgtgggccgcttctttg	11/18/03	11/22/03	120	cDNA	unknown
ss19118236	CSHL-HAPMAP\|CSHL-HuDD-200402.chr1.NT_004610.16_414491	rev/B	C/T	caaagaagcggcccacgggctgtttcccat	cttgtcctcatacttgtacttgccggtcag	02/20/04	03/04/04	120	Genomic	unknown
ss20529516	SSAHASNP\|WGSA-200403-chr1.chr1.NT_004610.16_414491	rev/B	C/T	caaagaagcggcccacgggctgtttcccat	cttgtcctcatacttgtacttgccggtcag	03/18/04	03/18/04	121	Genomic	unknown
ss23178723	PERLEGEN\|afd3978524	rev/B	C/T	caaagaagcggcccacgggctgtttcccat	cttgtcctcatacttgtacttgccggtcag	08/10/04	09/13/04	124	Genomic	unknown
ss28511033	MGC_GENOME_DIFF\|BC025709x37548632-T414491C	rev/B	C/T	caaagaagcggcccacgggctgtttcccat	cttgtcctcatacttgtacttgccggtcag	08/25/04	08/25/04	126	cDNA	unknown
ss48402884	APPLERA_GI\|hCV11644667	rev/B	C/T	caaagaagcggcccacgggctgtttcccat	cttgtcctcatacttgtacttgccggtcag	09/28/05	11/03/06	126	Genomic	unknown
ss65730814	ILLUMINA\|Human1-rs1738023	fwd/T	A/G	ctgaccggcaagtacaagtatgaggacaag	atgggaaacagcccgtgggccgcttctttg	10/10/06	10/10/06	127	Genomic	unknown
ss66673530	ILLUMINA\|HumanHap300v1.1_rs1738023	fwd/B	A/G	ctgaccggcaagtacaagtatgaggacaag	atgggaaacagcccgtgggccgcttctttg	11/09/06	11/09/06	127	Genomic	unknown
ss67185108	ILLUMINA\|HumanHap550v1.1_rs1738023	fwd/T	A/G	ctgaccggcaagtacaagtatgaggacaag	atgggaaacagcccgtgggccgcttctttg	11/14/06	11/14/06	127	Genomic	unknown
ss67558452	ILLUMINA\|HumanHap650Yv1.0_rs1738023	fwd/T	A/G	ctgaccggcaagtacaagtatgaggacaag	atgggaaacagcccgtgggccgcttctttg	11/14/06	11/14/06	127	Genomic	unknown
ss68405700	CSHL-HAPMAP\|sanger:assay:1731504:1	rev/B	C/T	caaagaagcggcccacgggctgtttcccat	cttgtcctcatacttgtacttgccggtcag	01/11/07	01/16/07	127	NA	unknown
ss68760424	PERLEGEN\|PGP03978524	rev/B	C/T	caaagaagcggcccacgggctgtttcccat	cttgtcctcatacttgtacttgccggtcag	01/30/07	08/14/07	127	Genomic	unknown
ss70663170	ILLUMINA\|HumanHap550v3.0__rs1738023	rev/B	C/T	caaagaagcggcccacgggctgtttcccat	cttgtcctcatacttgtacttgccggtcag	04/20/07	03/30/08	130	Genomic	unknown
ss71224631	ILLUMINA\|HumanHap650Yv3.0_rs1738023	fwd/T	A/G	ctgaccggcaagtacaagtatgaggacaag	atgggaaacagcccgtgggccgcttctttg	04/23/07	04/23/07	127	Genomic	unknown
ss75601787	ILLUMINA\|ILMN_Human_1M_rs1738023	fwd/T	A/G	ctgaccggcaagtacaagtatgaggacaag	atgggaaacagcccgtgggccgcttctttg	08/28/07	08/29/07	129	Genomic	unknown
ss77755200	HGSV\|Cor12156_SNV_20070510.chr1_19356547	rev/B	C/T	caaagaagcggcccacgggctgtttcccat	cttgtcctcatacttgtacttgccggtcag	10/09/07	10/14/07	129	Genomic	unknown
ss79090760	ILLUMINA\|HumanHap300v2.0_rs1738023	fwd/T	A/G	ctgaccggcaagtacaagtatgaggacaag	atgggaaacagcccgtgggccgcttctttg	04/18/07	11/18/07	130	Genomic	unknown
ss83868097	KRIBB_YJKIM\|KHS561015	fwd/T	A/G	ctgaccggcaagtacaagtatgaggacaag	atgggaaacagcccgtgggccgcttctttg	12/04/07	12/05/07	130	Genomic	unknown
ss85837410	HGSV\|Cor19129_SNV_20070510.chr1_19356547	rev/B	C/T	caaagaagcggcccacgggctgtttcccat	cttgtcctcatacttgtacttgccggtcag	12/06/07	12/10/07	130	Genomic	unknown
ss86068019	HGSV\|Cor18956_SNV_20070510.chr1_19356547	rev/B	C/T	caaagaagcggcccacgggctgtttcccat	cttgtcctcatacttgtacttgccggtcag	11/30/07	12/11/07	130	Genomic	unknown
ss87275155	BCMHGSC_JDW\|JWB-0019728	rev/B	C/T	caaagaagcggcccacgggctgtttcccat	cttgtcctcatacttgtacttgccggtcag	02/26/08	02/26/08	129	Genomic	unknown
ss97923174	HUMANGENOME_JCVI\|1103675037949	rev/B	C/T	caaagaagcggcccacgggctgtttcccat	cttgtcctcatacttgtacttgccggtcag	03/30/08	03/30/08	130	Genomic	unknown
ss105128281	BGI\|BGI_rs1738023	rev/B	C/T	caaagaagcggcccacgggctgtttcccat	cttgtcctcatacttgtacttgccggtcag	08/06/08	06/16/09	130	Genomic	unknown
ss108038062	1000GENOMES\|CEU.trio.12.15.2008_25319_chr1_19483828	rev/B	C/T	caaagaagcggcccacgggctgtttcccat	cttgtcctcatacttgtacttgccggtcag	12/15/08	12/15/08	130	Genomic	unknown
ss118541784	ILLUMINA-UK\|NA18507_000024033_NCBI36.1_chr1_19483828	rev/B	C/T	caaagaagcggcccacgggctgtttcccat	cttgtcctcatacttgtacttgccggtcag	01/21/09	01/21/09	130	Genomic	99 %

Fasta sequence (Legend)

 TGAGGTTCTA TGCCTTCAAC CCTCTGGCTG GTACGTGGAG CATTCCTGGC CCTGTCTCAG
 CCTATTCCCG ACCCACAGAT GCCCAGCCCA GGACCTGGGA AGCAAGGAGG GTTTGACAAA
 CTTTGACCTC TCAGGTCAAA GACGTAAAGG CTGCATCTTC AGCCCTCCTG GGTCCCTGCC
 CCTCCCCTAG ACCAGAGCCC TGAGGGATGT GGCAGCTTCT GGGGCACTCT AGGCCCCGGG
 GCTGATTGCT GCTTTCCCTC AGGGGGCCTG CTGACCGGCA AGTACAAGTA TGAGGACAAG
 R
 ATGGGAAACA GCCCGTGGGC CGCTTCTTTG GGAATACCTG GGCAGAGATG TACAGGAATC
 GGTAAGCTGT GGGTGCTTGG TGTGGATGGC TGGGGTGGGG TCAGCTTTAT GTGGAATGAA
 GTCCTGGGCT GCTCCTGGGG TAAGGCCTTT CCTCGCTGCT GCACCTACTC CCCTGAATTT
 CTTCGGGAAT TTCCAAACCC TCCATCGGTT TTCTTGTTGT CTTGGGACCT CCAGGAGGAA
 AGGAGACTCC CTGGACCTCG GGGTCTTGAA GTCGTTGCTC TTTCCTGAGC AATCACCTGC

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_004610 ABBA01059756 AL360017 BC025709 BI759582

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
ss23178723	AFD_EUR_PANEL	European	48	IG		0.375	0.625	0.273	0.188	0.812

	AFD_AFR_PANEL	African American	46	IG	0.174	0.391	0.435	0.479	0.370	0.630

	AFD_CHN_PANEL	Asian	48	IG		0.250	0.750	0.527	0.125	0.875

ss2871801	CHMJ	Asian	74	IG					0.189	0.811

ss48402884	HapMap-CEU	European	108	IG		0.278	0.722	0.655	0.139	0.861

	HapMap-HCB	Asian	90	IG	0.067	0.289	0.644	0.403	0.211	0.789

	HapMap-JPT	Asian	88	IG	0.068	0.295	0.636	0.403	0.216	0.784

	HapMap-YRI	Sub-Saharan African	110	IG		0.564	0.436	0.005	0.282	0.718

	AGI_ASP population	multiple	44	IG	0.045	0.318	0.636	1.000	0.205	0.795

ss68760424	HapMap-CEU	European	120	GF	0.017	0.283	0.700		0.158	0.842

	HapMap-HCB	Asian	90	GF	0.044	0.311	0.644		0.200	0.800

	HapMap-JPT	Asian	90	GF	0.067	0.289	0.644		0.211	0.789

	HapMap-YRI	Sub-Saharan African	120	GF	0.117	0.450	0.433		0.342	0.658

Concordant Genotype	Total Sample	A/A	A/G	G/G
ss23178723	71
ss48402884	1212
ss97923174	1

RefSNP Genotype Summary	Total Individual	A/A	A/G	G/G
rs1738023	1287

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
410	ss48402884	T/T	CSHL-HAPMAP	HapMap-CEU	NA12155	CEPH1408.12	r27_ch1_CEU_illumina:human_1m_beadchip
5133	ss48402884	N/N	CSHL-HAPMAP	HapMap-YRI	NA18502	YOR004.02	r27_ch1_YRI_illumina:human_1m_beadchip
5145	ss48402884	T/T	CSHL-HAPMAP	HapMap-YRI	NA19240	YOR117.01	r27_ch1_YRI_illumina:human_1m_beadchip
5146	ss48402884	T/T	CSHL-HAPMAP	HapMap-YRI	NA19238	YOR117.02	r27_ch1_YRI_illumina:human_1m_beadchip
5181	ss48402884	T/T	CSHL-HAPMAP	HapMap-HCB	NA18576	CH18576	r27_ch1_CHB_illumina:human_1m_beadchip
5182	ss48402884	T/T	CSHL-HAPMAP	HapMap-HCB	NA18577	CH18577	r27_ch1_CHB_illumina:human_1m_beadchip
5193	ss48402884	T/T	CSHL-HAPMAP	HapMap-JPT	NA18942	JA18942	r27_ch1_JPT_illumina:human_1m_beadchip
5195	ss48402884	T/T	CSHL-HAPMAP	HapMap-JPT	NA18951	JA18951	r27_ch1_JPT_illumina:human_1m_beadchip
5205	ss48402884	C/T	CSHL-HAPMAP	HapMap-JPT	NA18953	JA18953	r27_ch1_JPT_illumina:human_1m_beadchip
5224	ss48402884	T/T	CSHL-HAPMAP	HapMap-JPT	NA18974	JA18974	r27_ch1_JPT_illumina:human_1m_beadchip
5239	ss48402884	T/T	CSHL-HAPMAP	HapMap-YRI	NA18505	YOR005.02	r27_ch1_YRI_illumina:human_1m_beadchip
5244	ss48402884	T/T	CSHL-HAPMAP	HapMap-YRI	NA18860	YOR012.01	r27_ch1_YRI_illumina:human_1m_beadchip
5246	ss48402884	T/T	CSHL-HAPMAP	HapMap-YRI	NA18859	YOR012.03	r27_ch1_YRI_illumina:human_1m_beadchip
5257	ss48402884	T/T	CSHL-HAPMAP	HapMap-YRI	NA18852	YOR018.02	r27_ch1_YRI_illumina:human_1m_beadchip
5265	ss48402884	T/T	CSHL-HAPMAP	HapMap-YRI	NA18914	YOR028.01	r27_ch1_YRI_illumina:human_1m_beadchip
5267	ss48402884	T/T	CSHL-HAPMAP	HapMap-YRI	NA18913	YOR028.03	r27_ch1_YRI_illumina:human_1m_beadchip
5286	ss48402884	T/T	CSHL-HAPMAP	HapMap-YRI	NA19211	YOR050.01	r27_ch1_YRI_illumina:human_1m_beadchip
5294	ss48402884	T/T	CSHL-HAPMAP	HapMap-YRI	NA19160	YOR056.03	r27_ch1_YRI_illumina:human_1m_beadchip

Genotype data submitted for	1302	samples from	1287	individuals	Individual with multiple genotypes submission:	15

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: ILLUMINA

UNKNOWN

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Revised: May 25, 2006 1:38 PM .