Reference SNP(refSNP) Cluster Report: rs40837

Reference SNP(refSNP) Cluster Report: rs40837

refSNP ID: rs40837
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	76/129
Map to Genome Build:	36.3

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

HGVS Names
NM_145659.3:c.*127T>C
NT_010393.15:g.19823924A>G

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss40681368 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs40837 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
ss46152	KWOK\|OVLP-10201	fwd/T	A/G	ggaccagaggggctttcagttactgggtag	gcctggggcagggggctggaagagccctcc	04/28/00	04/07/04	76	Genomic	91 %
ss240042	KWOK\|OVLP-000621-344904	fwd/T	A/G	ggaccagaggggctttcagttactgggtag	gcctggggcagggggctggaagagccctcc	06/30/00	10/10/03	79	Genomic	94 %
ss240650	KWOK\|OVLP-000621-367168	fwd/T	A/G	ggaccagaggggctttcagttactgggtag	gcctggggcagggggctggaagagccctcc	06/30/00	10/10/03	79	Genomic	94 %
ss299042	KWOK\|OVLP-000621-309540	fwd/T	A/G	ggaccagaggggctttcagttactgggtag	gcctggggcagggggctggaagagccctcc	06/30/00	10/10/03	79	Genomic	97 %
ss309935	KWOK\|OVLP-000621-369000	rev/B	C/T	ggagggctcttccagccccctgccccaggc	ctacccagtaactgaaagcccctctggtcc	06/30/00	10/10/03	79	Genomic	97 %
ss327112	KWOK\|OVLP-000621-42268	rev/B	C/T	ggagggctcttccagccccctgccccaggc	ctacccagtaactgaaagcccctctggtcc	06/30/00	10/10/03	79	Genomic	99 %
ss619288	SC_JCM\|AC002425.1_74624	rev/B	C/T	ggagggctcttccagccccctgccccaggc	ctacccagtaactgaaagcccctctggtcc	07/12/00	10/10/03	80	Genomic	unknown
ss1173377	KWOK\|OVLP-000804-556045	rev/B	C/T	ggagggctcttccagccccctgccccaggc	ctacccagtaactgaaagcccctctggtcc	09/02/00	10/10/03	86	Genomic	99 %
ss1252723	KWOK\|OVLP-000804-547269	fwd/T	A/G	ggaccagaggggctttcagttactgggtag	gcctggggcagggggctggaagagccctcc	09/02/00	10/10/03	86	Genomic	97 %
ss1254635	KWOK\|OVLP-000804-564412	rev/B	C/T	ggagggctcttccagccccctgccccaggc	ctacccagtaactgaaagcccctctggtcc	09/02/00	10/10/03	86	Genomic	97 %
ss1276145	KWOK\|OVLP-000804-542041	rev/B	C/T	ggagggctcttccagccccctgccccaggc	ctacccagtaactgaaagcccctctggtcc	09/02/00	10/10/03	86	Genomic	94 %
ss1276280	KWOK\|OVLP-000804-557381	rev/B	C/T	ggagggctcttccagccccctgccccaggc	ctacccagtaactgaaagcccctctggtcc	09/02/00	10/10/03	86	Genomic	94 %
ss1279534	KWOK\|OVLP-000804-530882	fwd/T	A/G	ggaccagaggggctttcagttactgggtag	gcctggggcagggggctggaagagccctcc	09/02/00	10/10/03	86	Genomic	92 %
ss1862514	KWOK\|OVLP-000925-18185	rev/B	C/T	ggagggctcttccagccccctgccccaggc	ctacccagtaactgaaagcccctctggtcc	10/06/00	10/10/03	87	Genomic	99 %
ss1940896	KWOK\|OVLP-000925-23275	fwd/T	A/G	ggaccagaggggctttcagttactgggtag	gcctggggcagggggctggaagagccctcc	10/06/00	10/10/03	87	Genomic	97 %
ss1942405	KWOK\|OVLP-000925-48235	rev/B	C/T	ggagggctcttccagccccctgccccaggc	ctacccagtaactgaaagcccctctggtcc	10/06/00	10/10/03	87	Genomic	97 %
ss1971463	KWOK\|OVLP-000925-32030	rev/B	C/T	ggagggctcttccagccccctgccccaggc	ctacccagtaactgaaagcccctctggtcc	10/06/00	10/10/03	87	Genomic	94 %
ss1971623	KWOK\|OVLP-000925-51347	rev/B	C/T	ggagggctcttccagccccctgccccaggc	ctacccagtaactgaaagcccctctggtcc	10/06/00	10/10/03	87	Genomic	94 %
ss1975609	KWOK\|OVLP-000925-40749	fwd/T	A/G	ggaccagaggggctttcagttactgggtag	gcctggggcagggggctggaagagccctcc	10/06/00	10/10/03	87	Genomic	92 %
ss40681368	ABI\|hCV614195	rev/B	C/T	ggagggctcttccagccccctgccccaggc	ctacccagtaactgaaagcccctctggtcc	07/17/05	07/17/05	126	Genomic	unknown
ss75197513	ILLUMINA\|ILMN_Human_1M_rs40837	fwd/T	A/G	ggaccagaggggctttcagttactgggtag	gcctggggcagggggctggaagagccctcc	08/28/07	08/29/07	129	Genomic	unknown
ss90361341	BCMHGSC_JDW\|JWB-0936383	fwd/T	A/G	ggaccagaggggctttcagttactgggtag	gcctggggcagggggctggaagagccctcc	02/26/08	02/29/08	129	Genomic	unknown

Fasta sequence (Legend)

 GGAAGGTGGG CCAGAGACCC CAAAAATGTA GGAGCAGAGA GGGGTTCAGG ATGGCTAGAG
 GTTGCTGACC CCGTTCCAGG CTGCCCTGCC CTCTGGGTGT CAGACAGCCC TTACCCGAAG
 AGAAGCGGAG GCCAGGGGTG GATGAGAGTG CTTTATTGGG CACCCAGCAT GGGGGCTTGG
 CCCGAGGAGG ACCATCGGGC CCCAAGACAA TAAATAAACC ATCATCTCCC TAAACAATAA
 ATAAATATCC AAGAAATAAA TAGCTGGCGA GGACCAGAGG GGCTTTCAGT TACTGGGTAG
 R
 GCCTGGGGCA GGGGGCTGGA AGAGCCCTCC CTTGTCCAAG GCTGATGATG CGAAGGCTGC
 CCTGATGCCA AGACTCCAGT CCTAAAGTTC TAAAGGGTGG GGGGCAGGGG GCTAAGAAGC
 CACCGATCAG GGCTGGGGGC TCAATGTTGG GAACCCCAAG GGCCAGACTG AGTGCCCAGC
 CTTGGACAGC AGCAGCAACT CCCGCACGGC CCGAGATAAG ACGAGCTCCA AGGAGTGCAG
 CAGGCGGTAG GTGGAGAGGA GCTGGGGCCA GGACACCTGG GCCGGGCCCT GTAAGGCGCT

GeneView

GeneView via analysis of contig annotation: APOB48R apolipoprotein B48 receptor

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

GeneView via analysis of contig annotation: IL27 interleukin 27

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

HuRef

NW_001838230->NM_018690

function

Celera

NW_926262->NM_018690

function

reference

NT_010393->NM_145659

function

HuRef

NW_001838230->NM_145659

function

Celera

NW_926262->NM_145659

function

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


HuRef	NW_001838230->NM_018690->NP_061160	142440	reverse		3' near gene

Celera	NW_926262->NM_018690->NP_061160	133683	reverse		3' near gene

reference	NT_010393->NM_145659->	19823924	reverse	882	3' UTR

HuRef	NW_001838230->NM_145659->	142440	forward	882	3' UTR

Celera	NW_926262->NM_145659->	133683	forward	882	3' UTR

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs40837 maps exactly once on NCBI human chromosome 16

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
16	NW_001838230.2	142440	26536763	minus	T	alt_assembly_8	HuRef	HuRef	view	300
16	NW_926262.1	133683	27692922	minus	T	alt_assembly_1	Celera	Celera	view	300
16	NT_010393.15	19823924	28418346	plus	A	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
AC008956.6 AC002544 AC002544.1 AC008956 AC008956.6 AC020765.4 AC026411.5

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC002425.1 AC002544.1 AC008956.8 AC020765.8 AC026411.7 AC136948.2 AC138894.2 AC138934.3 NC_000016.8	AC130463.1 AC138814.1 AC145283.1 AC145284.1

UniGene Cluster ID
528111

Population Diversity

	Sample Ascertainment				Genotypes	Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	HWP	A	G
ss46152	B		60	AF		0.800	0.200

	A		60	AF		0.750	0.250

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.349+/-0.230	0	0	0	0

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

DoubleHit found by: NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .