Reference SNP(refSNP) Cluster Report: rs2428705

Reference SNP(refSNP) Cluster Report: rs2428705

refSNP ID: rs2428705
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:	A/G
Ancestral Allele:	A
Clinical Association:	unknown

HGVS Names
NM_000868.1:c.350-54188C>T
NT_028405.11:g.460710C>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss8280725 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2428705 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
ss3403305	SC_JCM\|AC004822.1_2676	fwd/T	A/G	tatattcaccactctagctgcaatgattag	agagtgtataatacaaagtagtaagtgctt	09/24/01	10/10/03	100	Genomic	unknown
ss5986233	SC_JCM\|NT_028405.6_381282	rev/B	C/T	aagcacttactactttgtattatacactct	ctaatcattgcagctagagtggtgaatata	01/10/03	10/10/03	111	Genomic	unknown
ss8280725	SC_SNP\|NT_028405.7_463240	rev/B	C/T	aagcacttactactttgtattatacactct	ctaatcattgcagctagagtggtgaatata	04/17/03	10/30/04	114	Genomic	unknown
ss12036556	WI_SSAHASNP\|chrX.NT_028405.9_460710	rev/B	C/T	aagcacttactactttgtattatacactct	ctaatcattgcagctagagtggtgaatata	07/04/03	10/10/03	116	Genomic	unknown
ss19818456	CSHL-HAPMAP\|CSHL-HuDD-200402.chrX.NT_028405.9_460710	rev/B	C/T	aagcacttactactttgtattatacactct	ctaatcattgcagctagagtggtgaatata	02/20/04	03/04/04	120	Genomic	unknown
ss23831272	PERLEGEN\|afd4197964	rev/B	C/T	aagcacttactactttgtattatacactct	ctaatcattgcagctagagtggtgaatata	08/10/04	09/13/04	123	Genomic	unknown
ss43539291	ABI\|hCV15795445	rev/B	C/T	aagcacttactactttgtattatacactct	ctaatcattgcagctagagtggtgaatata	07/18/05	07/18/05	126	Genomic	unknown
ss94373071	BCMHGSC_JDW\|JWB-2699139	rev/B	C/T	aagcacttactactttgtattatacactct	ctaatcattgcagctagagtggtgaatata	02/26/08	03/06/08	129	Genomic	unknown

Fasta sequence (Legend)

 ACACATCTAG AAATAAGGTG CAGGCATTTT GGTTATATAA TTTTGGGGTT TGAATTATTA
 GTGAGTCTTC CTTAAGCTTT TGCTATTTTC ATGTTATTTT CTGATTGAGG CAGGAAACAG
 TAAAGCATAG ACTTTTAAAG TTGTCACAAA CACTAATCAA ATACTAAAAT CACTGATCAT
 GATCAAGTGA TCTTGTACAG GCATCACTAA CAAAACACTG TACATACTTC Tctctctctc
 tctgatactc gctattctca ccattttatt ttttttcata gcactcacta acatctaact
 tactctatac tgactccttt attttattta ttgtctctct tctcccatga atataagctt
 tatgtctgtt tatattcacc actctagctg caatgattag
 R
 agagtgtata atacaaagta gtaagtgctt aatatatatt ggctgaatTA atggatggat
 ggatggatgg atgaatAAAT AAAAAAAAAA GCCTAAGGTG TTGTTTACTG ATTTTTCTGT
 GTTTATGCAT TATtcaataa tagagccaga tctagatacc agatttcctg actttcaatc
 ccgtactccc tatgAATGAA AGAGAAAGAT AAGTATGAAA ATCCATAATA ATCTCCCATT
 AAAGGAGGGT GGGAATAGGA TAATACAGCT AATAAATGTA ATGAAAAGAT TATTCTTTGA
 GGACTATTTG ATTTGAAAAC TATTTGAAGA CTATTAATTG ATCTAGGAAC ATTTCCTATG
 AAAAGTTAAT TGTCCTATGT CCAAGAAACA AAAAGAAGAC

GeneView

GeneView via analysis of contig annotation: HTR2C 5-hydroxytryptamine (serotonin) receptor 2C

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_028405->NM_000868

function

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


reference	NT_028405->NM_000868->NP_000859	460710	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs2428705 maps exactly once on NCBI human chromosome X

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
X	NW_001842393.1	465042	103615870	minus	C	alt_assembly_8	HuRef	HuRef	view	400
X	NT_028405.11	460710	113934634	minus	C	ref_assembly	reference	reference	view	400
X	NW_927717.1	10748055	114463537	minus	C	alt_assembly_1	Celera	Celera	view	400

NCBI Resource Links

Submitter-Referenced
GenBank
NT_028405.6 AL590097

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
ss23831272	AFD_EUR_PANEL	European	48	IG	0.083	0.208	0.708	0.150	0.188	0.812

	AFD_AFR_PANEL	African American	46	IG	0.261	0.304	0.435	0.100	0.413	0.587

	AFD_CHN_PANEL	Asian	48	IG	0.042		0.958	0.001	0.042	0.958

ss8280725	HapMap-CEU	European	120	IG	0.067	0.150	0.783	1.000	0.142	0.858

	HapMap-HCB	Asian	90	IG	0.022	0.022	0.956	1.000	0.033	0.967

	HapMap-JPT	Asian	86	IG	0.023	0.023	0.953	1.000	0.035	0.965

	HapMap-YRI	Sub-Saharan African	120	IG	0.283	0.317	0.400	0.150	0.442	0.558

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.308+/-0.243	332	260	9	0

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, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .