Reference SNP(refSNP) Cluster Report: rs35353912

Reference SNP(refSNP) Cluster Report: rs35353912

refSNP ID: rs35353912
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	126/129
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_004187.2:c.1794C>T
NP_004178.2:p.P598P
NT_011630.14:g.785193G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss48417422 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs35353912 during BLAST analysis for the current build.

NCBI Assay ID	Handle\|Submitter ID	Validation Status	ss to rs Orientation /Strand	Alleles	5' Near Seq 30 bp	3' Near Seq 30 bp	Entry Date	Update Date	Build Added	Molecule Type	Freq Warning	Ancestral Allele	Success Rate
ss48417422	APPLERA_GI\|hCV25762137		fwd/T	A/G	gccttggttgaagccgctgtggtaagcacg	gggaaggtgatgacaaactctcctgcacac	09/28/05	11/03/06	126	Genomic			unknown

Fasta sequence (Legend)

 AGGTTCAGGT CTAGCTTCTC TGGGCAGGCA GCCATCTTGC AGATAAGCTC CTCATGGGAG
 AAGACGCAGT ATCTCCGGAG CCGGCGGTAG TGCTCAATGC ACTGGCGCCC AGCAGGCAAC
 TGTGGGCAGG TTCAAGGTTG AGTGTGGCCA AGTCTGGAGG CCATGATGCC CCAGCTTCTC
 TACAACCCTC CTGCTTCTCC CCACCATCCC ACCACATTCT AGACTCACCC AGTCAGCAGT
 GCAAAAGTTG ACAGCCTCGG CAAAGTTGTA GCCTTGGTTG AAGCCGCTGT GGTAAGCACG
 R
 GGGAAGGTGA TGACAAACTC TCCTGCACAC TGGTTTGTGC GGACAACCTG AAGAACACAA
 AAGGCCATGG CTGTTGAGAT AGAGATTTTC CTGTATACAG ACCTGACTTA AGTGCAAGGT
 AATTAAGGAG ACAAAGAAAA GCCTCAGGGA ACACAGTCTG ACAACAGAAT CCCAGACTCT
 CCAACTCTGA AAGGAAGGAC CACTGGTCTC TGCTCTCAAG GTTTTGATGT GTGTTGAGAT
 GATAGGAAGA TTTGAGATTA AAAAATATAT CTGTCAAAAT ATTCCAACTT CCTTAGTAAT

GeneView

GeneView via analysis of contig annotation: JARID1C jumonji, AT rich interactive domain 1C

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_011630->NM_004187

function

HuRef

NW_001842369->NM_004187

function

Celera

NW_927709->NM_004187

function

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


reference	NT_011630->NM_004187->NP_004178	785194	reverse	2327	synonymous	T	Pro [P]	3	598
					contig reference	C	Pro [P]	3	598

HuRef	NW_001842369->NM_004187->NP_004178	410454	reverse	2249	synonymous	T	Pro [P]	3	598
					contig reference	C	Pro [P]	3	598

Celera	NW_927709->NM_004187->NP_004178	221585	reverse	2327	synonymous	T	Pro [P]	3	598
					contig reference	C	Pro [P]	3	598

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs35353912 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_001842369.1	410454	50295883	plus	G	alt_assembly_8	HuRef	HuRef	view	300
X	NT_011630.14	785194	53247833	plus	G	ref_assembly	reference	reference	view	300
X	NW_927709.1	221585	57060347	plus	G	alt_assembly_1	Celera	Celera	view	300

NCBI Resource Links

Submitter-Referenced

dbSNP Blast Analysis
GenBank HTGS Finished:
AL139396.18 NC_000023.9

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/G	G/G	HWP	A	G
ss48417422	AGI_ASP population	African American	74	IG	0.054	0.946	1.000	0.027	0.973

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.053+/-0.153	38	38	0	0

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 .