Reference SNP(refSNP) Cluster Report: rs11954174

Reference SNP(refSNP) Cluster Report: rs11954174

refSNP ID: rs11954174
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	120/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	C/T
Ancestral Allele:	C
Clinical Association:	unknown

HGVS Names
NM_000949.2:c.855+89G>A
NT_006576.15:g.35040986C>T

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss17846814 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs11954174 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
ss17846814	CSHL-HAPMAP\|CSHL-HuCC-200402.chr5.NT_006576.14_17520335		fwd/B	C/T	agtccaaaaaggctggctgaaactaccagg	tgaactgacggggactgtgtgtgagtgtgt	02/19/04	03/04/04	120	Genomic			unknown

Fasta sequence (Legend)

 TTGTATAAAA TGTTTATCTC TATGCTTATG AGTAGATCTG ATAAATCAAT AAATGTGTTT
 CCATGTTTTC TTGGCTTTCT CTCCTTGCCC TCTGACATTT AGTGTGTGAA AGTAAGTACC
 CTCATCCTTC ACACAACTTT CTGTTAACAC ACATGCTGAC CAGGAGAGAC AGTCCAAAAA
 GGCTGGCTGA AACTACCAGG
 Y
 TGAACTGACG GGGACTGTGT GTGAGTGTGT AGAGTTAATT ACTACAGAGC AGTGAGTCAC
 ACTCCATTTT TTTGCCTCCT GTACTTACCT CCAACAGATG AGCATCAAAT CCTTTTATTT
 TTGGCCCAGG AACTGGCGGA AAGATGCAGG TCACCATGCT ATAAAATAAT TCATGAGATT
 GGCTAAATGA CTCATTTCTG

GeneView

GeneView via analysis of contig annotation: PRLR prolactin receptor

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_006576->NM_000949

function

HuRef

NW_001838932->NM_000949

function

Celera

NW_922596->NM_000949

function

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


reference	NT_006576->NM_000949->NP_000940	35040986	reverse	intron

HuRef	NW_001838932->NM_000949->NP_000940	640166	forward	intron

Celera	NW_922596->NM_000949->NP_000940	660930	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs11954174 maps exactly once on NCBI human chromosome 5

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
5	NW_922596.1	660930	34950416	plus	C	alt_assembly_1	Celera	Celera	view	200
5	NW_001838932.2	640166	35017124	minus	G	alt_assembly_8	HuRef	HuRef	view	200
5	NT_006576.15	35040986	35103986	plus	C	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_006576

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail		Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	HWP	C
ss17846814	HapMap-CEU	European	118	IG	1.000		1.000

	HapMap-HCB	Asian	88	IG	1.000		1.000

	HapMap-JPT	Asian	88	IG	1.000		1.000

	HapMap-YRI	Sub-Saharan African	120	IG	1.000		1.000

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
		270	210	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 .