Reference SNP(refSNP) Cluster Report: rs10038062

Reference SNP(refSNP) Cluster Report: rs10038062

refSNP ID: rs10038062
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	119/129
Map to Genome Build:	36.3

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

HGVS Names
NM_000949.2:c.-106+9851G>A
NT_006576.15:g.35193276C>T

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss13885624 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs10038062 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
ss13885624	WI_SSAHASNP\|chr5.NT_006576.14_17672625	fwd/B	C/T	ccagctctcggcatgcttttctttttagta	tgatgtgctagcttgaagggcacctcctca	11/05/03	10/25/06	119	Genomic	unknown
ss17061046	CSHL-HAPMAP\|CSHL-HuAA-200402.chr5.NT_006576.14_17672625	fwd/B	C/T	ccagctctcggcatgcttttctttttagta	tgatgtgctagcttgaagggcacctcctca	02/17/04	03/04/04	120	Genomic	unknown
ss22298529	SSAHASNP\|WGSA-200403-chr5.chr5.NT_006576.14_17672625	fwd/B	C/T	ccagctctcggcatgcttttctttttagta	tgatgtgctagcttgaagggcacctcctca	03/21/04	03/21/04	121	Genomic	unknown
ss42643182	ABI\|hCV1438976	fwd/B	C/T	ccagctctcggcatgcttttctttttagta	tgatgtgctagcttgaagggcacctcctca	07/18/05	07/18/05	126	Genomic	unknown
ss66060749	AFFY\|SNP_A-1855254	rev/T	A/G	tcaagctagcacatca	tactaaaaagaaaagc	10/27/06	03/31/08	127	Genomic	unknown
ss75979301	AFFY\|AFFY_6_1M_SNP_A-1855254	rev/T	A/G	tcaagctagcacatca	tactaaaaagaaaagc	08/28/07	08/29/07	130	Genomic	unknown
ss77815230	HGSV\|Cor12156_SNV_20070510.chr5_35256276	fwd/B	C/T	ccagctctcggcatgcttttctttttagta	tgatgtgctagcttgaagggcacctcctca	10/09/07	10/14/07	129	Genomic	unknown
ss78799042	HGSV\|Cor12878_SNV_20070510.chr5_35256276	fwd/B	C/T	ccagctctcggcatgcttttctttttagta	tgatgtgctagcttgaagggcacctcctca	10/17/07	10/20/07	129	Genomic	unknown
ss85220622	HGSV\|Cor19240_SNV_20070510.chr5_35256276	fwd/B	C/T	ccagctctcggcatgcttttctttttagta	tgatgtgctagcttgaagggcacctcctca	11/30/07	12/08/07	130	Genomic	unknown
ss93058823	BCMHGSC_JDW\|JWB-1962701	fwd/B	C/T	ccagctctcggcatgcttttctttttagta	tgatgtgctagcttgaagggcacctcctca	02/26/08	03/03/08	129	Genomic	unknown

Fasta sequence (Legend)

 AGGTTTTCCA GCACTTTCGC TGGTCCCCtc catctgaaag ccatgctggc catacctcca
 aattccatcc tgaatccaac acctcttcca ccttgcttgc tgtcaccttg gcatgatcca
 ccctcccctc ttgcttgtac ttccgatcag cctcctacaa accctctgct ttcagtcttc
 aagccattct ccacacagaa gctgggaaga gctctcaaag gcaatgccaa ccatgatcct
 accctgctga aaacctccca atgagttagg atgttaggct ctcaaagcac ttaacagcct
 aactccatcc catgacctcg ggccctcctt gctcttttcc cacctttccc tcattgcttc
 ttacctcggg tccagccacA ATGGTCTCAT TTCTGTTTCC TGAACAACTC AGACCTTTTC
 CAGTCTTAGG ACTTTTGCTG TTGTTCTTTC TGCCTGAAGC CTTCTTTCTG CCAGCTCTCG
 GCATGCTTTT CTTTTTAGTA
 Y
 TGATGTGCTA GCTTGAAGGG CACCTCCTCA GACAGTGCAA CTTGTACAAG CTATTGAAAG
 CAGCCTTCAG CAAACTCTAT TCCCTTCAGT TCATTGCATT TTTTTCATAG TACTGACTAA
 TTTATTGGGT TTTATTTATT GTTTGTTTTT AGTGTGGATA TCTGTTTCCT CTTACTGGAA
 TCTAAACTAC ACTAGAGTAG GAACTTCATC CTTCTATCTC CAGCTCCTAT AATGGGTCCT
 TGGAACAAAG CAGAACCTCC ATAAACATTA GTTGAGTGAA TAAAGAAATT CTGATGCCCA
 TGATAGTTGA CTAACAGGAG GCCTCTGTCC ATCGTTCTCC CCTGCGATCT TTTTTCTTAT
 TTTCTCCTAA TCCCACAATC TCAGCACCCC AGAAAACAAA ATGCTACATC ACCTTCTGTC
 CCCCAGCCTC TTCCATCAAA TCTAATACAA AAACCTGGTT TCTTTTTGTT ATTAATACAA
 CCTT

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	35193276	reverse	intron

HuRef	NW_001838932->NM_000949->NP_000940	488114	forward	intron

Celera	NW_922596->NM_000949->NP_000940	813121	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs10038062 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	813121	35102607	plus	T	alt_assembly_1	Celera	Celera	view	500
5	NW_001838932.2	488114	35169176	minus	A	alt_assembly_8	HuRef	HuRef	view	500
5	NT_006576.15	35193276	35256276	plus	C	ref_assembly	reference	reference	view	500

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	C/T	T/T	HWP	C	T
ss13885624	HapMap-CEU	European	120	IG		0.200	0.800	0.403	0.100	0.900

	HapMap-HCB	Asian	90	IG	0.222	0.467	0.311	0.752	0.456	0.544

	HapMap-JPT	Asian	90	IG	0.244	0.600	0.156		0.544	0.456

	HapMap-YRI	Sub-Saharan African	120	IG	0.017	0.050	0.933	0.005	0.042	0.958

ss66060749	HapMap-CEU	European	118	GF		0.220	0.780		0.110	0.890

	HapMap-HCB	Asian	90	GF	0.222	0.467	0.311		0.456	0.544

	HapMap-JPT	Asian	90	GF	0.244	0.600	0.156		0.544	0.456

	HapMap-YRI	Sub-Saharan African	120	GF	0.017	0.050	0.933		0.042	0.958

Concordant Genotype	Total Sample	C/C	C/T	T/T
ss13885624	268	23	70	175
ss66060749	267

RefSNP Genotype Summary	Total Individual	C/C	C/T	T/T
rs10038062	270	23	70	175

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
239	ss13885624	T/T	CSHL-HAPMAP	HapMap-CEU	NA11882	CEPH1347.15	r23_ch5_CEU_perlegen:genotyping_1.0.0	2867915
239	ss66060749	A/G	CSHL-HAPMAP	HapMap-CEU	NA11882	CEPH1347.15	chr5-HapMap-CEU
5244	ss13885624	T/T	CSHL-HAPMAP	HapMap-YRI	NA18860	YOR012.01	r23_ch5_YRI_perlegen:genotyping_1.0.0	2867915
5244	ss66060749	A/G	CSHL-HAPMAP	HapMap-YRI	NA18860	YOR012.01	chr5-HapMap-YRI

Genotype data submitted for	270	samples from	270	individuals	Individual with multiple genotypes submission:	269

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

UNKNOWN

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Revised: May 25, 2006 1:38 PM .