Reference SNP(refSNP) Cluster Report: rs554821

Reference SNP(refSNP) Cluster Report: rs554821

refSNP ID: rs554821
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	83/129
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_130386.1:c.2064-376C>T
NT_010859.14:g.312183G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44090421 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs554821 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
ss725823	SC_JCM\|AP000900.3_158617	fwd/T	A/G	tatatatgtgtgtgaatatctattcattat	aggacatgatacacacacacacacacacac	07/27/00	10/10/03	83	Genomic	unknown
ss1984405	KWOK\|OVLP-000925-46198	fwd/T	A/G	tatatatgtgtgtgaatatctattcattat	aggacatgatacacacacacacacacacac	10/06/00	04/07/04	87	Genomic	99 %
ss1985023	KWOK\|OVLP-000925-56509	fwd/T	A/G	tatatatgtgtgtgaatatctattcattat	aggacatgatacacacacacacacacacac	10/06/00	10/10/03	87	Genomic	99 %
ss20047825	CSHL-HAPMAP\|CSHL-HuFF-200402.chr18.NT_010859.13_312183	fwd/T	A/G	tatatatgtgtgtgaatatctattcattat	aggacatgatacacacacacacacacacac	02/21/04	03/04/04	120	Genomic	unknown
ss24013002	PERLEGEN\|afd1763287	fwd/T	A/G	tatatatgtgtgtgaatatctattcattat	aggacatgatacacacacacacacacacac	08/10/04	09/13/04	123	Genomic	unknown
ss44090421	ABI\|hCV634108	fwd/T	A/G	tatatatgtgtgtgaatatctattcattat	aggacatgatacacacacacacacacacac	07/18/05	11/03/06	126	Genomic	unknown
ss65999720	AFFY\|SNP_A-1730852	fwd/T	A/G	atgtgtgtgaatatctattcattat	aggacatgatacacacacacacaca	10/26/06	10/26/06	127	Genomic	unknown
ss66844773	ILLUMINA\|HumanHap300v1.1_rs554821	fwd/T	A/G	tatatatgtgtgtgaatatctattcattat	aggacatgatacacacacacacacacacac	11/09/06	11/09/06	127	Genomic	unknown
ss67417104	ILLUMINA\|HumanHap550v1.1_rs554821	fwd/T	A/G	tatatatgtgtgtgaatatctattcattat	aggacatgatacacacacacacacacacac	11/14/06	11/14/06	127	Genomic	unknown
ss67779486	ILLUMINA\|HumanHap650Yv1.0_rs554821	fwd/T	A/G	tatatatgtgtgtgaatatctattcattat	aggacatgatacacacacacacacacacac	11/14/06	11/14/06	127	Genomic	unknown
ss69204365	PERLEGEN\|PGP01763287	fwd/T	A/G	tatatatgtgtgtgaatatctattcattat	aggacatgatacacacacacacacacacac	01/30/07	08/14/07	127	Genomic	unknown
ss70845372	ILLUMINA\|HumanHap550v3.0__rs554821	fwd/T	A/G	tatatatgtgtgtgaatatctattcattat	aggacatgatacacacacacacacacacac	04/20/07	03/31/08	130	Genomic	unknown
ss71429886	ILLUMINA\|HumanHap650Yv3.0_rs554821	fwd/T	A/G	tatatatgtgtgtgaatatctattcattat	aggacatgatacacacacacacacacacac	04/23/07	04/23/07	127	Genomic	unknown
ss75870215	ILLUMINA\|ILMN_Human_1M_rs554821	fwd/T	A/G	tatatatgtgtgtgaatatctattcattat	aggacatgatacacacacacacacacacac	08/28/07	08/29/07	129	Genomic	unknown
ss76552416	AFFY\|AFFY_6_1M_SNP_A-8413436	fwd/T	A/G	aatatctattcattat	aggacatgatacacac	08/28/07	08/30/07	129	Genomic	unknown
ss77437931	HGSV\|Cor12156_SNV_20070510.chr18_312183	fwd/T	A/G	tatatatgtgtgtgaatatctattcattat	aggacatgatacacacacacacacacacac	10/09/07	10/13/07	129	Genomic	unknown
ss79208546	ILLUMINA\|HumanHap300v2.0_rs554821	fwd/T	A/G	tatatatgtgtgtgaatatctattcattat	aggacatgatacacacacacacacacacac	04/18/07	11/18/07	130	Genomic	unknown
ss82735162	HGSV\|Cor18555_SNV_20070510.chr18_312183	fwd/T	A/G	tatatatgtgtgtgaatatctattcattat	aggacatgatacacacacacacacacacac	11/27/07	12/03/07	130	Genomic	unknown
ss83482227	KRIBB_YJKIM\|KHS472047	fwd/T	A/G	tatatatgtgtgtgaatatctattcattat	aggacatgatacacacacacacacacacac	12/04/07	12/05/07	130	Genomic	unknown

Fasta sequence (Legend)

 TATAAAAAAA CAAAATTGAA GCATGTCATT TATCCTGGAA TGAAAATGCA GTTTAAAAAT
 CAGTACATGC TCTTATTCAG AGAAAGGAGC AGCTGTTTTG CAGAGTAATG CATAATGCGG
 CATCTCCCTG CGCGCTTGTG ATCTTTGCTA CCATGAACCA AACTCACTAG GCTGGTTCAT
 CAGAATGCAG AGGGAGCGAA TCTTGCTTTG GGACAGTTAG ATGAATAACT TTCTAATGTG
 TACTGGAATG CTGACTTCTG GGCATGAGTG TATATATGTG TGTGAATATC TATTCATTAT
 R
 AGGACATGAT ACACACACAC ACACACACAC ACACGCACAC ATGATCTTGT GAGAACCCAG
 AGGGACCTTG TACATTTCAA TATCTTGCCT CTAACAAGTC CAAGAGCCAG GAAGAGAAAG
 TGAAAGACTT TTGATATACA TTTACAAGAA CCTACAATTA CAAATAACTG GTTATGATTG
 TCTGGGTGAG TTGTAGAAGG TTGATTGCTT TAGAAAGAAA TAGTAACTTA ATCTTACTGA
 AAATGACTCC TACATTTCAC TCCCTTTTTT GGGAGAGAGA TTCTTAAAAA CAAGTTTTCT

GeneView

GeneView via analysis of contig annotation: COLEC12 collectin sub-family member 12

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_010859->NM_130386

function

HuRef

NW_001838461->NM_130386

function

Celera

NW_926940->NM_130386

function

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


reference	NT_010859->NM_130386->NP_569057	312183	reverse	intron

HuRef	NW_001838461->NM_130386->NP_569057	270327	reverse	intron

Celera	NW_926940->NM_130386->NP_569057	197334	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs554821 maps exactly once on NCBI human chromosome 18

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
18	NW_926940.1	197334	197334	plus	G	alt_assembly_1	Celera	Celera	view	300
18	NW_001838461.1	270327	281967	plus	G	alt_assembly_8	HuRef	HuRef	view	300
18	NT_010859.14	312183	312183	plus	G	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_010859 AP000915 AP000939 AP001022 AP001022.2

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AP000915.5 NC_000018.8	AC016128.4 AP000900.3 AP000939.3 AP001022.2

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss1984405	AfAm	African American	12	IG		0.167	0.833	1.000	0.083	0.917

	Caucasian	European	20	IG		0.400	0.600	0.439	0.200	0.800

	Asian	Asian	12	IG	0.167	0.167	0.667	0.200	0.250	0.750

	CEPH	European	12	IG		0.667	0.333	0.251	0.333	0.667

	PDpanel	Global	46	IG		0.348	0.652	0.317	0.174	0.826

	CHMJ	Asian	74	IG					0.338	0.662

ss24013002	AFD_EUR_PANEL	European	44	IG	0.091	0.273	0.636	0.317	0.227	0.773

	AFD_AFR_PANEL	African American	44	IG		0.136	0.864	0.752	0.068	0.932

	AFD_CHN_PANEL	Asian	42	IG	0.095	0.381	0.524	1.000	0.286	0.714

ss44090421	HapMap-CEU	European	120	IG	0.033	0.383	0.583	0.479	0.225	0.775

	HapMap-HCB	Asian	90	IG	0.111	0.400	0.489	0.254	0.311	0.689

	HapMap-JPT	Asian	90	IG	0.067	0.556	0.378	0.584	0.344	0.656

	HapMap-YRI	Sub-Saharan African	120	IG			1.000			1.000

ss69204365	HapMap-CEU	European	120	GF	0.033	0.383	0.583		0.225	0.775

	HapMap-HCB	Asian	90	GF	0.111	0.400	0.489		0.311	0.689

	HapMap-JPT	Asian	90	GF	0.067	0.556	0.378		0.344	0.656

	HapMap-YRI	Sub-Saharan African	120	GF			1.000			1.000

Concordant Genotype	Total Sample	A/A	A/G	G/G
ss1984405	51	1	18	32
ss24013002	70	3	17	44
ss44090421	268	11	77	180
ss69204365	268	11	77	180

RefSNP Genotype Summary	Total Individual	A/A	A/G	G/G
rs554821	377	15	108	248

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
188	ss24013002	A/A	PERLEGEN	AFD_EUR_PANEL	NA10851		71_IND_CHR_18
188	ss44090421	A/G	CSHL-HAPMAP	HapMap-CEU	NA10851	CEPH1344.01	r23_ch18_CEU_illumina:infinium_genotyping_2.0.0	108928
188	ss69204365	A/G	CSHL-HAPMAP	HapMap-CEU	NA10851	CEPH1344.01	chr18-HapMap-CEU
5253	ss44090421	G/G	CSHL-HAPMAP	HapMap-YRI	NA18872	YOR017.01	r23_ch18_YRI_illumina:infinium_genotyping_2.0.0	108928
5253	ss69204365	A/G	CSHL-HAPMAP	HapMap-YRI	NA18872	YOR017.01	chr18-HapMap-YRI

Genotype data submitted for	392	samples from	377	individuals	Individual with multiple genotypes submission:	276

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 .