Reference SNP(refSNP) Cluster Report: rs17211022

Search for SNP on NCBI Reference Assembly

Search Entrez for

BUILD 129

Have a question about dbSNP? Try searching the SNP FAQ Archive!

Reference SNP(refSNP) Cluster Report: rs17211022

refSNP ID: rs17211022
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	123/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	C/T
Ancestral Allele:	Not available
Clinical Association:	unknown

HGVS Names

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss23138929 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs17211022 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
ss23138929	FHCRC\|2JJ05_7684		fwd/B	C/T	tagctcagcacccacaatgtgcacttacgt	tggtgtccccagccaaagccagtggggagc	04/15/04	04/28/04	123	Genomic			unknown

Fasta sequence (Legend)

 GTCACAATTT CTTAAGGTAC ATGGCCTGGG CACAATGTTA ACAAAACTCC CTATTTTCCC
 CACCCCATAG TAGCTCAGCA CCCACAATGT GCACTTACGT
 Y
 TGGTGTCCCC AGCCAAAGCC AGTGGGGAGC TCAGCACCAT CAGTGTCACT GTCAGAACTG
 CCATGCAGGA GCCTCCAGGG AGCCTCAGAC ACACCATGCT

GeneView

GeneView via analysis of contig annotation: HLA-DRB1 major histocompatibility complex, class II, DR beta 1

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

GeneView via analysis of contig annotation: LOC730415 hypothetical protein LOC730415

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

GeneView via analysis of contig annotation: HLA-DRB4 major histocompatibility complex, class II, DR beta 4

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

c6_COX

NT_113891->NM_002124

function

HuRef

NW_001838980->XM_001720834

function

HuRef

NW_001838980->XM_001720835

function

HuRef

NW_001838980->XM_001720843

function

Celera

NW_923073->XM_001124749

function

c6_QBL

NT_113896->XM_001723414

function

c6_QBL

NT_113896->XM_001723417

function

c6_QBL

NT_113896->XM_001723419

function

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


c6_COX	NT_113891->NM_002124->NP_002115	3947869	reverse	160	missense	A	Lys [K]	2	33
					contig reference	G	Arg [R]	2	33

HuRef	NW_001838980->XM_001720834->XP_001720886	5575104	reverse	162	missense	A	Lys [K]	2	33
					contig reference	G	Arg [R]	2	33

HuRef	NW_001838980->XM_001720835->XP_001720887	5575104	reverse	175	missense	A	Lys [K]	2	33
					contig reference	G	Arg [R]	2	33

HuRef	NW_001838980->XM_001720843->XP_001720895	5575104	reverse	162	missense	A	Lys [K]	2	33
					contig reference	G	Arg [R]	2	33

Celera	NW_923073->XM_001124749->XP_001124749	5572577	reverse	202	missense	A	Lys [K]	2	33
					contig reference	G	Arg [R]	2	33

c6_QBL	NT_113896->XM_001723414->XP_001723466	428782	reverse	202	missense	A	Lys [K]	2	33
					contig reference	G	Arg [R]	2	33

c6_QBL	NT_113896->XM_001723417->XP_001723469	428782	reverse	161	missense	A	Lys [K]	2	33
					contig reference	G	Arg [R]	2	33

c6_QBL	NT_113896->XM_001723419->XP_001723471	428782	reverse	202	missense	A	Lys [K]	2	33
					contig reference	G	Arg [R]	2	33

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: See all two hits of rs17211022 on the NCBI human genome map
!WARNING: Several map positions found! The map position is found by blasting with the contig sequences.

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
6	NW_001838980.1	5575104	32302795	plus	C	alt_assembly_8	HuRef	HuRef	view	100
6	NG_002433.1	146154	32387788	plus	C	alt_haplotype_7	DR53	DR53	view	100
6	NT_007592.14	23356154	32605882	plus	C	ref_assembly	reference	reference	view	100
6	NT_113891.1	3947869	32636412	plus	C	alt_assembly_3	c6_COX	c6_COX	view	100
6	NT_113896.1	428782	32637277	plus	C	alt_assembly_4	c6_QBL	c6_QBL	view	100
6	NT_007592.14	23415672	32665400	plus	C	ref_assembly	reference	reference	view	100
6	NW_923073.1	5572577	34108256	plus	C	alt_assembly_1	Celera	Celera	view	100

NCBI Resource Links

Submitter-Referenced
GenBank
NT_007592.13

dbSNP Blast Analysis
GenBank HTGS Finished:
AL662842.3 AL929581.5 Z84489.1

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	T/T	HWP	C	T
ss23138929	POPU2		56	IG	0.643	0.357	0.001	0.643	0.357

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.459+/-0.137	28	28	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

Disclaimer Privacy statement

Revised: May 25, 2006 1:38 PM .