Reference SNP(refSNP) Cluster Report: rs175138

Reference SNP(refSNP) Cluster Report: rs175138

refSNP ID: rs175138
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	79/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	A/G
Ancestral Allele:	A
Clinical Association:	unknown

HGVS Names

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss2066569 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs175138 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
ss233083	KWOK\|OVLP-000621-115809	fwd/T	A/G	cataagctacagtttccacatctgtacaat	ataacatcattagaatcttcctggggagat	06/30/00	10/10/03	79	Genomic	94 %
ss781735	SC_JCM\|AC007064.2_62945	fwd/T	A/G	cataagctacagtttccacatctgtacaat	ataacatcattagaatcttcctggggagat	07/27/00	10/10/03	85	Genomic	unknown
ss1277279	KWOK\|OVLP-000804-621395	fwd/T	A/G	cataagctacagtttccacatctgtacaat	ataacatcattagaatcttcctggggagat	09/02/00	10/10/03	86	Genomic	94 %
ss2066569	KWOK\|OVLP-000925-316686	fwd/T	A/G	cataagctacagtttccacatctgtacaat	ataacatcattagaatcttcctggggagat	10/07/00	04/07/04	87	Genomic	94 %
ss2460384	SC_JCM\|AC007064.27_62945	fwd/T	A/G	cataagctacagtttccacatctgtacaat	ataacatcattagaatcttcctggggagat	11/03/00	10/10/03	92	Genomic	unknown
ss7994872	SC_SNP\|NT_011519.9_456189	fwd/T	A/G	cataagctacagtttccacatctgtacaat	ataacatcattagaatcttcctggggagat	04/15/03	10/10/03	114	Genomic	unknown
ss13344677	SC_SNP\|NT_011519.10_456282	fwd/T	A/G	cataagctacagtttccacatctgtacaat	ataacatcattagaatcttcctggggagat	10/22/03	10/31/03	119	Genomic	unknown
ss21841205	SSAHASNP\|WGSA-200403-chr22.chr22.NT_011519.10_456282	fwd/T	A/G	cataagctacagtttccacatctgtacaat	ataacatcattagaatcttcctggggagat	03/20/04	03/20/04	121	Genomic	unknown
ss44319197	ABI\|hCV3269244	fwd/T	A/G	cataagctacagtttccacatctgtacaat	ataacatcattagaatcttcctggggagat	07/18/05	07/18/05	126	Genomic	unknown
ss65716600	ILLUMINA\|Human1-rs175138	fwd/T	A/G	cataagctacagtttccacatctgtacaat	ataacatcattagaatcttcctggggagat	10/10/06	10/10/06	127	Genomic	unknown
ss65825273	KRIBB_YJKIM\|KHS1057	fwd/T	A/G	cataagctacagtttccacatctgtacaat	ataacatcattagaatcttcctggggagat	10/17/06	12/16/06	127	Genomic	unknown
ss69277762	PERLEGEN\|PGP13186868	fwd/T	A/G	cataagctacagtttccacatctgtacaat	ataacatcattagaatcttcctggggagat	01/30/07	08/14/07	127	Genomic	unknown
ss69379151	SI_EXO\|NT_011519.10_456282	fwd/T	A/G	cataagctacagtttccacatctgtacaat	ataacatcattagaatcttcctggggagat	04/12/07	04/12/07	127	Genomic	unknown
ss74859371	ILLUMINA\|ILMN_Human_1M_rs175138	fwd/T	A/G	cataagctacagtttccacatctgtacaat	ataacatcattagaatcttcctggggagat	08/28/07	08/29/07	129	Genomic	unknown
ss85655840	HGSV\|Cor19129_SNV_20070510.chr22_15678686	fwd/T	A/G	cataagctacagtttccacatctgtacaat	ataacatcattagaatcttcctggggagat	12/06/07	12/09/07	130	Genomic	unknown
ss85824466	HGSV\|Cor18517_SNV_20070510.chr22_15678686	fwd/T	A/G	cataagctacagtttccacatctgtacaat	ataacatcattagaatcttcctggggagat	12/06/07	12/10/07	130	Genomic	unknown
ss91869097	BCMHGSC_JDW\|JWB-1507546	fwd/T	A/G	cataagctacagtttccacatctgtacaat	ataacatcattagaatcttcctggggagat	02/26/08	03/02/08	129	Genomic	unknown

Fasta sequence (Legend)

 GCAATTTTGT ATGTTAATTT TAGACTTTTT TCTTTAATCA AATCTTTGAA AAATGCAATT
 GACTGTTGAA ATAATAAAAT ATTGTGGTTA TATAATTTTA AAAATGCATG TAGCACAGAG
 GCTGAGAGGG GATAATGGTA CATGTTATTT TAGTGTTTTA ACATTGTCCA TAGAGAAGTG
 TAATACCTCT TCAAGGTAGG TTGTGGTAAA TTTGAGATGT ACACTACAAA CCTCAAAGCA
 AGAACTAAAG TAACAGTAAC AGCTAAGAAA CCAACAAAGG CCATAATAGG AAATTaaaaa
 aataaataaa taatagaaaa gaagacagat aagagaaaat ggaacaagta acacatggag
 aaaacagaaa gctacatcaa tcagcacatt aactgtaaat ggcttatata ccacaactaa
 aaggtaaagc ctataagaga aataaaaata gtaaaatcca gttatatgtt gtctcctgga
 aacccatact tgacataaag acacaattac tacggaagag atggaataaa gctgtgcact
 actaacccta gtgataagac tgctggaatg gctatattaa tatcagacaa agtagaGCAA
 AAAAAATGGA AAATATCAAC TGATGCTCAA GTTGTTCtgg ttagcagtac aaactctgga
 accagacttt ctgagttaca atactgtcac ttctatttTT TTCTTTTAAC TATAAAATAA
 ATGTCCACAT TGCTAACAAG CATATTAACT AGCTTATTAT GCTTGCTTCC TTTGCTTTTG
 GTTGTGGTGG GTAtttattt gtttattttt taagacatga tctgcccttg tcacccaggt
 tggagtgcag tggcgtgacc tagactcact gaagcctcaa cctccaggac tcaaatgatc
 ctcctgcctt agcctcccaa gtagctggga ccacaggtgc atgccaccat gtacactaat
 ttttgtgttt tttgaggaga tggggtttga ccatcttcct ggtctcaaac tcatgagcta
 aagtgatcca cctgcctcag ccttccagtg ttgggattac aagcatgagc taccacacTG
 CCAGAATCCT GTCATTTCCT TGAATTGCAA AATTAAAACC TCATAAGCTA CAGTTTCCAC
 ATCTGTACAA T
 R
 ATAACATCAT TAGAATCTTC CTGGGGAGAT AGCAGTGTAG AGAAAATAAT ACATCGGCAG
 CAGGAAGAAG AGTTCGTGGT ACACAGTGAA GTTTGGAAAG GTGTTCCTAT TGATATCATT
 ATAATCATGA CCACCATCAT CATTTCTTAG AAACACAGAA TTGACAGGAC TCACTGATTA
 AGAGTATTTG ACAGTGAAAT ATGAGAGAAG AGATTGCCTT GGTCAATTCT TGAGTATCCA
 TCTGGTAGAG CTTGGAAAAG TGGTGGAAGC AGAATTTTTG GGAAAAACA

GeneView

GeneView via analysis of contig annotation: XKR3 XK, Kell blood group complex subunit-related family, member 3

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

HuRef

NW_001838735->NM_175878

function

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


HuRef	NW_001838735->NM_175878->NP_787074	1356667	forward	5' near gene

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs175138 maps exactly once on NCBI human chromosome 22

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
22	NW_927406.1	259403	926403	plus	A	alt_assembly_1	Celera	Celera	view	1151
22	NW_001838735.2	1356667	1123667	minus	T	alt_assembly_8	HuRef	HuRef	view	1151
22	NT_011519.10	456282	15684132	plus	G	ref_assembly	reference	reference	view	1151

NCBI Resource Links

Submitter-Referenced
GenBank
NT_011519.10 AC006548 AC007064.27

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss2066569	CEPH		184	AF					0.690	0.310

	HapMap-CEU	European	120	IG	0.300	0.550	0.150	0.343	0.575	0.425

	HapMap-HCB	Asian	90	IG	0.333	0.556	0.111	0.273	0.611	0.389

	HapMap-JPT	Asian	88	IG	0.341	0.409	0.250	0.251	0.545	0.455

	HapMap-YRI	Sub-Saharan African	120	IG	0.400	0.433	0.167	0.527	0.617	0.383

ss65825273	KHP1		168	AF	0.333	0.512	0.155	0.655	0.589	0.411

ss69277762	HapMap-CEU	European	120	GF	0.333	0.517	0.150		0.592	0.408

	HapMap-HCB	Asian	90	GF	0.489	0.400	0.111		0.689	0.311

	HapMap-JPT	Asian	90	GF	0.356	0.400	0.244		0.556	0.444

	HapMap-YRI	Sub-Saharan African	120	GF	0.400	0.433	0.167		0.617	0.383

Concordant Genotype	Total Sample	A/A	A/G	G/G
ss2066569	253	92	120	40
ss69277762	253	92	121	40

RefSNP Genotype Summary	Total Individual	A/A	A/G	G/G
rs175138	270	92	121	40

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
172	ss2066569	A/G	CSHL-HAPMAP	HapMap-CEU	NA07056	CEPH1340.12	r23_ch22_CEU_illumina:golden_gate_1.0.0	961620
172	ss69277762	A/A	CSHL-HAPMAP	HapMap-CEU	NA07056	CEPH1340.12	chr22-HapMap-CEU
252	ss2066569	A/G	CSHL-HAPMAP	HapMap-CEU	NA11839	CEPH1349.13	r23_ch22_CEU_illumina:golden_gate_1.0.0	961620
252	ss69277762	A/A	CSHL-HAPMAP	HapMap-CEU	NA11839	CEPH1349.13	chr22-HapMap-CEU
254	ss2066569	A/G	CSHL-HAPMAP	HapMap-CEU	NA10856	CEPH1350.01	r23_ch22_CEU_illumina:golden_gate_1.0.0	961620
254	ss69277762	A/A	CSHL-HAPMAP	HapMap-CEU	NA10856	CEPH1350.01	chr22-HapMap-CEU
265	ss2066569	A/A	CSHL-HAPMAP	HapMap-CEU	NA11832	CEPH1350.13	r23_ch22_CEU_illumina:golden_gate_1.0.0	961620
265	ss69277762	A/G	CSHL-HAPMAP	HapMap-CEU	NA11832	CEPH1350.13	chr22-HapMap-CEU
399	ss2066569	A/G	CSHL-HAPMAP	HapMap-CEU	NA10830	CEPH1408.01	r23_ch22_CEU_illumina:golden_gate_1.0.0	961620
399	ss69277762	A/A	CSHL-HAPMAP	HapMap-CEU	NA10830	CEPH1408.01	chr22-HapMap-CEU
546	ss2066569	A/G	CSHL-HAPMAP	HapMap-CEU	NA12761	CEPH1447.10	r23_ch22_CEU_illumina:golden_gate_1.0.0	961620
546	ss69277762	A/A	CSHL-HAPMAP	HapMap-CEU	NA12761	CEPH1447.10	chr22-HapMap-CEU
5139	ss2066569	A/G	CSHL-HAPMAP	HapMap-YRI	NA19100	YOR105.01	r23_ch22_YRI_illumina:golden_gate_1.1.0	961620
5139	ss69277762	A/A	CSHL-HAPMAP	HapMap-YRI	NA19100	YOR105.01	chr22-HapMap-YRI
5144	ss2066569	A/A	CSHL-HAPMAP	HapMap-YRI	NA19192	YOR112.03	r23_ch22_YRI_illumina:golden_gate_1.1.0	961620
5144	ss69277762	A/G	CSHL-HAPMAP	HapMap-YRI	NA19192	YOR112.03	chr22-HapMap-YRI
5153	ss2066569	A/G	CSHL-HAPMAP	HapMap-HCB	NA18561	CH18561	r23_ch22_HCB_illumina:golden_gate_1.1.0	961620
5153	ss69277762	A/A	CSHL-HAPMAP	HapMap-HCB	NA18561	CH18561	chr22-HapMap-HCB
5161	ss2066569	A/G	CSHL-HAPMAP	HapMap-HCB	NA18572	CH18572	r23_ch22_HCB_illumina:golden_gate_1.1.0	961620
5161	ss69277762	A/A	CSHL-HAPMAP	HapMap-HCB	NA18572	CH18572	chr22-HapMap-HCB
5174	ss2066569	A/G	CSHL-HAPMAP	HapMap-HCB	NA18571	CH18571	r23_ch22_HCB_illumina:golden_gate_1.1.0	961620
5174	ss69277762	A/A	CSHL-HAPMAP	HapMap-HCB	NA18571	CH18571	chr22-HapMap-HCB
5176	ss2066569	A/G	CSHL-HAPMAP	HapMap-HCB	NA18621	CH18621	r23_ch22_HCB_illumina:golden_gate_1.1.0	961620
5176	ss69277762	A/A	CSHL-HAPMAP	HapMap-HCB	NA18621	CH18621	chr22-HapMap-HCB
5180	ss2066569	A/G	CSHL-HAPMAP	HapMap-HCB	NA18623	CH18623	r23_ch22_HCB_illumina:golden_gate_1.1.0	961620
5180	ss69277762	A/A	CSHL-HAPMAP	HapMap-HCB	NA18623	CH18623	chr22-HapMap-HCB
5181	ss2066569	A/G	CSHL-HAPMAP	HapMap-HCB	NA18576	CH18576	r23_ch22_HCB_illumina:golden_gate_1.1.0	961620
5181	ss69277762	A/A	CSHL-HAPMAP	HapMap-HCB	NA18576	CH18576	chr22-HapMap-HCB
5187	ss2066569	A/G	CSHL-HAPMAP	HapMap-HCB	NA18633	CH18633	r23_ch22_HCB_illumina:golden_gate_1.1.0	961620
5187	ss69277762	A/A	CSHL-HAPMAP	HapMap-HCB	NA18633	CH18633	chr22-HapMap-HCB
5199	ss2066569	A/G	CSHL-HAPMAP	HapMap-JPT	NA18945	JA18945	r23_ch22_JPT_illumina:golden_gate_1.1.0	961620
5199	ss69277762	A/A	CSHL-HAPMAP	HapMap-JPT	NA18945	JA18945	chr22-HapMap-JPT
5272	ss2066569	A/G	CSHL-HAPMAP	HapMap-YRI	NA19102	YOR042.02	r23_ch22_YRI_illumina:golden_gate_1.1.0	961620
5272	ss69277762	A/A	CSHL-HAPMAP	HapMap-YRI	NA19102	YOR042.02	chr22-HapMap-YRI

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

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, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .