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Reference SNP (refSNP) Cluster Report: rs333                 ** With other allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:36/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Allele
Variation Class:DIV:
deletion/insertion variation
RefSNP Alleles:-/GTCAGTATCAATTCTGGAAGAATTTCCAGACA (FWD)
Allele Origin:
Ancestral Allele:Not available
Variation Viewer:link to VariationViewer
Clinical Significance:With other allele [ClinVar]
MAF/MinorAlleleCount:-=0.0726/8805 (ExAC)
-=0.0292/146 (1000 Genomes)
HGVS Names
  • CM000665.2:g.46373456_46373487del32
  • NC_000003.11:g.46414947_46414978del32
  • NC_000003.12:g.46373456_46373487del32
  • NG_012637.1:g.8315_8346del32
  • NM_000579.3:c.554_585del32
  • NM_001100168.1:c.554_585del32
  • NP_000570.1:p.Ser185Ilefs
  • NP_001093638.1:p.Ser185Ilefs
  • NR_125406.1:n.392-2070_392-2039del32
  • XP_005264911.1:p.Ser185Ilefs
  • XP_005264912.1:p.Tyr184_Ile185(?)
Links , Linkout
SNP Details are organized in the following sections:
GeneView Map Submission Fasta Resource Diversity Validation

  Integrated Maps (Hint: click on 'Chr Pos' to see variant in the new NCBI variation viewer) back to top

  GeneView back to top

GeneView via direct blast against RefSeq sequences (used when no gene model is available): N/A


  Submitter records for this RefSNP Cluster back to top
The submission ss334 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs333 during BLAST analysis for the current build.


NCBI
Assay ID		Handle|Submitter IDValidation
Status		ss to rs
Orientation
/Strand		Alleles5' Near Seq 30 bp3' Near Seq 30 bpEntry
Date		Update
Date		Build
Added		Molecule
Type		Freq
Warning		Ancestral
Allele		Success
Rate
ss334NCBI|CCR5-largedelfwd/B-/GTCAGTATCAATTCTGGAAGAATTTCCAGACAattacacctgcagctctcattttccatacattaaagatagtcatcttggggctggtcctg11/24/9810/10/0336Genomicunknown
ss5586335SNP500CANCER|CCR5-01byFreqfwd/B-/GTCAGTATCAATTCTGGAAGAATTTCCAGACAattacacctgcagctctcattttccatacattaaagatagtcatcttggggctggtcctg09/26/0204/07/04113Genomicunknown
ss6312538KIDDLAB|SI000676TbyFreqfwd/B-/GTCAGTATCAATTCTGGAAGAATTTCCAGACAattacacctgcagctctcattttccatacattaaagatagtcatcttggggctggtcctg01/17/0308/05/04113Genomicunknown
ss76868272CGM_KYOTO|9656fwd/-/GTCAGTATCAATTCTGGAAGAATTTCCAGACAattacacctgcagctctcattttccatacattaaagatagtcatcttggggctggtcctg09/12/0709/12/07131cDNAunknown
ss95210450CNG|29947915fwd/-/GTCAGTATCAATTCTGGAAGAATTTCCAGACAattacacctgcagctctcattttccatacattaaagatagtcatcttggggctggtcctg03/13/0803/13/08130Genomicunknown
ss13702917081000GENOMES|PHASE3_V1_15082169byFreqfwd/-/ACAGTCAGTATCAATTCTGGAAGAATTTCCAGtacacctgcagctctcattttccatacattaaagatagtcatcttggggc08/16/1408/07/15136Genomicunknown
ss1505810862OMIM-CURATED-RECORDS|SCV000028872fwd/-/GTCAGTATCAATTCTGGAAGAATTTCCAGACAattacacctgcagctctcattttccatacattaaagatagtcatcttggggctggtcctg12/08/1412/08/14142Genomicunknown
ss1578018880EVA_GENOME_DK|rs333fwd/-/ACAGTCAGTATCAATTCTGGAAGAATTTCCAGtacacctgcagctctcattttccatacattaaagatagtcatcttggggc02/19/1502/19/15136Genomicunknown
ss1588016654EVA_DECODE|EVA_DECODE_3_46389947_394287_rs333fwd/-/ACAGTCAGTATCAATTCTGGAAGAATTTCCAGtacacctgcagctctcattttccatacattaaagatagtcatcttggggc03/02/1503/03/15136Genomicunknown
ss1703610048EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_3_46414943_8344538fwd/-/ACAGTCAGTATCAATTCTGGAAGAATTTCCAGtacacctgcagctctcattttccatacattaaagatagtcatcttggggc03/04/1503/06/15136Genomicunknown
ss1703610076EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_3_46414943_8344538fwd/-/ACAGTCAGTATCAATTCTGGAAGAATTTCCAGtacacctgcagctctcattttccatacattaaagatagtcatcttggggc03/04/1503/06/15136Genomicunknown
ss1711720988EVA_EXAC|EVA_EXAC_1884255fwd/-/ACAGTCAGTATCAATTCTGGAAGAATTTCCAGtacacctgcagctctcattttccatacattaaagatagtcatcttggggc03/04/1503/10/15136Genomicunknown
ss1958559336ILLUMINA|3:46414944-TACAGTCAGTATCAATTCTGGAAGAATTTCCAG-T-0_P_F_2301523412fwd/-/ACAGTCAGTATCAATTCTGGAAGAATTTCCAGtacacctgcagctctcattttccatacattaaagatagtcatcttggggc11/13/1511/13/15136Genomicunknown
ss2094812410ILLUMINA|Immuno_BeadChip_11419691_B_seq-rs333-128_P_F_1767008738fwd/-/GTCAGTATCAATTCTGGAAGAATTTCCAGACAacctgcagctctcattttccatacattaaagatagtcatcttggggctgg09/27/1611/05/16150Genomicunknown
ss2095129519ILLUMINA|InfiniumImmunoArray-24v2-0_A_seq-rs333-128_P_F_2310772969fwd/-/GTCAGTATCAATTCTGGAAGAATTTCCAGACAacctgcagctctcattttccatacattaaagatagtcatcttggggctgg09/27/1611/05/16150Genomicunknown
ss2136299196ILLUMINA|3:46414944-TACAGTCAGTATCAATTCTGGAAGAfwd/-/ACAGTCAGTATCAATTCTGGAAGAATTTCCAGtacacctgcagctctcattttccatacattaaagatagtcatcttggggc11/13/1511/05/16136Genomicunknown
ss2633944651ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_rs333-131_P_F_1889916408fwd/-/GTCAGTATCAATTCTGGAAGAATTTCCAGACAacctgcagctctcattttccatacattaaagatagtcatcttggggctgg02/02/1702/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs333|allelePos=287|totalLen=629|taxid=9606|snpclass=2|alleles='over_30bp'|mol=Genomic|build=151
 GCTGCCGCCC AGTGGGACTT TGGAAATACA ATGTGTCAAC TCTTGACAGG GCTCTATTTT
 ATAGGCTTCT TCTCTGGAAT CTTCTTCATC ATCCTCCTGA CAATCGATAG GTACCTGGCT
 GTCGTCCATG CTGTGTTTGC TTTAAAAGCC AGGACGGTCA CCTTTGGGGT GGTGACAAGT
 GTGATCACTT GGGTGGTGGC TGTGTTTGCG TCTCTCCCAG GAATCATCTT TACCAGATCT
 CAAAAAGAAG GTCTTCATTA CACCTGCAGC TCTCATTTTC CATACA
 N
 TTAAAGATAG TCATCTTGGG GCTGGTCCTG CCGCTGCTTG TCATGGTCAT CTGCTACTCG
 GGAATCCTAA AAACTCTGCT TCGGTGTCGA AATGAGAAGA AGAGGCACAG GGCTGTGAGG
 CTTATCTTCA CCATCATGAT TGTTTATTTT CTCTTCTGGG CTCCCTACAA CATTGTCCTT
 CTCCTGAACA CCTTCCAGGA ATTCTTTGGC CTGAATAATT GCAGTAGCTC TAACAGGTTG
 GACCAAGCTA TGCAGGTGAC AGAGACTCTT GGGATGACGC ACTGCTGCAT CAACCCCATC
 ATCTATGCCT TTGTCGGGGA GAAGTTCAGA AACTACCTCT TA

  NCBI Resource Links back to top
Submitter-Referenced
dbSTSGenBank
UniSTS:9458(D4S1 U83326 U66285
dbSNP Blast Analysis
UniGene Cluster ID
546245
OMIM
609423

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
Source+/+
+/-
HWP+
-
ACAGTCAGTATCAATTCTGGAAGAATTTCCAG
ss1370291708EAS 1008AF 1.00000000
EUR 1006AF 0.110300000.88970000
AFR 1322AF 0.003000000.99700004
AMR 694AF 0.031700000.96829998
SAS 978AF 0.009200000.99079996
ss5586335P1 202AF0.959999980.040000001.000000000.980000020.02000000
CAUC1 62AF0.903000000.097000001.000000000.951999960.04800000
AFR1 48AF1.00000000 1.00000000
HISP1 46AF0.956999960.043000001.000000000.977999990.02200000
PAC1 46AF1.00000000 1.00000000

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict		Additional Freq. Data
0.039+/-0.1340000ALFRED: The Allele Frequency Database

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byClusterbyFreqWith1000GenomeDataUNKNOWNYESYES

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