NCBI
dbSNP
dbVar ClinVar GaP PubMed Nucleotide Protein
Search small variations in dbSNP or large structural variations in dbVar
transparent GIF
Re-designed RefSNP Report page!
Clean, modern design that makes it easy to find the information that you are looking for. Report any problems by sending us an email.
Spacer gif
Have a question about dbSNP? Try searching the SNP FAQ Archive!

Spacer gif
Reference SNP (refSNP) Cluster Report: rs6519442                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:116/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqwith2hitWith1000GenomeData
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:G/T (FWD)
Allele Origin:
Ancestral Allele:T
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:G=0.1743/873 (1000 Genomes)
G=0.2461/30907 (TOPMED)
HGVS Names
  • CM000684.2:g.23471071T>G
  • NC_000022.10:g.23813258T>G
  • NC_000022.11:g.23471071T>G
  • NR_110539.1:n.465A>C
  • NT_187632.1:g.117029T>G
  • XR_109751.2:n.465A>C
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 ss44308756 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs6519442 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
ss11003219BCM_SSAHASNP|chr22.NT_011520.9_3203827fwd/BG/Tgtacagaagcctcattagagatatctacaggtcctcatcagagatgtctacagcatcctc06/30/0310/10/03116Genomicunknown
ss12526664WI_SSAHASNP|chr22.NT_011520.9_3203827fwd/BG/Tgtacagaagcctcattagagatatctacaggtcctcatcagagatgtctacagcatcctc07/04/0310/10/03116Genomicunknown
ss21867135SSAHASNP|WGSA-200403-chr22.chr22.NT_011520.9_3203827fwd/BG/Tgtacagaagcctcattagagatatctacaggtcctcatcagagatgtctacagcatcctc03/20/0403/20/04121Genomicunknown
ss24568664PERLEGEN|afd0110745byFreqfwd/BG/Tgtacagaagcctcattagagatatctacaggtcctcatcagagatgtctacagcatcctc08/10/0409/13/04123Genomicunknown
ss44308756ABI|hCV25744591byFreqfwd/BG/Tgtacagaagcctcattagagatatctacaggtcctcatcagagatgtctacagcatcctc07/18/0511/03/06126Genomicunknown
ss66784194ILLUMINA|HumanHap300v1.1_rs6519442fwd/TG/Tgtacagaagcctcattagagatatctacaggtcctcatcagagatgtctacagcatcctc11/09/0611/09/06127Genomicunknown
ss67466293ILLUMINA|HumanHap550v1.1_rs6519442fwd/BG/Tgtacagaagcctcattagagatatctacaggtcctcatcagagatgtctacagcatcctc11/14/0611/14/06127Genomicunknown
ss67820563ILLUMINA|HumanHap650Yv1.0_rs6519442fwd/BG/Tgtacagaagcctcattagagatatctacaggtcctcatcagagatgtctacagcatcctc11/14/0611/14/06127Genomicunknown
ss69276441PERLEGEN|PGP00110745byFreqfwd/BG/Tgtacagaagcctcattagagatatctacaggtcctcatcagagatgtctacagcatcctc01/30/0703/31/08127Genomicunknown
ss70870282ILLUMINA|HumanHap550v3.0__rs6519442rev/TA/Cgaggatgctgtagacatctctgatgaggacctgtagatatctctaatgaggcttctgtac04/20/0703/31/08130Genomicunknown
ss71459032ILLUMINA|HumanHap650Yv3.0_rs6519442fwd/BG/Tgtacagaagcctcattagagatatctacaggtcctcatcagagatgtctacagcatcctc04/23/0704/23/07127Genomicunknown
ss74810914AFFY|SNP_M-184608fwd/BG/Tgtacagaagcctcattagagatatctacaggtcctcatcagagatgtctacagcatcctc08/09/0708/09/07128Genomicunknown
ss75802518ILLUMINA|ILMN_Human_1M_rs6519442fwd/BG/Tgtacagaagcctcattagagatatctacaggtcctcatcagagatgtctacagcatcctc08/28/0708/29/07129Genomicunknown
ss79224032ILLUMINA|HumanHap300v2.0_rs6519442fwd/BG/Tgtacagaagcctcattagagatatctacaggtcctcatcagagatgtctacagcatcctc04/18/0711/18/07130Genomicunknown
ss81296071HGSV|Cor18507_SNV_20070510.chr22_22137812fwd/BG/Tgtacagaagcctcattagagatatctacaggtcctcatcagagatgtctacagcatcctc11/26/0711/29/07130Genomicunknown
ss84495217KRIBB_YJKIM|KHS725661fwd/BG/Tgtacagaagcctcattagagatatctacaggtcctcatcagagatgtctacagcatcctc12/04/0712/07/07130Genomicunknown
ss86252752CORNELL|hCV25744591byFreqfwd/BG/Tgtacagaagcctcattagagatatctacaggtcctcatcagagatgtctacagcatcctc01/21/0809/05/14129Genomicunknown
ss91888821BCMHGSC_JDW|JWB-1514680fwd/BG/Tgtacagaagcctcattagagatatctacaggtcctcatcagagatgtctacagcatcctc02/26/0803/02/08129Genomicunknown
ss96117187HUMANGENOME_JCVI|1103691014798fwd/BG/Tgtacagaagcctcattagagatatctacaggtcctcatcagagatgtctacagcatcctc03/25/0803/25/08130Genomicunknown
ss1125701851000GENOMES|CEU.trio.12.15.2008_3790214_chr22_22143258fwd/BG/Tgtacagaagcctcattagagatatctacaggtcctcatcagagatgtctacagcatcctc12/17/0812/17/08130Genomicunknown
ss117371350ILLUMINA-UK|NA18507_000008408_NCBI36.1_chr22_22143258fwd/BG/Tgtacagaagcctcattagagatatctacaggtcctcatcagagatgtctacagcatcctc01/19/0901/19/09130Genomic99 %
ss122559616ILLUMINA|HumanCNV370v1_C_rs6519442fwd/BG/Tgtacagaagcctcattagagatatctacaggtcctcatcagagatgtctacagcatcctc04/14/0904/15/09131Genomicunknown
ss138339580ENSEMBL|ENSSNP11911260fwd/BG/Tgtacagaagcctcattagagatatctacaggtcctcatcagagatgtctacagcatcctc05/15/0905/17/09131Genomicunknown
ss154365506ILLUMINA|Human610_Quadv1_B_rs6519442-127_T_R_1501832702rev/TA/Cgaggatgctgtagacatctctgatgaggacctgtagatatctctaatgaggcttctgtac06/18/0906/20/09131Genomicunknown
ss159541696ILLUMINA|Human660W-Quad_v1_A_rs6519442-128_T_R_1501832702rev/TA/Cgaggatgctgtagacatctctgatgaggacctgtagatatctctaatgaggcttctgtac07/06/0907/07/09131Genomicunknown
ss160782807ILLUMINA|HumanOmni1-Quad_v1-0_B_rs6519442-128_T_R_1501832702rev/TA/Cgaggatgctgtagacatctctgatgaggacctgtagatatctctaatgaggcttctgtac08/04/0910/04/09131Genomicunknown
ss171858366COMPLETE_GENOMICS|NA20431_36_chr22_22143258fwd/BG/Tgtacagaagcctcattagagatatctacaggtcctcatcagagatgtctacagcatcctc10/01/0910/01/09132Genomicunknown
ss172140761ILLUMINA|HumanCNV370-Quadv3_C_rs6519442-127_T_R_1501832702rev/TA/Cgaggatgctgtagacatctctgatgaggacctgtagatatctctaatgaggcttctgtac10/01/0910/04/09132Genomicunknown
ss174024138ILLUMINA|Human1M-Duov3_B_rs6519442-127_T_R_1501832702rev/TA/Cgaggatgctgtagacatctctgatgaggacctgtagatatctctaatgaggcttctgtac10/01/0910/04/09132Genomicunknown
ss208826526BCM-HGSC-SUB|BCM_CMT_1011-3281961fwd/BG/Tgtacagaagcctcattagagatatctacaggtcctcatcagagatgtctacagcatcctc03/15/1003/20/10132Genomicunknown
ss2286313021000GENOMES|pilot_1_YRI_10440985_chr22_22143258fwd/G/Tgtacagaagcctcattagagatatctacaggtcctcatcagagatgtctacagcatcctc04/22/1004/22/10132Genomicunknown
ss2380322231000GENOMES|pilot_1_CEU_7636852_chr22_22143258fwd/G/Tgtacagaagcctcattagagatatctacaggtcctcatcagagatgtctacagcatcctc05/01/1005/01/10132Genomicunknown
ss255856600BL|SNP10821_22_22143258fwd/BG/Tgtacagaagcctcattagagatatctacaggtcctcatcagagatgtctacagcatcctc08/20/1008/20/10134Genomicunknown
ss292741773PJP|SNP_2248131_chr22_22143258fwd/G/Tgtacagaagcctcattagagatatctacaggtcctcatcagagatgtctacagcatcctc01/21/1101/21/11134Genomicunknown
ss481270169ILLUMINA|HumanOmni2.5-4v1_B_rs6519442-128_T_R_1767840465fwd/BG/Tgaagcctcattagagatatctacaggtcctcatcagagatgtctacagca01/30/1210/28/16137Genomicunknown
ss481294587ILLUMINA|HumanOmniExpress-12v1_C_rs6519442-128_T_R_1854666694fwd/BG/Tgaagcctcattagagatatctacaggtcctcatcagagatgtctacagca01/30/1210/27/16137Genomicunknown
ss482278268ILLUMINA|HumanOmni1-Quad_v1-0_C_rs6519442-128_T_R_1854666694fwd/BG/Tgaagcctcattagagatatctacaggtcctcatcagagatgtctacagca01/30/1208/28/15146Genomicunknown
ss485430358ILLUMINA|HumanOmni2.5-4v1_D_rs6519442-128_T_R_1854666694fwd/BG/Tgaagcctcattagagatatctacaggtcctcatcagagatgtctacagca01/30/1210/28/16137Genomicunknown
ss491821022CLINSEQ_SNP|SNV-chr22-22143258byFreqfwd/BG/Tgaagcctcattagagatatctacaggtcctcatcagagatgtctacagca03/06/1209/05/14137Genomicunknown
ss537359609ILLUMINA|HumanOmni5-4v1_B_rs6519442-128_T_R_1908482029fwd/BG/Tgaagcctcattagagatatctacaggtcctcatcagagatgtctacagca06/22/1208/29/15146Genomicunknown
ss566577170TISHKOFF|snp_chr22_23813258fwd/BG/Tgaagcctcattagagatatctacaggtcctcatcagagatgtctacagca11/22/1211/23/12138Genomicunknown
ss662505317SSMP|22_23813258fwd/BG/Tgaagcctcattagagatatctacaggtcctcatcagagatgtctacagca12/14/1202/14/15138Genomicunknown
ss778942816ILLUMINA|HumanOmni25Exome-8v1_A_rs6519442-128_T_R_1854666694fwd/BG/Tgaagcctcattagagatatctacaggtcctcatcagagatgtctacagca05/30/1307/10/15146Genomicunknown
ss783160622ILLUMINA|HumanOmni2.5-4v1_H_rs6519442-128_T_R_1854666694fwd/BG/Tgaagcctcattagagatatctacaggtcctcatcagagatgtctacagca05/30/1307/29/15146Genomicunknown
ss784116395ILLUMINA|HumanOmniExpressExome-8v1_A_rs6519442-128_T_R_1908482029fwd/BG/Tgaagcctcattagagatatctacaggtcctcatcagagatgtctacagca05/31/1306/19/15146Genomicunknown
ss825554550ILLUMINA|HumanCNV370v1_C_rs6519442-126_T_R_IFB1136815292:0fwd/BG/Tgaagcctcattagagatatctacaggtcctcatcagagatgtctacagca06/24/1311/21/14147Genomicunknown
ss832419986ILLUMINA|HumanOmniExpress-12v1_H_rs6519442-128_T_R_1854666694fwd/BG/Tgaagcctcattagagatatctacaggtcctcatcagagatgtctacagca09/17/1306/18/15146Genomicunknown
ss834404548ILLUMINA|HumanOmni2.5-8v1_A_rs6519442-128_T_R_1854666694fwd/BG/Tgaagcctcattagagatatctacaggtcctcatcagagatgtctacagca09/18/1307/29/15146Genomicunknown
ss995249667EVA-GONL|EVA-GONL_rs6519442fwd/BG/Tgaagcctcattagagatatctacaggtcctcatcagagatgtctacagca04/23/1405/01/14142Genomicunknown
ss1082587948JMKIDD_LAB|HGDP_WGS_chr22_23813258fwd/BG/Tgaagcctcattagagatatctacaggtcctcatcagagatgtctacagca07/10/1407/12/14142Genomicunknown
ss13667900711000GENOMES|PHASE3_V1_80665498fwd/G/Tgaagcctcattagagatatctacaggtcctcatcagagatgtctacagca08/16/1408/16/14142Genomicunknown
ss1397782761HAMMER_LAB|HAMMER_LAB_rs6519442fwd/BG/Tgaagcctcattagagatatctacaggtcctcatcagagatgtctacagca09/30/1409/30/14146Genomicunknown
ss1579714663EVA_GENOME_DK|EVA_GENOME_DK_snv_rs6519442fwd/BG/Tgaagcctcattagagatatctacaggtcctcatcagagatgtctacagca02/19/1502/20/15144Genomicunknown
ss1639799677EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_22_23813258_44432772fwd/G/Tgaagcctcattagagatatctacaggtcctcatcagagatgtctacagca03/04/1503/04/15144Genomicunknown
ss1682793710EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_22_23813258_44432772fwd/G/Tgaagcctcattagagatatctacaggtcctcatcagagatgtctacagca03/04/1503/04/15144Genomicunknown
ss1711563438EVA_MGP|EVA_XIMO_679198fwd/BG/Tgaagcctcattagagatatctacaggtcctcatcagagatgtctacagca03/09/1503/09/15144Genomicunknown
ss1713733155EVA_SVP|EVA_SVP_1427234fwd/BG/Tgaagcctcattagagatatctacaggtcctcatcagagatgtctacagca03/12/1503/12/15144Genomicunknown
ss1752415193ILLUMINA|OmniExpressExome-8v1-1_B_rs6519442-128_T_R_1908482029fwd/BG/Tgaagcctcattagagatatctacaggtcctcatcagagatgtctacagca05/27/1506/09/15146Genomicunknown
ss1938815692WEILL_CORNELL_DGM|SNV:chr22:23813258fwd/BG/Tgaagcctcattagagatatctacaggtcctcatcagagatgtctacagca10/16/1510/19/15147Genomicunknown
ss1946580061ILLUMINA|HumanCoreExome-12v1-0_C_rs6519442-128_T_R_1908482029fwd/BG/Tgaagcctcattagagatatctacaggtcctcatcagagatgtctacagca10/29/1510/29/15147Genomicunknown
ss1959968912ILLUMINA|rs6519442-128_T_R_1908482029fwd/BG/Tgaagcctcattagagatatctacaggtcctcatcagagatgtctacagca11/13/1511/13/15147Genomicunknown
ss2030180451JJLAB|SNP10683006fwd/BG/Tgaagcctcattagagatatctacaggtcctcatcagagatgtctacagca08/29/1608/31/16149Genomicunknown
ss2158792220USC_VALOUEV|NC_000022.10:g.23813258T>Gfwd/G/Tgaagcctcattagagatatctacaggtcctcatcagagatgtctacagca11/17/1611/17/16150Genomicunknown
ss2413495145TOPMED|22_23813258_T/Gfwd/G/Tgaagcctcattagagatatctacaggtcctcatcagagatgtctacagca11/19/1611/19/16150Genomicunknown
ss2633865446ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_rs6519442-128_T_R_19084820fwd/G/Tgaagcctcattagagatatctacaggtcctcatcagagatgtctacagca02/02/1702/02/17151Genomicunknown
ss2710662493ILLUMINA|Consortium-OncoArray_15047405_A_rs6519442-128_T_R_1908482029fwd/G/Tgaagcctcattagagatatctacaggtcctcatcagagatgtctacagca03/22/1703/22/17151Genomicunknown
ss2973321903GNOMAD|rs6519442fwd/G/Tgaagcctcattagagatatctacaggtcctcatcagagatgtctacagca05/23/1705/23/17151Genomicunknown
ss2985234649AFFY|Axiom_PsorMich_Affx-19203869fwd/G/Tgaagcctcattagagatatctacaggtcctcatcagagatgtctacagca05/24/1705/24/17151Genomicunknown
ss3019145342SWEGEN|NC_000022.10:g.23813258T>Gfwd/G/Tgaagcctcattagagatatctacaggtcctcatcagagatgtctacagca05/30/1705/30/17151Genomicunknown
ss3022175129ILLUMINA|MEGA_Consortium_v2_15070954_A2_rs6519442-138_T_R_2269315430fwd/G/Tgaagcctcattagagatatctacaggtcctcatcagagatgtctacagca06/28/1706/28/17151Genomicunknown
ss3028927463BIOINF_KMB_FNS_UNIBA|22.23471071T>Gfwd/G/Tgaagcctcattagagatatctacaggtcctcatcagagatgtctacagca07/05/1707/05/17151Genomicunknown
ss3352792012CSHL|rs6519442fwd/G/Tgaagcctcattagagatatctacaggtcctcatcagagatgtctacagca10/02/1710/02/17151Genomicunknown
ss3374747048TOPMED|TOPMed_freeze_5?chr22:23,471,071fwd/G/Tgaagcctcattagagatatctacaggtcctcatcagagatgtctacagca10/03/1710/03/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs6519442|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='G/T'|mol=Genomic|build=151
 GCAACATTTC TGTTCAAGAC AAAGGAAAGT GTCTTACCTT GGTAGCATCT TTTTTACAGA
 GGTATCGTAC AGCATCCTCA TTAGTGATGT CGTATACAGT GTCCTCATAA GAAATGTCTT
 CTATAGTGTC CTCATTAGAG ATGTCATGTA CAGCAGCCTC ATTACAGATG TCTACAGCGT
 CATTAGAGAT GTCACGTACA GCAGCCTCAT TAGAGATGTT TACGGCATCG TTAGAGATGT
 CACATACAGC AGCCTCATTA GAGATGTCAT GTACAGAAGC CTCATTAGAG ATATCTACAG
 K
 GTCCTCATCA GAGATGTCTA CAGCATCCTC ATTACAGATG TCATATACAG TGTCTTCTTT
 AGAGATGTCT TGTACAGCGT ACCCACAAAG AGCTAGGAGA ACACAGAGTA AAGGTCAGTG
 CCCTGGTGGT GAATCACCCA GGGAGCTTGC TTGGTGTGGG TGCCTGGAGG TGGCTGATCA
 CAGCATGGGC CCAGCTGATG CTAGGCCATC CTCCCGGGTG GACCTGCACT AGTGAAGCTA
 AGGGACATGA CTCAGAACAC TTTCTGCAGT GGGAATCAGT TTCCAGGTTC AGATATGCAT

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_011520 ABBA01055111
dbSNP Blast Analysis
UniGene Cluster ID
126178

  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.
SourceG/G
G/T
T/T
HWPG
T
ss117371350YRI 2IG1.00000000 1.00000000
ss1366790071EAS 1008AF 0.003000000.99700004
EUR 1006AF 0.307200010.69279999
AFR 1322AF 0.202699990.79730004
AMR 694AF 0.214700000.78530002
SAS 978AF 0.147199990.85280001
ss138339580ENSEMBL_Watson 2IG 1.00000000 0.500000000.50000000
ss171858366PGP 2IG 1.00000000 0.500000000.50000000
ss228631302pilot_1_YRI_low_coverage_panel 118AF 0.211864410.78813559
ss238032223pilot_1_CEU_low_coverage_panel 120AF 0.291666660.70833331
ss24568664AFD_EUR_PANELEuropean 48IG0.041666670.416666660.541666690.654721000.250000000.75000000
AFD_AFR_PANELAfrican American 46IG 0.478260870.521739130.342782000.239130440.76086956
AFD_CHN_PANELAsian 48IG 1.00000000 1.00000000
ss44308756HapMap-CEUEuropean 226IG0.061946900.495575220.442477880.099721000.309734520.69026548
HapMap-HCBAsian 90IG 1.00000000 1.00000000
HapMap-JPTAsian 88IG 1.00000000 1.00000000
HapMap-YRISub-Saharan African 226IG0.035398230.318584080.646017671.000000000.194690270.80530971
HAPMAP-ASW 98IG0.040816330.326530610.632653061.000000000.204081640.79591835
HAPMAP-GIH 174IG0.011494250.321839090.666666690.250592000.172413800.82758623
HAPMAP-LWK 180IG0.022222220.355555560.622222240.294266000.200000000.80000001
HAPMAP-MEX 100IG0.020000000.300000010.680000010.751830000.170000000.82999998
HAPMAP-MKK 286IG0.146853150.398601410.454545470.200325000.346153860.65384614
HAPMAP-TSI 176IG0.090909090.443181810.465909091.000000000.312500000.68750000
ss491821022CSAgilent 592GF0.094094090.461461420.444444420.371093000.324824810.67517519
ss86252752AGI_ASP_populationmultiple 74IG0.108108110.189189200.702702700.020022000.202702700.79729730
ss96117187J. Craig Venter 2IG 1.00000000 0.500000000.50000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
Additional Freq. Data
0.288+/-0.2470000ALFRED: 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
byClusterbyFreqwith2hitWith1000GenomeData
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

GENERAL: Contact Us | Homepage | Announcements |dbSNP Summary | Genome | FTP SERVER | Build History | Handle Request
DOCUMENTATION: FAQ | Searchable FAQ Archive | Overview | How to Submit | RefSNP Summary Info | Database Schema
SEARCH: Entrez SNP | Blast SNP | Batch Query | By Submitter |New Batches | Method | Population | Publication | Batch | Locus Info | Between Marker
NCBI: PubMed | Entrez | BLAST | OMIM | Taxonomy | Structure

Disclaimer     Privacy statement