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Reference SNP (refSNP) Cluster Report: rs16856202                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:123/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Association:NHGRI GWAS PheGenI
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=0.0611/306 (1000 Genomes)
G=0.0371/4657 (TOPMED)
HGVS Names
  • CM000663.2:g.232019405T>G
  • NC_000001.10:g.232155151T>G
  • NC_000001.11:g.232019405T>G
  • NG_011681.1:g.397591T>G
  • NM_001012957.1:c.2242-7030T>G
  • NM_001164537.1:c.2404-7030T>G
  • NM_001164540.1:c.1942-7030T>G
  • NM_018662.2:c.2308-7030T>G
  • NR_028393.1:n.2974-7030T>G
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 ss276259690 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs16856202 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
ss23890750PERLEGEN|afd1200369byFreqfwd/BG/Tttgctgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacactttgaaat08/10/0409/13/04123Genomicunknown
ss66207159AFFY|SNP_A-2300497byFreqfwd/BG/Tgcctgacaagacaaatactggagagtcttcaa10/27/0603/31/08127Genomicunknown
ss66831240ILLUMINA|HumanHap300v1.1_rs16856202fwd/TG/Tttgctgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacactttgaaat11/09/0611/09/06127Genomicunknown
ss67150405ILLUMINA|HumanHap550v1.1_rs16856202fwd/BG/Tttgctgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacactttgaaat11/14/0611/14/06127Genomicunknown
ss67494098ILLUMINA|HumanHap650Yv1.0_rs16856202fwd/BG/Tttgctgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacactttgaaat11/14/0611/14/06127Genomicunknown
ss68796293PERLEGEN|PGP01200369byFreqfwd/BG/Tttgctgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacactttgaaat01/30/0703/31/08127Genomicunknown
ss70448315ILLUMINA|HumanHap300v2.0_rs16856202fwd/BG/Tttgctgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacactttgaaat04/18/0711/18/07127Genomicunknown
ss70641183ILLUMINA|HumanHap550v3.0__rs16856202rev/TA/Catttcaaagtgtctttgaagactctccagtatttgtcttgtcaggcggtcctttcagcaa04/20/0703/30/08130Genomicunknown
ss71193170ILLUMINA|HumanHap650Yv3.0_rs16856202fwd/BG/Tttgctgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacactttgaaat04/23/0704/23/07127Genomicunknown
ss75900873ILLUMINA|ILMN_Human_1M_rs16856202fwd/BG/Tttgctgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacactttgaaat08/28/0708/29/07129Genomicunknown
ss76301206AFFY|AFFY_6_1M_SNP_A-2300497fwd/BG/Tgcctgacaagacaaatactggagagtcttcaa08/28/0708/30/07129Genomicunknown
ss85327639KRIBB_YJKIM|KHS964654fwd/BG/Tttgctgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacactttgaaat12/04/0712/09/07130Genomicunknown
ss121775962ILLUMINA|HumanCNV370v1_C_rs16856202fwd/BG/Tttgctgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacactttgaaat04/14/0904/14/09131Genomicunknown
ss153560639ILLUMINA|Human610_Quadv1_B_rs16856202-128_T_R_1501682118rev/TA/Catttcaaagtgtctttgaagactctccagtatttgtcttgtcaggcggtcctttcagcaa06/18/0906/19/09131Genomicunknown
ss159294008ILLUMINA|Human660W-Quad_v1_A_rs16856202-128_T_R_1501682118rev/TA/Catttcaaagtgtctttgaagactctccagtatttgtcttgtcaggcggtcctttcagcaa07/06/0907/06/09131Genomicunknown
ss160387742ILLUMINA|HumanOmni1-Quad_v1-0_B_rs16856202-128_T_R_1501682118rev/TA/Catttcaaagtgtctttgaagactctccagtatttgtcttgtcaggcggtcctttcagcaa08/04/0910/02/09131Genomicunknown
ss170713690ILLUMINA|HumanCNV370-Quadv3_C_rs16856202-128_T_R_1501682118rev/TA/Catttcaaagtgtctttgaagactctccagtatttgtcttgtcaggcggtcctttcagcaa10/01/0910/03/09132Genomicunknown
ss172632867ILLUMINA|Human1M-Duov3_B_rs16856202-128_T_R_1501682118rev/TA/Catttcaaagtgtctttgaagactctccagtatttgtcttgtcaggcggtcctttcagcaa10/01/0910/02/09132Genomicunknown
ss173182391AFFY|GenomeWideSNP_5_SNP_A-2300497fwd/BG/Tgcctgacaagacaaatactggagagtcttcaa10/01/0910/03/09132Genomicunknown
ss2309446891000GENOMES|pilot_1_CEU_549318_chr1_230221774fwd/G/Tttgctgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacactttgaaat05/01/1005/01/10132Genomicunknown
ss2385506221000GENOMES|pilot_1_CHB+JPT_435699_chr1_230221774fwd/G/Tttgctgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacactttgaaat05/01/1005/01/10132Genomicunknown
ss276259690GMI|GMI_AK_SNP_579857fwd/G/Tttgctgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacactttgaaat12/16/1012/16/10137Genomicunknown
ss480079037ILLUMINA|HumanOmni2.5-4v1_B_rs16856202-128_T_R_1765402949fwd/BG/Tgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacacttt01/30/1210/28/16137Genomicunknown
ss480087802ILLUMINA|HumanOmniExpress-12v1_C_rs16856202-131_T_R_1857651962fwd/BG/Tgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacacttt01/30/1210/27/16137Genomicunknown
ss480768090ILLUMINA|HumanOmni1-Quad_v1-0_C_rs16856202-131_T_R_1865606501fwd/BG/Tgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacacttt01/30/1208/28/15146Genomicunknown
ss484837359ILLUMINA|HumanOmni2.5-4v1_D_rs16856202-131_T_R_1857651962fwd/BG/Tgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacacttt01/30/1210/27/16137Genomicunknown
ss491312502EXOME_CHIP|.GWAS._28729_chr_1_232155151fwd/BG/Tttgctgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacactttgaaat03/05/1203/05/12137Genomicunknown
ss536910927ILLUMINA|HumanOmni5-4v1_B_rs16856202-131_T_R_1885473653fwd/BG/Tgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacacttt06/22/1208/28/15146Genomicunknown
ss555206539TISHKOFF|snp_chr1_232155151fwd/BG/Tgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacacttt11/22/1211/23/12138Genomicunknown
ss648779293SSMP|1_232155151fwd/BG/Tgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacacttt12/14/1202/10/15138Genomicunknown
ss778817971ILLUMINA|HumanOmni25Exome-8v1_A_rs16856202-131_T_R_1865606501fwd/BG/Tgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacacttt05/30/1307/09/15146Genomicunknown
ss780682224ILLUMINA|HumanOmni25Exome-8v1_A_exm-rs16856202-131_T_R_1990489002fwd/BG/Tgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacacttt05/30/1307/09/15146Genomicunknown
ss782865251ILLUMINA|HumanOmni2.5-4v1_H_rs16856202-131_T_R_1857651962fwd/BG/Tgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacacttt05/30/1307/28/15146Genomicunknown
ss783355568ILLUMINA|HumanOmniExpressExome-8v1_A_exm-rs16856202-131_T_R_1990489002fwd/BG/Tgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacacttt05/31/1306/18/15146Genomicunknown
ss783829456ILLUMINA|HumanOmniExpressExome-8v1_A_rs16856202-131_T_R_1885473653fwd/BG/Tgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacacttt05/31/1306/18/15146Genomicunknown
ss825417048ILLUMINA|HumanCNV370v1_C_rs16856202-123_T_R_IFB1137780020:0fwd/BG/Tgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacacttt06/24/1311/21/14144Genomicunknown
ss832119338ILLUMINA|HumanOmniExpress-12v1_H_rs16856202-131_T_R_1857651962fwd/BG/Tgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacacttt09/17/1306/18/15146Genomicunknown
ss834278294ILLUMINA|HumanOmni2.5-8v1_A_rs16856202-131_T_R_1865606501fwd/BG/Tgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacacttt09/18/1307/28/15146Genomicunknown
ss976256294EVA-GONL|EVA-GONL_rs16856202fwd/BG/Tgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacacttt04/23/1404/23/14142Genomicunknown
ss1068686032JMKIDD_LAB|HGDP_WGS_chr1_232155151fwd/BG/Tgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacacttt07/10/1407/10/14142Genomicunknown
ss12950721541000GENOMES|PHASE3_V1_5971480fwd/G/Tgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacacttt08/16/1408/16/14142Genomicunknown
ss1426143748DDI|DDI_rs16856202fwd/BG/Tgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacacttt11/04/1411/04/14144Genomicunknown
ss1574749197EVA_GENOME_DK|EVA_GENOME_DK_snv_rs16856202fwd/BG/Tgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacacttt02/19/1502/19/15144Genomicunknown
ss1585656114EVA_DECODE|EVA_DECODE_1_230221774_1526874_rs16856202fwd/BG/Tgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacacttt03/02/1503/02/15144Genomicunknown
ss1602364636EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_1_232155151_3285951fwd/G/Tgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacacttt03/04/1503/04/15144Genomicunknown
ss1645358669EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_1_232155151_3285951fwd/G/Tgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacacttt03/04/1503/04/15144Genomicunknown
ss1712413681EVA_SVP|EVA_SVP_108233fwd/BG/Tgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacacttt03/12/1503/12/15144Genomicunknown
ss1751905009ILLUMINA|OmniExpressExome-8v1-1_B_exm-rs16856202-131_T_R_1990489002fwd/BG/Tgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacacttt05/27/1506/09/15146Genomicunknown
ss1751905010ILLUMINA|OmniExpressExome-8v1-1_B_rs16856202-131_T_R_1885473653fwd/BG/Tgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacacttt05/27/1506/09/15146Genomicunknown
ss1917743910ILLUMINA|HumanExome-12v1-1_B_exm-rs16856202-131_T_R_1990489002fwd/BG/Tgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacacttt10/16/1510/16/15147Genomicunknown
ss1919477563WEILL_CORNELL_DGM|SNV:chr1:232155151fwd/BG/Tgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacacttt10/16/1510/16/15147Genomicunknown
ss1946026640ILLUMINA|HumanCoreExome-12v1-0_C_exm-rs16856202-131_T_R_1990489002fwd/BG/Tgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacacttt10/29/1510/29/15147Genomicunknown
ss1958367103ILLUMINA|exm-rs16856202-131_T_R_1990489002fwd/BG/Tgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacacttt11/13/1511/13/15147Genomicunknown
ss1966999058GENOMED|rs16856202fwd/BG/Tgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacacttt02/16/1602/16/16147Genomicunknown
ss2020264044JJLAB|SNP766599fwd/BG/Tgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacacttt08/29/1608/30/16149Genomicunknown
ss2136845980CSHL|rs16856202fwd/BG/Tgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacacttt12/02/1612/02/16151Genomicunknown
ss2148300125USC_VALOUEV|NC_000001.10:g.232155151T>Gfwd/G/Tgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacacttt11/17/1611/17/16150Genomicunknown
ss2170956943HUMAN_LONGEVITY|HLI-1-232019405-T-Gfwd/G/Tgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacacttt11/18/1611/18/16150Genomicunknown
ss2333606488TOPMED|1_232155151_T/Gfwd/G/Tgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacacttt11/19/1611/19/16150Genomicunknown
ss2624644166SYSTEMSBIOZJU|SYSTEMSBIOZJU_SNV488292fwd/G/Tgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacacttt01/06/1701/06/17151Genomicunknown
ss2632643028ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_rs16856202-131_T_R_1885473fwd/G/Tgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacacttt02/02/1702/02/17151Genomicunknown
ss2635008336ILLUMINA|Cancer_BeadChip_11459870_A_rs16856202-128_T_R_1765402949fwd/G/Tgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacacttt02/02/1702/02/17151Genomicunknown
ss2698300568GRF|rs16856202fwd/G/Tgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacacttt02/13/1702/13/17151Genomicunknown
ss2767413918GNOMAD|rs16856202fwd/G/Tgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacacttt05/17/1705/17/17151Genomicunknown
ss2984897642AFFY|Axiom_PsorMich_Affx-7640969fwd/G/Tgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacacttt05/24/1705/24/17151Genomicunknown
ss2985541581AFFY|Axiom_Smokesc1_Affx-7640969fwd/G/Tgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacacttt05/24/1705/24/17151Genomicunknown
ss2988624026SWEGEN|NC_000001.10:g.232155151T>Gfwd/G/Tgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacacttt05/30/1705/30/17151Genomicunknown
ss3021191166ILLUMINA|MEGA_Consortium_v2_15070954_A2_exm-rs16856202-131_T_R_1990489002fwd/G/Tgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacacttt06/28/1706/28/17151Genomicunknown
ss3106136533TOPMED|TOPMed_freeze_5?chr1:232,019,405fwd/G/Tgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacacttt09/28/1709/28/17151Genomicunknown
ss3343961245CSHL|rs16856202fwd/G/Tgaaaggaccgcctgacaagacaaatactggagagtcttcaaagacacttt10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs16856202|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='G/T'|mol=Genomic|build=151
 AGCATCCAGA AAGGTTCTTC TTGTTGGTTT TCCTTCCTGG CTCTTTATAC TTGGGTGAAA
 TGATCTCTTG GAAGTGTAGT CTGAAAAACA GCATAGCTTC TTCCAAGTTC TCATAAGATA
 CAGGAGTCTC CATTCATTAC TTCAATAAGC ATTACTGAGC ACCTTTTATG AGCAAGGTAG
 GACGACGGAG GCAGGGCCAG GACCTCATCA TCTGGTGAGG GAGACAGGCG GTTACACACA
 CAGGGAGGAA CTCCTCCTAC CCAGAAGTAG GCAGGGTTGG AGATTCGGGA TTGAAGCGTT
 CCTGGAAGAA GTGGAATCTG CAGAGTTTTG AAAAGAGGGG GTGTTAGGTG TAGCAATCAG
 ACCATTTACC TGTTATAACT GCTTTTCATT CTGACCCACA GGGAAAACAA TTATTCCTAG
 GGTTAAATGA TGGGACGGAT GTTCAGAAAG GAAAAAAATA ATAATTTGAA TTGCTGAAAG
 GACCGCCTGA CAAGACAAAT
 K
 ACTGGAGAGT CTTCAAAGAC ACTTTGAAAT GCCGAGCAAC CTGTACTTTA AATGATCCGT
 TCAGAATTGC AAATCCTACA GAACTCCATT TCTGCTAGGA ATCCCAGTGG CTTTGTAGTG
 GGTGGTATTT TTAATTATCA AGTATCAGTC TTGCAGGCTT TCTCTTTTTT GTCACATTTG
 ATTTAAAGTA CAAATGGGAG CAAAAGTTAC AAATTGCACA CAGAGAGACA CTCAGTGTGT
 GAAATTGTGG ACATGGTTCA GAATATGTTT ATTTGGAATC CGCTGAGGTG ATGGGAGAGA
 TGGGACTGGA TACTCATGTT CTTATTTGGA AAGGAGACAT TCTCGCCGCC TTTCCCATGT
 GCCCGCTTGC TTTTCTCTGC TTCCAGCCTG ATATTTTATG GACTTGTGGA TGAGAGGTCC
 TGTGCCCATC ATTGCATTCC AGATTGTCAT GGCTGTTATC ATTGTCACCT CCACTCATTA
 TGCCTCTGAG TCCTGGAGGG

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000001.8
dbSNP Blast Analysis

  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
ss1295072154EAS 1008AF 0.150799990.84920001
EUR 1006AF 0.028800000.97120005
AFR 1322AF 0.004500000.99550003
AMR 694AF 0.077800000.92219996
SAS 978AF 0.066500000.93349999
ss230944689pilot_1_CEU_low_coverage_panel 120AF 0.033333340.96666664
ss238550622pilot_1_CHB+JPT_low_coverage_panel 120AF 0.108333330.89166665
ss23890750AFD_EUR_PANELEuropean 48IG 1.00000000 1.00000000
AFD_AFR_PANELAfrican American 46IG 0.043478260.956521751.000000000.021739130.97826087
AFD_CHN_PANELAsian 48IG 0.166666670.833333311.000000000.083333340.91666669
HapMap-CEUEuropean 220IG 0.072727270.927272741.000000000.036363640.96363634
HapMap-HCBAsian 86IG0.023255810.162790700.813953460.402784000.104651160.89534885
HapMap-JPTAsian 172IG0.034883720.174418600.790697690.099721000.122093020.87790698
HapMap-YRISub-Saharan African 120IG 1.00000000 1.00000000
HAPMAP-ASW 98IG 0.020408160.979591851.000000000.010204080.98979592
HAPMAP-CHBAsian 82IG0.048780490.414634140.536585390.583882000.256097560.74390244
HAPMAP-CHD 170IG0.035294120.223529410.741176490.317310000.147058830.85294116
HAPMAP-GIH 176IG 0.159090910.840909060.751830000.079545450.92045456
HAPMAP-LWK 180IG 0.033333340.966666641.000000000.016666670.98333335
HAPMAP-MEX 100IG0.040000000.200000000.759999990.250592000.140000000.86000001
HAPMAP-MKK 286IG 0.041958040.958041971.000000000.020979020.97902095
HAPMAP-TSI 176IG 0.045454550.954545441.000000000.022727270.97727275
ss66207159HapMap-CEUEuropean 118IG 0.084745760.915254241.000000000.042372880.95762712
HapMap-HCBAsian 90IG0.022222220.155555560.822222230.371093000.100000000.89999998
HapMap-JPTAsian 90IG0.022222220.200000000.777777790.654721000.122222220.87777776
HapMap-YRISub-Saharan African 120IG 1.00000000 1.00000000
ss76301206ICMHP 8IG 1.00000000 1.00000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
Additional Freq. Data
0.115+/-0.2100000ALFRED: 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
byClusterbyFreqWith1000GenomeDataUNKNOWNUNKNOWNUNKNOWN

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