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BUILD 130
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Reference SNP(refSNP) Cluster Report: rs406113          
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:80/130
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/C
Ancestral Allele:C
Clinical Association:unknown
HGVS Names
NM_182701.1:c.39T>G
NP_874360.1:p.Phe13Leu
NT_007592.14:g.19341733A>C
Links , Linkout

SNP Details are organized in the following sections:
Submission Fasta Resource GeneView Map Diversity Validation

  Submitter records for this RefSNP Cluster back to top
The submission ss1473062 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs406113 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
ss530553SC_JCM|AL049543.14_5686fwd/TA/Ctagggtctgctgagcaaagccaaccaggaaaacaggacaagacaggaggcctggaactgc07/12/0010/10/0380Genomicunknown
ss1473062TSC-CSHL|TSC0089849byFreqfwd/TA/Ctagggtctgctgagcaaagccaaccaggaaaacaggacaagacaggaggcctggaactgc09/07/0008/14/0786Genomic95 %
ss1854633KWOK|OVLP-000925-675836fwd/TA/Ctagggtctgctgagcaaagccaaccaggaaaacaggacaagacaggaggcctggaactgc10/06/0010/10/0387Genomic94 %
ss10309631BCM_SSAHASNP|chr6.NT_007592.13_19341733fwd/TA/Ctagggtctgctgagcaaagccaaccaggaaaacaggacaagacaggaggcctggaactgc06/29/0310/10/03116Genomicunknown
ss17902985CSHL-HAPMAP|CSHL-HuCC-200402.chr6.NT_007592.13_19341733fwd/TA/Ctagggtctgctgagcaaagccaaccaggaaaacaggacaagacaggaggcctggaactgc02/19/0403/04/04120Genomicunknown
ss20287731CSHL-HAPMAP|CSHL-HuFF-200402.chr6.NT_007592.13_19341733fwd/TA/Ctagggtctgctgagcaaagccaaccaggaaaacaggacaagacaggaggcctggaactgc02/21/0403/04/04120Genomicunknown
ss22442612SSAHASNP|WGSA-200403-chr6.chr6.NT_007592.13_19341733fwd/TA/Ctagggtctgctgagcaaagccaaccaggaaaacaggacaagacaggaggcctggaactgc03/21/0403/21/04121Genomicunknown
ss38347255EGP_SNPS|GPX6-002035byFreqrev/BG/Tgcagttccaggcctcctgtcttgtcctgttttcctggttggctttgctcagcagacccta07/07/0511/02/06126Genomicunknown
ss44680668ABI|hCV2491865byFreqfwd/TA/Ctagggtctgctgagcaaagccaaccaggaaaacaggacaagacaggaggcctggaactgc07/19/0511/03/06126Genomicunknown
ss65728157ILLUMINA|Human1-rs406113fwd/TA/Ctagggtctgctgagcaaagccaaccaggaaaacaggacaagacaggaggcctggaactgc10/10/0610/10/06127Genomicunknown
ss66617665ILLUMINA|HumanHap300v1.1_rs406113fwd/BA/Ctagggtctgctgagcaaagccaaccaggaaaacaggacaagacaggaggcctggaactgc11/09/0611/09/06127Genomicunknown
ss67313382ILLUMINA|HumanHap550v1.1_rs406113fwd/TA/Ctagggtctgctgagcaaagccaaccaggaaaacaggacaagacaggaggcctggaactgc11/14/0611/14/06127Genomicunknown
ss67719467ILLUMINA|HumanHap650Yv1.0_rs406113fwd/TA/Ctagggtctgctgagcaaagccaaccaggaaaacaggacaagacaggaggcctggaactgc11/14/0611/14/06127Genomicunknown
ss68970000PERLEGEN|PGP04484066byFreqfwd/TA/Ctagggtctgctgagcaaagccaaccaggaaaacaggacaagacaggaggcctggaactgc01/30/0708/14/07127Genomicunknown
ss70792008ILLUMINA|HumanHap550v3.0__rs406113rev/BG/Tgcagttccaggcctcctgtcttgtcctgttttcctggttggctttgctcagcagacccta04/20/0703/30/08130Genomicunknown
ss71369623ILLUMINA|HumanHap650Yv3.0_rs406113fwd/TA/Ctagggtctgctgagcaaagccaaccaggaaaacaggacaagacaggaggcctggaactgc04/23/0704/23/07127Genomicunknown
ss74812877AFFY|SNP_M-288443fwd/TA/Ctagggtctgctgagcaaagccaaccaggaaaacaggacaagacaggaggcctggaactgc08/09/0708/09/07128Genomicunknown
ss75473001ILLUMINA|ILMN_Human_1M_rs406113fwd/TA/Ctagggtctgctgagcaaagccaaccaggaaaacaggacaagacaggaggcctggaactgc08/28/0708/29/07129Genomicunknown
ss79174229ILLUMINA|HumanHap300v2.0_rs406113fwd/TA/Ctagggtctgctgagcaaagccaaccaggaaaacaggacaagacaggaggcctggaactgc04/18/0711/18/07130Genomicunknown
ss83447640KRIBB_YJKIM|KHS463924fwd/TA/Ctagggtctgctgagcaaagccaaccaggaaaacaggacaagacaggaggcctggaactgc12/04/0712/05/07130Genomicunknown
ss84169033PHARMGKB_AB_DME|PS206039_PA147495299_301fwd/TA/Ctagggtctgctgagcaaagccaaccaggaaaacaggacaagacaggaggcctggaactgc12/06/0712/09/07130Genomicunknown
ss86031164HGSV|Cor18517_SNV_20070510.chr6_28591461fwd/TA/Ctagggtctgctgagcaaagccaaccaggaaaacaggacaagacaggaggcctggaactgc12/06/0712/11/07130Genomicunknown
ss93429359BCMHGSC_JDW|JWB-2114442fwd/TA/Ctagggtctgctgagcaaagccaaccaggaaaacaggacaagacaggaggcctggaactgc02/26/0803/04/08129Genomicunknown
ss98483942HUMANGENOME_JCVI|1103652816205fwd/TA/Ctagggtctgctgagcaaagccaaccaggaaaacaggacaagacaggaggcctggaactgc04/01/0804/01/08130Genomicunknown
ss105439840SNP500CANCER|GPX6-02rev/BG/Tgcagttccwggcctcctgtcttgtcctgttttcctggttggctttgctcagcagacccta09/05/0809/05/08130Genomicunknown
ss1098601031000GENOMES|CEU.trio.12.15.2008_1476568_chr6_28591461fwd/TA/Ctagggtctgctgagcaaagccaaccaggaaaacaggacaagacaggaggcctggaactgc12/15/0812/16/08130Genomicunknown
ss1140790881000GENOMES|NA19240_2008_12_16_1327046_chr6_28591461fwd/TA/Ctagggtctgctgagcaaagccaaccaggaaaacaggacaagacaggaggcctggaactgc12/18/0812/18/08130Genomicunknown
ss116371546ILLUMINA-UK|NA18507_000041279_NCBI36.1_chr6_28591461fwd/TA/Ctagggtctgctgagcaaagccaaccaggaaaacaggacaagacaggaggcctggaactgc01/17/0901/17/09130Genomic99 %

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs406113|allelePos=65|totalLen=3351|taxid=9606|snpclass=1|alleles='A/C'|mol=Genomic|build=130
 CCTGCCCCAT GCTCACCTTC CTATTTTGAG GCTTTAGGGT CTGCTGAGCA AAGCCAACCA
 GGAA
 M
 AACAGGACAA GACAGGAGGC CTGGAACTGC TGGAACATGG CTAGGAGTTT TAGACGACTC
 TGAGGTCCCC AGGATTTCAG CCCCTTTTGA GCCCCTGGCA GGGACCAATT TGAAGAAGCA
 CCCTCCAATC GCAGAGTGGC ATTCATACAC ACCCACCTCC ACTCCCTACA CACACCCCCT
 TCCTCTTCAG TTGTAAACCC CTCACCATCG AGCCTGCTCC ACCTGCGTTG CCTCTGCCAG
 CTTCACACAA AAGGCATTCT CTGCCTCTTG AAACTAAAGT CTGGGTGGGG TTGAGTTCTT
 ATGAACTCTC TTGAAAGACA AGCTTTTAGT TATCTCAGAT TTCTGAACTC TTTTCAAAAG
 CCTATAATCT ATGTCCTGAT CACTGATACC TGATCCAGCT ATGCAGCTCC TTAAGGCAGC
 AGGTCAGATG CTTGCCTCTT ATGGAACAGA CCTACACACA TTCCCAAGTT CTTTACCCTT
 CTCCTGCTTT TAGCTCAAAA AAATGGCTGA AACTTTGACT ACGAGGCTAT AAAGACCATt
 gaattcaata cctgtcagtg ccactgacta gctccttgaa tctgaaatca aagttaatgt
 gtctgtcccc agttttctca tctgtgaaat cagaataata atattatcta ccttgtaggg
 ctgctgtaac aattaaatgt gataataact ataaagcact taccacatgg cctgacaatg
 gtaaacAACT AGAACTGTAT TCACATAGTT TCATGTATGA GAAAACTGAA GCTCAGAGAG
 AGAGATAACA TATAAAAAGT CACAAGGTGG GTAACAGTGA AATGAAGGCA ACTTCTGCGT
 CCTACTCCAG AGCTCTTGCT CTGGTTCCAT TTGGATCATA ATTACTGTGA TGAAATCTTT
 ACTATCTGGG ACAATTTACA TTTGCTCACC TTGTAGTAAT GAGCCCTTGA GAGGTAAGGA
 GACATTTCAT TATGGACCTC ATCAGTAGGT CAAATGGCCT AAAACCCCAA CTTCATAGGT
 TTTGGTGTTC CCACATTCTT GATAGACTTT TGAGTACCTT GGGTCCTTGC CTCCAGCAAT
 GAGAAGTGAA GGTACAGGAG CACACATGGA ACAGGAGGAA ACAAGGAACA TTTCATGTCC
 CTGGTGCACC TGAAGGTATC ATGGGGCTGC AATTGCCCTT CACCCATCCT TCTTTGGAGC
 CTTAGTTCCC TGTTATCTCC TTCCAGGAAT TTTGCTTTCA TCCCTTAGCT ATCTCCTCAC
 TTCCAGGATC TTCTCCAGTC CCTGTTTCCT TCACACTCTG CCTCTATGAC TTTTCTAAAG
 GTCAGGTTTG TTGATATCAC TTATGTTAAA GTGCCCCAAT TCCTCCTAAA TTCTTACACT
 TTTAGTTTGA AATTCTCCCA TGAAGCACTC AAGGTCCTTT CTGATTTGAC ATCGGCCAGA
 TTTCCCTGAT GTAACCTTCC CTCCAGAAAT GTTCTGATTC TGGTAGATAG AACTGTCTTC
 ATCACCAGAG TCCACCTATC TGGGGTTGAC TCTAGATCAA ATCTTGGCAA GTACTTTGGG
 ATCATTCCTG AGATATTTTA TGATATACAA ATTACATATT TTTATTCAAA ATGATGGATA
 TAGCTTTATC AAACAAGACT TCTGAGGTAA CTTTCTGAGA CTTGAGTCAC AAATCAGGGT
 TCTGGTGAGC TTGACCACGC CTTAATATAT ATTAGGAGCC AGTTCACATC CTCACCCTCC
 TCCTTAGAAT TTGGCTTGAT TTATTAATTT ACATTTTAAA ACCTATTCTG TCCACAGATA
 GAAACATTAT TTCAGGTCTG ATTTCATCAA TCAAGAGCAT ACTCTTTAGA TACTAATCAG
 TAGAGTCCAA GATGGCATTA TTTTCTCTAG TATCTTTGAA ACATTATTGG TTCACTTATT
 TTAGTTTTTA ATTTTTATTG GTTCACTTTT AACTTAAGGT CAAATAAACA TCAAAGTTTA
 TATGAATTGC CCCTGCAATG CTGGTGCCTA TTATTGTCTA TCCACCCAAG CAATTGATCT
 TTTAAATCTG AATTCTATCA TCTATCAGAC TAGCTATATT TATCATCTAT CAATGATCTA
 CACATTTGAT CAGCATACCT TTTGTGTCTT CCACCAAATA CATTAAAGTT TATAGGATAG
 AAAGAAGCCA AGTGAAGAAG TTTCTGCCCA GGACTAGAGT TTAACTTACT CCTTATTTCT
 TAATCAAGAT GCTTGTGGTT GATTTTTGGT TAAGCTATGT TCCCATTCAG TGATCAGCAC
 TCACATATGT TCATAACTCA CTTGTTTAAA ATTTGTCTTA AAAAGTAGTA GAAGCGCCAA
 GTGGAGCTTT TTCTTAGGTT CTGAAGTTCA TTTCCCCTGC TTTGGAAAGT CAAAACATTT
 GCATGTCTAC CAAGACATCT AGCATTCATG CTTGCAGGCA GGGATGGTCC TCAGTGTGTA
 TACACAGGAA TATGCACGGC AGTTGTTGGA GCCCAGGATT TGTTCTGATT GGTTGTGCCC
 ATGGCATACT TCTAAATATA TATGTACACA CACACAtttt gggacaaggt ctggctctgt
 cacccaggct ggagtgcagt ggtgtgatct cagctaactt gtaacctttg actccaaggc
 tcaagccatc ctcccacctc agccccctga gtagctggga ctacagtcgc atgccaccaa
 acccagctaa tttttgtatt tttggtagag atgggatttt gtcatgtttc ccagggtggt
 ctcgaagtgg tgatcttaaa tgatccaccc acctaggcat cccaaagtgc tgggattaca
 ggcatgagcc atccaaccca gccCTGCTAA ATATTTTAAT ATCAGCTTTG ATTGCAGAAC
 CAATACAGGC AATGTAAGGT TTTAATTTTT TATCTTGAGA TCTGCTTGTC TGTGCTGTGT
 CAACAAATTC ACATAGAACA AGTAGGTGAC TTTTATTAAT ATCTCAGGTT TAACTTTATA
 TTTCCTCTTT GTTCTACATT TTTTTCTTCT TTTAAATTTA AAAAATGCAT TTTTCTTACT
 GGAGAAGAAA GAAGCAAAGG ATGTGTTAAA GAGAGTAGCT TTTTATCATT GTCAAGGCGT
 AACACTCTAT CATTTTACTC AAATTCTGTA TTACCTCTTC CTTATTCCTG TTCTGTTATA
 ATTTAGCTTG AGcacacaca cacacacaca cacacacaca cacacacaga cacaAGAAGT
 CAGTGCAGGG CCATCAGAGG GGAGGCACAA ACATTTGGGA GATCAT

  GeneView back to top

GeneView via analysis of contig annotation:  

View more variation on this gene (click to hide).
Include clinically associated: in gene region cSNP has frequency double hit
Assembly SNP to Chr Chr Chr position Contig Contig position Allele
Function mRNA Protein
mRNA to Chr Accession Position Allele change Accession Position Residue change
on assembly: is labeled at position on chromosome .

GeneView via analysis of contig annotation: N/A.

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

Function Chr mRNA Protein
SNP to mRNA Accession Position Allele change Accession Position Residue change
on assembly: is labeled at position on chromosome .

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


  Integrated Maps: back to top
Genome Build Chr Chr Pos Contig Contig Pos SNP to
Chr		 Contig
allele		 Group term Group label Contig label Neighbor
SNP		 Map Method
doesn't map to any assembly.

  NCBI Resource Links back to top
Resource
Submitter-Referenced
GenBank
NT_007592 ABBA01038020 AC005678 AL049543.15
dbSNP Blast Analysis
UniGene Cluster ID
448570

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss# Population Individual
Group		 Chrom.
Sample Cnt.
 Source A/A
 A/C
 C/C
 HWP A
 C
ss105439840 P1 202 GF 0.337 0.376 0.287 0.525 0.475
CAUC1 62 GF 0.613 0.323 0.065 0.774 0.226
AFR1 48 GF 0.125 0.375 0.500 0.312 0.688
HISP1 44 GF 0.136 0.545 0.318 0.409 0.591
PAC1 48 GF 0.375 0.292 0.333 0.521 0.479
P2 420 GF 0.267 0.405 0.329 0.469 0.531
CAUC2 120 GF 0.450 0.367 0.183 0.633 0.367
AFR2 120 GF 0.100 0.350 0.550 0.275 0.725
P3 554 GF 0.238 0.484 0.278 0.480 0.520
CAUC3 130 GF 0.462 0.508 0.031 0.715 0.285
AFR3 150 GF 0.080 0.347 0.573 0.253 0.747
HISP3 98 GF 0.184 0.490 0.327 0.429 0.571
PAC3 176 GF 0.239 0.580 0.182 0.528 0.472
ASI2 180 GF 0.256 0.467 0.278 0.489 0.511
ss1473062 HapMap-CEU European 120 IG 0.450 0.367 0.183 0.633 0.367
HapMap-HCB Asian 90 IG 0.378 0.422 0.200 0.589 0.411
HapMap-JPT Asian 90 IG 0.111 0.533 0.356 0.378 0.622
HapMap-YRI Sub-Saharan African 120 IG 0.100 0.350 0.550 0.275 0.725
ss38347255 EGP_YORUB-PANEL Sub-Saharan African 24 AF 0.083 0.167 0.750 0.200 0.167 0.833
EGP_HISP-PANEL Hispanic 42 AF 0.381 0.476 0.143 1.000 0.619 0.381
EGP_CEPH-PANEL European 40 AF 0.450 0.400 0.150 0.655 0.650 0.350
EGP_AD-PANEL African American 30 AF 0.267 0.133 0.600 0.010 0.333 0.667
EGP_ASIAN-PANEL Asian 48 AF 0.125 0.458 0.417 1.000 0.354 0.646
ss44680668 AoD_African_American 90 AF 0.330 0.670
AoD_Caucasian 92 AF 0.680 0.320
AoD_Chinese 90 AF 0.520 0.480
AoD_Japanese 90 AF 0.480 0.520
ss68970000 HapMap-CEU European 120 GF 0.400 0.450 0.150 0.625 0.375
HapMap-HCB Asian 88 GF 0.364 0.432 0.205 0.580 0.420
HapMap-JPT Asian 90 GF 0.067 0.578 0.356 0.356 0.644
HapMap-YRI Sub-Saharan African 120 GF 0.100 0.400 0.500 0.300 0.700
ss84169033 PA147495300 352 AF 0.511 0.489
Concordant Genotype Total Sample A/A A/C C/C
ss1473062 1195 265 528 378
ss38347255 92
ss68970000 258 59 115 83
ss98483942 1 1
RefSNP Genotype Summary Total Individual A/A A/C C/C
rs406113 1245 269 538 388
Discordant Genotypes:
Indiviudal
SampleID		 SubSNP(ss) Genotype Population
Handle		 Submitter
Population		 Submitter
SampleID		 SampleID
Alias		 Submission
Batch		 NCBI
ProbeID
170 ss1473062 C/C CSHL-HAPMAP HapMap-CEU NA07000 CEPH1340.10 r27_ch6_CEU_illumina:human_1m_beadchip
170 ss68970000 A/C CSHL-HAPMAP HapMap-CEU NA07000 CEPH1340.10 chr6-HapMap-CEU
214 ss1473062 A/A CSHL-HAPMAP HapMap-CEU NA07345 CEPH1345.13 r27_ch6_CEU_illumina:human_1m_beadchip
214 ss68970000 A/C CSHL-HAPMAP HapMap-CEU NA07345 CEPH1345.13 chr6-HapMap-CEU
239 ss38347255 T/T EGP_SNPS EGP_CEPH-PANEL E103 NA11882 GPX6-EGP_CEPH-061605
239 ss1473062 A/A CSHL-HAPMAP HapMap-CEU NA11882 CEPH1347.15 r27_ch6_CEU_illumina:human_1m_beadchip
239 ss68970000 A/C CSHL-HAPMAP HapMap-CEU NA11882 CEPH1347.15 chr6-HapMap-CEU
255 ss1473062 A/C CSHL-HAPMAP HapMap-CEU NA10855 CEPH1350.02 r27_ch6_CEU_illumina:human_1m_beadchip
255 ss68970000 C/C CSHL-HAPMAP HapMap-CEU NA10855 CEPH1350.02 chr6-HapMap-CEU
264 ss1473062 C/C CSHL-HAPMAP HapMap-CEU NA11831 CEPH1350.12 r27_ch6_CEU_illumina:human_1m_beadchip
264 ss68970000 A/C CSHL-HAPMAP HapMap-CEU NA11831 CEPH1350.12 chr6-HapMap-CEU
577 ss38347255 T/T EGP_SNPS EGP_CEPH-PANEL E122 NA12813 GPX6-EGP_CEPH-061605
577 ss1473062 A/A CSHL-HAPMAP HapMap-CEU NA12813 CEPH1454.13 r27_ch6_CEU_illumina:human_1m_beadchip
577 ss68970000 A/C CSHL-HAPMAP HapMap-CEU NA12813 CEPH1454.13 chr6-HapMap-CEU
5177 ss1473062 A/A CSHL-HAPMAP HapMap-HCB NA18594 CH18594 r27_ch6_CHB_illumina:human_1m_beadchip
5177 ss68970000 A/C CSHL-HAPMAP HapMap-HCB NA18594 CH18594 chr6-HapMap-HCB
5222 ss1473062 A/A CSHL-HAPMAP HapMap-JPT NA18981 JA18981 r27_ch6_JPT_illumina:human_1m_beadchip
5222 ss68970000 A/C CSHL-HAPMAP HapMap-JPT NA18981 JA18981 chr6-HapMap-JPT
5222 ss38347255 T/T EGP_SNPS EGP_ASIAN-PANEL X118 NA18981 GPX6-EGP_ASIAN-061605
5225 ss1473062 A/A CSHL-HAPMAP HapMap-JPT NA18987 JA18987 r27_ch6_JPT_illumina:human_1m_beadchip
5225 ss68970000 A/C CSHL-HAPMAP HapMap-JPT NA18987 JA18987 chr6-HapMap-JPT
5257 ss1473062 C/C CSHL-HAPMAP HapMap-YRI NA18852 YOR018.02 r27_ch6_YRI_illumina:human_1m_beadchip
5257 ss68970000 A/C CSHL-HAPMAP HapMap-YRI NA18852 YOR018.02 chr6-HapMap-YRI
5284 ss1473062 C/C CSHL-HAPMAP HapMap-YRI NA19204 YOR048.02 r27_ch6_YRI_illumina:human_1m_beadchip
5284 ss68970000 A/C CSHL-HAPMAP HapMap-YRI NA19204 YOR048.02 chr6-HapMap-YRI
5296 ss1473062 C/C CSHL-HAPMAP HapMap-YRI NA19222 YOR058.02 r27_ch6_YRI_illumina:human_1m_beadchip
5296 ss68970000 A/C CSHL-HAPMAP HapMap-YRI NA19222 YOR058.02 chr6-HapMap-YRI
Genotype data submitted for1303 samples from1245 individualsIndividual with multiple genotypes submission:270

  Validation Summary: back to top
Validation status Marker displays
Mendelian segregation		 PCR results confirmed
in multiple reactions		 Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
DoubleHit found by:  BCM_SSAHASNP
 UNKNOWN UNKNOWN YES

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Revised: May 25, 2006 1:38 PM .