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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs35601          
refSNP ID: rs35601
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:76/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:C/T
Ancestral Allele:Not available
Clinical Association:unknown
HGVS Names
NM_004996.3:c.1678-2262C>T
NM_019862.2:c.1678-2262C>T
NM_019898.2:c.1678-2262C>T
NM_019899.2:c.1678-2262C>T
NM_019900.2:c.1678-2262C>T
NT_010393.15:g.7472830C>T
Links

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 ss1609942 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs35601 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
ss39131KWOK|OVLP-70221fwd/BC/Ttaccatgccgatcgaaatgtatttttttaaggaggtataattcaccatttaaaagtgtgc04/28/0010/10/0376Genomic99 %
ss279470KWOK|OVLP-000621-209960fwd/BC/Ttaccatgccgatcgaaatgtatttttttaaggaggtataattcaccatttaaaagtgtgc06/30/0010/10/0379Genomic97 %
ss320846KWOK|OVLP-000621-22160rev/TA/Ggcacacttttaaatggtgaattatacctccttaaaaaaatacatttcgatcggcatggta06/30/0010/10/0379Genomic99 %
ss610632SC_JCM|AC025778.2_180632fwd/BC/Ttaccatgccgatcgaaatgtatttttttaaggaggtataattcaccatttaaaagtgtgc07/12/0010/10/0380Genomicunknown
ss707276SC_JCM|AC026452.5_139935rev/TA/Ggcacacttttaaatggtgaattatacctccttaaaaaaatacatttcgatcggcatggta07/27/0010/10/0385Genomicunknown
ss1139502KWOK|OVLP-000804-402311fwd/BC/Ttaccatgccgatcgaaatgtatttttttaaggaggtataattcaccatttaaaagtgtgc09/02/0010/10/0392Genomic99 %
ss1140208KWOK|OVLP-000804-408027fwd/BC/Ttaccatgccgatcgaaatgtatttttttaaggaggtataattcaccatttaaaagtgtgc09/02/0010/10/0386Genomic99 %
ss1237953KWOK|OVLP-000804-409989fwd/BC/Ttaccatgccgatcgaaatgtatttttttaaggaggtataattcaccatttaaaagtgtgc09/02/0010/10/0392Genomic97 %
ss1609942KWOK|OVLP-000925-448985byFreqfwd/BC/Ttaccatgccgatcgaaatgtatttttttaaggaggtataattcaccatttaaaagtgtgc10/04/0010/25/0692Genomic99 %
ss1610273KWOK|OVLP-000925-452331fwd/BC/Ttaccatgccgatcgaaatgtatttttttaaggaggtataattcaccatttaaaagtgtgc10/04/0010/10/0387Genomic99 %
ss1642209KWOK|OVLP-000925-446292fwd/BC/Ttaccatgccgatcgaaatgtatttttttaaggaggtataattcaccatttaaaagtgtgc10/04/0010/10/0392Genomic97 %
ss3336362TSC-CSHL|TSC1550852fwd/BC/Ttaccatgccgatcgaaatgtatttttttaaggaggtataattcaccatttaaaagtgtgc09/20/0110/10/03100Genomicunknown
ss5336275TSC-CSHL|TSC1575715fwd/BC/Ttaccatgccgatcgaaatgtatttttttaaggaggtataattcaccatttaaaagtgtgc09/20/0210/10/03108Genomicunknown
ss14260933BCM_SSAHASNP|chr16.NT_010393.14_7471885fwd/BC/Ttaccatgccgatcgaaatgtatttttttaaggaggtataattcaccatttaaaagtgtgc11/05/0311/22/03119Genomicunknown
ss16706557CSHL-HAPMAP|CSHL-HuAA-200402.chr16.NT_010393.14_7471885fwd/BC/Ttaccatgccgatcgaaatgtatttttttaaggaggtataattcaccatttaaaagtgtgc02/17/0403/04/04120Genomicunknown
ss21347831SSAHASNP|WGSA-200403-chr16.chr16.NT_010393.14_7471885fwd/BC/Ttaccatgccgatcgaaatgtatttttttaaggaggtataattcaccatttaaaagtgtgc03/19/0403/19/04121Genomicunknown
ss40702504ABI|hCV3188914fwd/BC/Ttaccatgccgatcgaaatgtatttttttaaggaggtataattcaccatttaaaagtgtgc07/17/0507/17/05126Genomicunknown
ss75242968ILLUMINA|ILMN_Human_1M_rs35601fwd/BC/Ttaccatgccgatcgaaatgtatttttttaaggaggtataattcaccatttaaaagtgtgc08/28/0708/29/07129Genomicunknown
ss80173248HGSV|Cor18507_SNV_20070510.chr16_16067252fwd/BC/Ttaccatgccgatcgaaatgtatttttttaaggaggtataattcaccatttaaaagtgtgc11/23/0711/24/07130Genomicunknown
ss90334084BCMHGSC_JDW|JWB-0926266fwd/BC/Ttaccatgccgatcgaaatgtatttttttaaggaggtataattcaccatttaaaagtgtgc02/26/0802/29/08129Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs35601|allelePos=1326|totalLen=2759|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=130
 GATTGGTACT TGGCTCACCA AGGGGGCTGG TACGTTTTGG TGGTGAGATG CCTGAGGCCT
 GGTTTGCTTC ACTGCTGAAG AGACACCTGT GATGTGCTCT TCTGCCCTCA GGCAAATTCA
 CCTACCCCGT CCCCACCCAT TTATCCACTC CCACCCATCC Attatctatc cagcagacat
 tcactgagca ccatgatctg ggctctgtcc taggctctga caatacagca gtgcatacta
 caggtaataa tctccagtca tggaacattc atttttcacg gagagaaaca gacaaggaaa
 aataggcaca ataaataaat cctagtgcta gagaaagcca tcctaagtgc tatagaaaga
 aaagagtcag atctttggaa taagggcggc ttgcagtttt aagtagggtg gtccaagctc
 actgagaagg tgacacttga ggaaagactt gatggaggta aagaggccaa ccagggagta
 gcaagagcat gtgcaaaggc cctggggcat tactgtgccc attcataggt gggataacca
 tggaggctga aacagtggga gtgaggggag agtgacagat gacgccaaat gaggtacggg
 gaagggactt tacaaatcag ctgggccttg ggatccgagt cagcactttg acttctacac
 tgaaaaatag gttgactttg gagagGTACT TTTTTAAAAA TTACTTGTTT AGAGATGGgg
 gcctcactct gttacccagg ctggtgcggg ggcacagtaa tagctcactg cagcctcgac
 ctcctgggct caaatgattc tcctgcctca gcctccctag tagctaggac tacaggtgca
 tgccactatg cttgacttat ttATTAATAT TATTGTTGtt ttgagacgga gtcttgctct
 gttgcacacg ctggggtgca gtggtgcaat cttggctcac tgcaacctcc acctcccggg
 ttaaagtgat tctcctactt cagcctccct agtagctggg actacaggca catgccacca
 cacccggcta atttttgtat ttttagtaga gacagggttt tgccctgtca gacaggctgg
 tcttgaactc ctgacttcag gagatccacc tgccttggcc tcccaacatg ctgggattac
 aggcatgagc cattgagccc agccACCTGG CTTATTTTTT AAAAAAtttt gtagagacac
 aggcttgctt ttttgccctg gctctgctcg aacttctggc ctcaagtgat cctccctcct
 cggccttgca aagcatttgg attacaggca tgggctacca tgccGATCGA AATGTATTTT
 TTTAA
 Y
 GGAGGtataa ttcaccattt aaaagtgtgc aattcagtgg tttttTTGTG TGATGTGTGG
 TGGTGTGAAG GTCACCcagt gggttttttg tataaatgat aatgacaatc accactaatt
 ccaggacgtt ttcattaccc caaaaggaag ccctgtacct gttaccagtt gctccccaaa
 tcttccattc cattccaggc aaccagtaat ctgctttctg tctgtctctg tttatctact
 gtggactttt catataaatg gaatcaaaca acaggtggcc ttttctgact gttttctttt
 tttttgagac gaagtgtctc ccttgttgcc cacctgaagc gcaatggcat gaccttgcct
 cactacaacg tttgcctcct aggttcaagc gattctcctg cctcagccta ctgagtagct
 gggattatag gcatgcacca ccactcctgg ctaattgtgt atttttagta gagacggagt
 ttctccatgt tggtcaggct ggtctggaac tcccgacctc aagtgatccg cccgcctcag
 cctcccgaag tgctgggatt tcaggtgtga gccaccccgc ctggccatct gactggtttc
 ttagcatgat gttttcaagg tttatccatg ttttagcatg tataagaatt tcactccttt
 ttatggttga gaagtctatc atgtagatac aTGTAGACCC TTTCGAGTAA AGAATATCTC
 TGggctgggc atggtggctc atacctgtaa tcccagcatt ttgggaggcc gaggcagacg
 gatcacttga ggccaggagc tcaagaccag cctgaccaac atggcgaaac cccatctcta
 ctaagaaaaa tacaaaaaga ttagctgggc atggtggtgg gcgcctataa tcccagctac
 ttggagactg aggcatgaga atcgtttgac cttgggaggc agaggttgcg gtgaactgcg
 atcgcaccac tgcactccat cttgtgcaaa agaatgagac tgtgtctcaa aaaaaaaaaa
 aGTATCTTTA GGTAAGATGC CAGTGTTGCG TTACCGCTTA GAAGATGGGA GCCAGGATgg
 gtgcagtggc tcatgtctgt aatcccagca ctttaggtgg ccgaggcagg cagatggcct
 gagcccaggt gttcgagaac agcctaggaa gcatagggag accctgtctc tacaaaaata
 aaaaaactag ccgggcatgg tggtatgcgc ctgtagtcct agctactcgg gaggctgagg
 tgggaggaat gcttgagccc gggaggtcga ggctgtggtg agccatgatt gcaccactgc
 acccagGGAT CATGCGTCCC TGTCGTTTCG AGCACCTTGC CTCCCTCTTG ACATCGGAGC
 CTGGAAAATT TCTGTGCCAT GGCTCAGCGT CATCTGTCTT GTTAATGTCA GAG

  GeneView back to top
GeneView via analysis of contig annotation: ABCC1 ATP-binding cassette, sub-family C (CFTR/MRP), member 1
View variations for gene:
Include clinically associated: in gene region cSNP has frequency double hit
Group
Label		Contig->mRNAGene Model (contig mRNA transcript) Color Legend
referenceNT_010393->NM_004996
svfunction
referenceNT_010393->NM_019862
svfunction
referenceNT_010393->NM_019898
svfunction
referenceNT_010393->NM_019899
svfunction
referenceNT_010393->NM_019900
svfunction
HuRefNW_001838356->NM_004996
svfunction
HuRefNW_001838356->NM_019862
svfunction
HuRefNW_001838356->NM_019898
svfunction
HuRefNW_001838356->NM_019899
svfunction
HuRefNW_001838356->NM_019900
svfunction
CeleraNW_926051->NM_004996
svfunction
CeleraNW_926051->NM_019862
svfunction
CeleraNW_926051->NM_019898
svfunction
CeleraNW_926051->NM_019899
svfunction
CeleraNW_926051->NM_019900
svfunction
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_010393->NM_004996->NP_0049877472830forwardintron
referenceNT_010393->NM_019862->NP_0639157472830forwardintron
referenceNT_010393->NM_019898->NP_0639537472830forwardintron
referenceNT_010393->NM_019899->NP_0639547472830forwardintron
referenceNT_010393->NM_019900->NP_0639557472830forwardintron
HuRefNW_001838356->NM_004996->NP_004987691754forwardintron
HuRefNW_001838356->NM_019862->NP_063915691754forwardintron
HuRefNW_001838356->NM_019898->NP_063953691754forwardintron
HuRefNW_001838356->NM_019899->NP_063954691754forwardintron
HuRefNW_001838356->NM_019900->NP_063955691754forwardintron
CeleraNW_926051->NM_004996->NP_004987692868forwardintron
CeleraNW_926051->NM_019862->NP_063915692868forwardintron
CeleraNW_926051->NM_019898->NP_063953692868forwardintron
CeleraNW_926051->NM_019899->NP_063954692868forwardintron
CeleraNW_926051->NM_019900->NP_063955692868forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs35601 maps exactly once on NCBI human chromosome 16
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
16NW_001838356.169175415553623plusTalt_assembly_8HuRefHuRefview1325
16NW_926051.169286815839888plusTalt_assembly_1CeleraCeleraview1325
16NT_010393.15747283016067252plusCref_assemblyreferencereferenceview1325

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_010393 AC025778 AC026452 AC026452.5
dbSNP Blast Analysis
GenBank HTGS Finished:GenBank HTGS Draft:
AC003026.1 AC025778.8 NC_000016.8 AC026452.5

  Population Diversity back to top

Sample AscertainmentGenotype Detailnew.gifAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
T
ss1609942HapMap-CEUEuropean 106IG 0.019 0.321 0.660 0.527 0.179 0.821
HapMap-HCBAsian 80IG 0.075 0.350 0.575 0.752 0.250 0.750
HapMap-JPTAsian 70IG 0.057 0.257 0.686 0.403 0.186 0.814
HapMap-YRISub-Saharan African 100IG 0.060 0.400 0.540 1.000 0.260 0.740

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict
0.342+/-0.23227021000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hitwithHapMapFreq
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .