Variant report

Variant	rs616279
Chromosome Location	chr6:140249466-140249467
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:140239712..140241213-chr6:140248206..140250375,2	K562	blood:
2	chr6:140242464..140245824-chr6:140246316..140249558,3	K562	blood:
3	chr6:140247524..140250315-chr6:140258612..140260750,2	K562	blood:
4	chr6:139693225..139698326-chr6:140245231..140252808,11	MCF-7	breast:
5	chr6:139695662..139697462-chr6:140248620..140250507,2	K562	blood:
6	chr6:139692080..139697357-chr6:140246933..140251926,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164442	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1028469	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12525047	0.99[ASN][1000 genomes]
rs12526885	0.99[ASN][1000 genomes]
rs12663217	0.93[ASN][1000 genomes]
rs12663483	0.97[ASN][1000 genomes]
rs12665399	0.95[ASN][1000 genomes]
rs13194827	0.95[ASN][1000 genomes]
rs13204837	0.89[CHB][hapmap];0.85[JPT][hapmap];0.96[ASN][1000 genomes]
rs1416289	0.90[CHB][hapmap];0.82[JPT][hapmap];0.95[ASN][1000 genomes]
rs1933742	0.95[ASN][1000 genomes]
rs1953788	0.99[ASN][1000 genomes]
rs1953789	0.99[ASN][1000 genomes]
rs586246	0.89[CHB][hapmap];0.85[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs587235	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs592056	0.89[CHB][hapmap];0.85[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs598498	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs609488	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs618515	0.90[CHB][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs622216	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62429515	0.96[ASN][1000 genomes]
rs62429516	0.96[ASN][1000 genomes]
rs62429517	0.96[ASN][1000 genomes]
rs647968	0.90[CHB][hapmap];0.80[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs648510	0.83[EUR][1000 genomes]
rs650774	0.83[EUR][1000 genomes]
rs67013338	0.96[ASN][1000 genomes]
rs679849	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs680290	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs681235	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6926807	0.99[ASN][1000 genomes]
rs6928433	0.95[ASN][1000 genomes]
rs724061	0.90[CHB][hapmap];0.82[JPT][hapmap];0.95[ASN][1000 genomes]
rs7743656	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs856646	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9373255	0.99[ASN][1000 genomes]
rs9376482	0.99[ASN][1000 genomes]
rs9385888	0.99[ASN][1000 genomes]
rs9389733	0.90[CHB][hapmap];0.82[JPT][hapmap];0.97[ASN][1000 genomes]
rs9399298	0.90[CHB][hapmap];0.82[JPT][hapmap];0.99[ASN][1000 genomes]
rs9399299	0.97[ASN][1000 genomes]
rs9403134	0.90[CHB][hapmap];0.82[JPT][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869066	chr6:139777114-140639695	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv830820	chr6:140059279-140255292	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
3	nsv1017015	chr6:140084137-140300565	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1019407	chr6:140087307-140304334	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1016532	chr6:140174639-141029988	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140239800-140251600	Weak transcription	Colon Smooth Muscle	Colon
2	chr6:140242400-140254000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:140242400-140260200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr6:140242800-140254400	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr6:140247200-140250000	Enhancers	K562	blood
6	chr6:140247800-140250000	Enhancers	Fetal Heart	heart
7	chr6:140248000-140249600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:140248000-140252400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr6:140248000-140252800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:140248200-140252800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr6:140248200-140254000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr6:140249200-140253000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr6:140249200-140253800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr6:140249400-140254000	Weak transcription	Osteobl	bone

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