Variant report

Variant	rs1553586
Chromosome Location	chr6:100820354-100820355
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:100820119..100822622-chr6:100822669..100824422,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs13193778	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13213077	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1506082	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1506083	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34729906	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35453882	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35502469	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4145403	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs714378	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs718268	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7743566	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7747189	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9376940	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9376941	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9376963	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9386117	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9390325	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949535	chr6:100740293-101469052	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1028122	chr6:100774245-100964347	Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv1023710	chr6:100810738-101001115	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv538388	chr6:100810738-101001115	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:100814200-100830000	Weak transcription	Aorta	Aorta
2	chr6:100819800-100820800	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr6:100820000-100820600	Enhancers	H9 Cell Line	embryonic stem cell
4	chr6:100820000-100821000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:100820000-100821000	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr6:100820000-100821000	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr6:100820000-100821000	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr6:100820000-100821000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:100820000-100821200	Enhancers	Dnd41	blood
10	chr6:100820200-100820600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr6:100820200-100820600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:100820200-100820600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:100820200-100820600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr6:100820200-100820600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr6:100820200-100820800	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr6:100820200-100821000	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr6:100820200-100821000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr6:100820200-100821000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr6:100820200-100821000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr6:100820200-100821200	Enhancers	HUES6 Cell Line	embryonic stem cell

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