Variant report

Variant	rs6097553
Chromosome Location	chr20:52347783-52347784
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:45988261..45989864-chr20:52347427..52350014,2	MCF-7	breast:
2	chr20:52345991..52347989-chr20:55837745..55840072,2	MCF-7	breast:

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12479726	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55993902	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6013777	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6022698	0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6022701	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6091737	0.81[ASN][1000 genomes]
rs6097552	0.90[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	nsv1055342	chr20:52126973-52352323	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	214 gene(s)	inside rSNPs	diseases
2	esv3412883	chr20:52176349-52393416	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	250 gene(s)	inside rSNPs	diseases
3	nsv834007	chr20:52213864-52404557	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	174 gene(s)	inside rSNPs	diseases
4	esv34060	chr20:52251863-52702186	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	296 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52331200-52352600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr20:52341800-52354800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr20:52342000-52352200	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr20:52344800-52348000	Weak transcription	Placenta	Placenta
5	chr20:52346400-52351600	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr20:52346400-52352800	Weak transcription	Spleen	Spleen
7	chr20:52346600-52349200	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr20:52346600-52350400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr20:52346600-52350600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr20:52346800-52352000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr20:52347000-52348200	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr20:52347200-52349800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr20:52347200-52350400	Weak transcription	HepG2	liver
14	chr20:52347200-52352000	Weak transcription	Fetal Thymus	thymus
15	chr20:52347200-52352200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr20:52347200-52352400	Weak transcription	Duodenum Mucosa	Duodenum
17	chr20:52347200-52352800	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr20:52347200-52353400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr20:52347400-52348200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr20:52347400-52350800	Weak transcription	GM12878-XiMat	blood
21	chr20:52347600-52350600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr20:52347600-52352000	Weak transcription	Primary B cells from cord blood	blood
23	chr20:52347600-52352000	Weak transcription	Primary B cells from peripheral blood	blood

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