Variant report

Variant	rs2870276
Chromosome Location	chr20:52350534-52350535
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:58602011..58604653-chr20:52349971..52352360,2	MCF-7	breast:
2	chr20:52349507..52351793-chr6:132662386..132665362,2	MCF-7	breast:
3	chr12:53773971..53776932-chr20:52348408..52351125,2	MCF-7	breast:
4	chr17:59475494..59478044-chr20:52349419..52353533,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000267131	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000185591	Chromatin interaction
ENSG00000062725	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000259349	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12479726	0.90[ASN][1000 genomes]
rs12480103	1.00[CEU][hapmap];0.90[AMR][1000 genomes]
rs55993902	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6022697	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6022698	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6091737	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6097549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6097552	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6126927	0.90[CEU][hapmap]
rs62206459	0.90[AMR][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:37 , 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	chr20:52346400-52351600	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr20:52346400-52352800	Weak transcription	Spleen	Spleen
6	chr20:52346600-52350600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr20:52346800-52352000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr20:52347200-52352000	Weak transcription	Fetal Thymus	thymus
9	chr20:52347200-52352200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr20:52347200-52352400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr20:52347200-52352800	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr20:52347200-52353400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr20:52347400-52350800	Weak transcription	GM12878-XiMat	blood
14	chr20:52347600-52350600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr20:52347600-52352000	Weak transcription	Primary B cells from cord blood	blood
16	chr20:52347600-52352000	Weak transcription	Primary B cells from peripheral blood	blood
17	chr20:52348200-52350600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr20:52348600-52350600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr20:52348600-52357600	Enhancers	Placenta	Placenta
20	chr20:52349800-52351600	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr20:52349800-52351800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr20:52350000-52350600	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr20:52350000-52352200	Weak transcription	NHLF	lung
24	chr20:52350000-52352600	Weak transcription	Brain Cingulate Gyrus	brain
25	chr20:52350200-52350600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr20:52350200-52353200	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr20:52350400-52350800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr20:52350400-52350800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr20:52350400-52351000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr20:52350400-52351000	Enhancers	Adipose Nuclei	Adipose
31	chr20:52350400-52351000	Enhancers	NH-A	brain
32	chr20:52350400-52351200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr20:52350400-52351400	Enhancers	NHDF-Ad	bronchial
34	chr20:52350400-52352400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr20:52350400-52353400	Enhancers	HepG2	liver
36	chr20:52350400-52353600	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr20:52350400-52354800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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