Variant report

Variant	rs599086
Chromosome Location	chr20:52576894-52576895
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:52576003..52577529-chr20:52812898..52814510,2	MCF-7	breast:
2	chr20:52575166..52577110-chr20:52817182..52819499,2	MCF-7	breast:
3	chr17:56706951..56709239-chr20:52571954..52576924,4	MCF-7	breast:
4	chr1:201118101..201120636-chr20:52576111..52577980,2	MCF-7	breast:
5	chr17:56735101..56737749-chr20:52575346..52577054,2	MCF-7	breast:
6	chr12:120729283..120731029-chr20:52576003..52578392,2	MCF-7	breast:
7	chr20:52574055..52577130-chr20:55839672..55843479,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000202538	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000226308	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs6013852	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6013853	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6022866	1.00[CEU][hapmap]
rs6022882	1.00[CEU][hapmap];0.85[YRI][hapmap];1.00[EUR][1000 genomes]
rs6022891	1.00[CEU][hapmap]
rs6022912	1.00[EUR][1000 genomes]
rs6091785	1.00[CEU][hapmap]
rs6091790	1.00[CEU][hapmap]
rs7260720	1.00[CEU][hapmap];1.00[EUR][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	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
2	nsv834009	chr20:52386050-52590795	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	182 gene(s)	inside rSNPs	diseases
3	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
4	nsv1055549	chr20:52555871-52586281	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52566400-52644800	Weak transcription	Gastric	stomach
2	chr20:52567000-52578200	Weak transcription	Brain Angular Gyrus	brain
3	chr20:52567000-52580200	Weak transcription	Stomach Mucosa	stomach
4	chr20:52570200-52591800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr20:52570200-52592400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr20:52570800-52590800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr20:52574200-52577400	Enhancers	Fetal Stomach	stomach
8	chr20:52574800-52578200	Weak transcription	Brain Substantia Nigra	brain
9	chr20:52575600-52578400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr20:52576200-52577000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr20:52576200-52577000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr20:52576200-52577000	Flanking Active TSS	Osteobl	bone
13	chr20:52576200-52577200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr20:52576200-52577400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr20:52576200-52577400	Enhancers	Muscle Satellite Cultured Cells	--
16	chr20:52576200-52577800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr20:52576400-52577000	Enhancers	H9 Cell Line	embryonic stem cell
18	chr20:52576400-52577000	Enhancers	Fetal Muscle Leg	muscle
19	chr20:52576400-52577000	Enhancers	NHLF	lung
20	chr20:52576400-52577200	Enhancers	HSMMtube	muscle
21	chr20:52576400-52577400	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr20:52576400-52577400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr20:52576400-52577400	Enhancers	NH-A	brain
24	chr20:52576400-52577600	Enhancers	Fetal Lung	lung
25	chr20:52576400-52577800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr20:52576400-52578200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr20:52576400-52578200	Enhancers	Fetal Kidney	kidney
28	chr20:52576400-52578400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr20:52576400-52578400	Enhancers	HSMM	muscle
30	chr20:52576400-52578600	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr20:52576400-52578600	Enhancers	Brain Hippocampus Middle	brain
32	chr20:52576400-52591400	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr20:52576600-52577000	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr20:52576600-52577000	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr20:52576600-52577000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr20:52576600-52577400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr20:52576600-52577400	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr20:52576600-52577400	Enhancers	Brain Anterior Caudate	brain
39	chr20:52576600-52578000	Enhancers	A549	lung
40	chr20:52576600-52578600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr20:52576600-52578600	Enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr20:52576800-52577400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr20:52576800-52577600	Enhancers	HepG2	liver
44	chr20:52576800-52577800	Enhancers	Adipose Nuclei	Adipose
45	chr20:52576800-52578200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr20:52576800-52579200	Enhancers	NHDF-Ad	bronchial

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