Variant report

Variant	rs3787559
Chromosome Location	chr20:52827038-52827039
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:49345330..49348251-chr20:52823191..52827147,4	MCF-7	breast:
2	chr20:52826695..52829423-chr20:53117360..53120091,2	MCF-7	breast:
3	chr20:52824614..52827050-chrX:153713627..153715899,2	MCF-7	breast:
4	chr17:57915224..57917032-chr20:52824163..52827087,2	MCF-7	breast:
5	chr16:765349..767993-chr20:52824649..52827443,2	MCF-7	breast:
6	chr20:52825632..52827601-chr20:53272621..53275494,2	MCF-7	breast:
7	chr20:52824488..52827444-chr3:64007659..64009363,3	MCF-7	breast:
8	chr20:52826556..52827403-chr8:38759473..38760087,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000103260	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000102178	Chromatin interaction
ENSG00000124171	Chromatin interaction
ENSG00000163636	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11698157	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs292112	0.84[ASN][1000 genomes]
rs292116	1.00[JPT][hapmap]
rs292117	1.00[JPT][hapmap]
rs6013926	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs6013927	1.00[ASN][1000 genomes]
rs6023079	0.92[JPT][hapmap]
rs6127146	0.80[ASN][1000 genomes]
rs73137406	0.96[ASN][1000 genomes]
rs986709	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv834010	chr20:52759824-52932939	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52825400-52828400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr20:52825400-52829800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr20:52825400-52838800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr20:52825600-52827200	Enhancers	Stomach Mucosa	stomach
5	chr20:52825600-52827400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr20:52825600-52833800	Weak transcription	Lung	lung
7	chr20:52825600-52839000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr20:52825800-52827200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr20:52825800-52831400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr20:52826000-52827200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr20:52826000-52827200	Enhancers	Right Atrium	heart
12	chr20:52826000-52827400	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr20:52826000-52827400	Enhancers	Ovary	ovary
14	chr20:52826000-52828400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr20:52826000-52828800	Weak transcription	Aorta	Aorta
16	chr20:52826000-52831200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr20:52826000-52831400	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr20:52826000-52831400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr20:52826000-52833400	Weak transcription	Esophagus	oesophagus
20	chr20:52826000-52833600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr20:52826000-52837200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr20:52826000-52837800	Weak transcription	Fetal Thymus	thymus
23	chr20:52826000-52838200	Weak transcription	Pancreas	Pancrea
24	chr20:52826000-52840000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr20:52826200-52827200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr20:52826200-52827400	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr20:52826200-52827600	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr20:52826200-52828200	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr20:52826200-52828600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr20:52826200-52828800	Weak transcription	HSMMtube	muscle
31	chr20:52826200-52828800	Weak transcription	HUVEC	blood vessel
32	chr20:52826200-52831000	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr20:52826200-52831200	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr20:52826200-52831200	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr20:52826200-52831200	Weak transcription	Primary B cells from cord blood	blood
36	chr20:52826200-52831200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr20:52826200-52831200	Weak transcription	Fetal Intestine Large	intestine
38	chr20:52826200-52831400	Weak transcription	Primary B cells from peripheral blood	blood
39	chr20:52826200-52831400	Weak transcription	Duodenum Mucosa	Duodenum
40	chr20:52826200-52831800	Weak transcription	Fetal Kidney	kidney
41	chr20:52826200-52836000	Weak transcription	Colonic Mucosa	Colon
42	chr20:52826200-52838800	Weak transcription	Gastric	stomach
43	chr20:52826400-52827200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr20:52826400-52827200	Enhancers	Brain Germinal Matrix	brain
45	chr20:52826400-52828000	Weak transcription	Hela-S3	cervix
46	chr20:52826400-52828000	Weak transcription	Osteobl	bone
47	chr20:52826400-52828200	Weak transcription	NH-A	brain
48	chr20:52826400-52828800	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr20:52826400-52828800	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr20:52826400-52829200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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