Variant report

Variant	rs6022786
Chromosome Location	chr20:52447303-52447304
allele	A/G
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52367432..52369907-chr20:52444310..52447312,3	K562	blood:
2	chr20:52436875..52438996-chr20:52445815..52447419,2	K562	blood:
3	chr20:52446917..52447817-chr20:53061273..53061918,2	MCF-7	breast:
4	chr20:52445461..52447922-chr22:31741028..31743008,2	MCF-7	breast:
5	chr20:52446635..52448369-chr6:26033029..26034926,2	MCF-7	breast:
6	chr20:52446642..52448632-chr8:144359909..144362720,2	MCF-7	breast:
7	chr20:52445630..52448175-chr20:52453269..52455432,3	K562	blood:
8	chr17:57917840..57922874-chr20:52444092..52449259,5	MCF-7	breast:
9	chr20:52444427..52449219-chr20:55839929..55843430,6	MCF-7	breast:
10	chr20:52445950..52448025-chr20:52488646..52490930,2	K562	blood:
11	chr17:56708142..56710971-chr20:52444323..52447306,3	MCF-7	breast:
12	chr20:52447059..52448791-chr20:53058974..53060532,2	MCF-7	breast:
13	chr20:52446291..52448679-chr20:52463374..52466298,2	K562	blood:
14	chr20:52445412..52448214-chr20:52672686..52675334,2	MCF-7	breast:
15	chr1:115052548..115055382-chr20:52445896..52448449,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000137259	Chromatin interaction
ENSG00000213888	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000100105	Chromatin interaction
ENSG00000199004	Chromatin interaction
ENSG00000197323	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs4809942	0.81[JPT][hapmap]
rs6013808	0.83[EUR][1000 genomes]
rs6013809	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6022757	0.81[CEU][hapmap]
rs6064010	0.84[ASN][1000 genomes]
rs6064011	0.81[JPT][hapmap]
rs6068684	0.90[JPT][hapmap]
rs6068691	0.81[JPT][hapmap]
rs6091756	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6097618	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6097632	0.85[CEU][hapmap];0.81[JPT][hapmap]
rs6126982	0.81[CEU][hapmap];0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv834008	chr20:52368660-52533410	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	185 gene(s)	inside rSNPs	diseases
3	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
4	nsv1060372	chr20:52409008-52502100	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	122 gene(s)	inside rSNPs	diseases
5	esv1831516	chr20:52437245-52514913	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	98 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Polycystic ovary syndrome	22885925	GWAS catalog

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52426200-52456200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr20:52443400-52456000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr20:52443800-52449000	Weak transcription	Lung	lung
4	chr20:52444000-52453200	Weak transcription	Small Intestine	intestine
5	chr20:52444800-52456000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr20:52445200-52447400	Flanking Active TSS	Primary hematopoietic stem cells	blood
7	chr20:52445200-52447400	Flanking Active TSS	GM12878-XiMat	blood
8	chr20:52445400-52447600	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr20:52445800-52447400	Enhancers	Fetal Stomach	stomach
10	chr20:52445800-52447400	Enhancers	Stomach Mucosa	stomach
11	chr20:52446000-52447400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr20:52446000-52447800	Enhancers	Fetal Thymus	thymus
13	chr20:52446000-52448000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr20:52446200-52448600	Enhancers	Primary B cells from peripheral blood	blood
15	chr20:52446400-52447400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr20:52446400-52447400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr20:52446400-52447600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr20:52446600-52447400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr20:52446600-52447400	Enhancers	HMEC	breast
20	chr20:52446600-52455400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr20:52446800-52447400	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr20:52446800-52447400	Enhancers	NH-A	brain
23	chr20:52446800-52447600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr20:52446800-52447600	Enhancers	Colonic Mucosa	Colon
25	chr20:52446800-52447800	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr20:52446800-52448000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr20:52446800-52450200	Weak transcription	Fetal Muscle Leg	muscle
28	chr20:52446800-52450600	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr20:52446800-52452000	Weak transcription	Thymus	Thymus
30	chr20:52447000-52447400	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr20:52447000-52447400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr20:52447000-52447400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr20:52447000-52447400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr20:52447000-52447400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr20:52447000-52447400	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr20:52447000-52447400	Enhancers	HUVEC	blood vessel
37	chr20:52447000-52447400	Enhancers	NHEK	skin
38	chr20:52447000-52447400	Enhancers	NHLF	lung
39	chr20:52447000-52447400	Enhancers	Osteobl	bone
40	chr20:52447000-52447600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr20:52447000-52447600	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr20:52447000-52447600	Enhancers	Liver	Liver
43	chr20:52447000-52447600	Enhancers	Dnd41	blood
44	chr20:52447000-52447600	Enhancers	Hela-S3	cervix
45	chr20:52447000-52447600	Enhancers	HSMM	muscle
46	chr20:52447000-52447600	Enhancers	HSMMtube	muscle
47	chr20:52447000-52447800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr20:52447000-52447800	Enhancers	Fetal Lung	lung
49	chr20:52447000-52447800	Enhancers	NHDF-Ad	bronchial
50	chr20:52447000-52448000	Enhancers	Primary hematopoietic stem cells short term culture	blood

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