Variant report

Variant	rs558291868
Chromosome Location	chr3:52443144-52443145
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr3:52443055-52444488	IMR90	lung:	n/a	n/a
2	MXI1	chr3:52443027-52445926	SK-N-SH	brain:	n/a	n/a
3	MTA3	chr3:52442995-52444180	GM12878	blood:	n/a	n/a
4	ESRRA	chr3:52442736-52445785	GM12878	blood:	n/a	chr3:52444629-52444645 chr3:52443225-52443237 chr3:52443981-52443994 chr3:52444631-52444641 chr3:52445485-52445504

No.	Distal block	Cell Line	Cell type
1	chr3:52441032..52443343-chr3:52444895..52446688,2	MCF-7	breast:
2	chr3:52420801..52424667-chr3:52442297..52446214,5	K562	blood:
3	chr3:52442610..52445343-chr3:52803282..52805357,2	K562	blood:
4	chr3:52324588..52327004-chr3:52442941..52444727,2	MCF-7	breast:
5	chr3:52271478..52274801-chr3:52443057..52446273,4	K562	blood:
6	chr3:52442891..52445847-chr3:52570573..52572369,2	K562	blood:
7	chr3:52272619..52275147-chr3:52443057..52446254,5	K562	blood:
8	chr3:52443115..52446014-chr3:52718098..52719635,2	K562	blood:

Variant related genes	Relation type
PHF7	TF binding region
BAP1	TF binding region
ENSG00000239732	Chromatin interaction
ENSG00000114904	Chromatin interaction
ENSG00000168237	Chromatin interaction
ENSG00000243224	Chromatin interaction
ENSG00000163939	Chromatin interaction
ENSG00000010318	Chromatin interaction
ENSG00000168273	Chromatin interaction
ENSG00000114841	Chromatin interaction
ENSG00000247596	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
3	nsv834696	chr3:52317478-52479537	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	45 gene(s)	inside rSNPs	diseases
4	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	esv3325653	chr3:52442937-52445885	Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52395000-52443200	Weak transcription	Right Atrium	heart
2	chr3:52438000-52443400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr3:52438200-52443200	Transcr. at gene 5' and 3'	NHEK	skin
4	chr3:52439600-52443200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr3:52440600-52443200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:52441800-52443200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr3:52441800-52443200	Weak transcription	Ovary	ovary
8	chr3:52441800-52443600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:52442000-52443200	Genic enhancers	Spleen	Spleen
10	chr3:52442200-52443200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:52442200-52443200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:52442200-52443200	Genic enhancers	Primary B cells from peripheral blood	blood
13	chr3:52442200-52443200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr3:52442400-52443200	Enhancers	Primary T cells fromperipheralblood	blood
15	chr3:52442400-52443400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:52442400-52443400	Genic enhancers	Lung	lung
17	chr3:52442400-52443800	Transcr. at gene 5' and 3'	Dnd41	blood
18	chr3:52442400-52445200	Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr3:52442600-52443200	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr3:52442600-52443200	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
21	chr3:52442600-52443200	Weak transcription	Esophagus	oesophagus
22	chr3:52442600-52443200	Enhancers	Gastric	stomach
23	chr3:52442600-52443200	Enhancers	Pancreas	Pancrea
24	chr3:52442600-52443400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:52442600-52443600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr3:52442600-52443600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr3:52442600-52443600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr3:52442600-52443600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr3:52442600-52443600	Flanking Active TSS	Brain Hippocampus Middle	brain
30	chr3:52442600-52443600	Flanking Active TSS	Colonic Mucosa	Colon
31	chr3:52442600-52443600	Flanking Active TSS	Colon Smooth Muscle	Colon
32	chr3:52442600-52443600	Flanking Active TSS	Hela-S3	cervix
33	chr3:52442600-52443800	Flanking Active TSS	Fetal Brain Male	brain
34	chr3:52442600-52443800	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
35	chr3:52442600-52445800	Active TSS	H9 Cell Line	embryonic stem cell
36	chr3:52442800-52443200	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr3:52442800-52443200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr3:52442800-52443200	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr3:52442800-52443200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
40	chr3:52442800-52443200	Flanking Active TSS	Brain Germinal Matrix	brain
41	chr3:52442800-52443200	Transcr. at gene 5' and 3'	Fetal Adrenal Gland	Adrenal Gland
42	chr3:52442800-52443200	Transcr. at gene 5' and 3'	Fetal Lung	lung
43	chr3:52442800-52443200	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
44	chr3:52442800-52443200	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
45	chr3:52442800-52443200	Enhancers	Placenta Amnion	Placenta Amnion
46	chr3:52442800-52443200	Transcr. at gene 5' and 3'	Osteobl	bone
47	chr3:52442800-52443400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr3:52442800-52443400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
49	chr3:52442800-52443400	Flanking Active TSS	GM12878-XiMat	blood
50	chr3:52442800-52443400	Flanking Active TSS	HepG2	liver

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