Variant report

Variant	rs556348059
Chromosome Location	chr3:28391589-28391590
allele	A/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	POLR2A	chr3:28389358-28391594	GM12891	blood:	n/a	n/a
2	POLR2A	chr3:28389421-28392084	GM12878	blood:	n/a	n/a
3	MAX	chr3:28388969-28391592	Hela-S3	cervix:	n/a	chr3:28389268-28389277
4	CUX1	chr3:28389078-28391644	K562	blood:	n/a	n/a
5	PML	chr3:28389703-28391590	K562	blood:	n/a	n/a
6	EP300	chr3:28389140-28391841	K562	blood:	n/a	chr3:28389265-28389279 chr3:28390526-28390533 chr3:28390482-28390498
7	POLR2A	chr3:28388873-28392054	IMR90	lung:	n/a	n/a
8	BRCA1	chr3:28389022-28391711	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr3:28388560-28395839	MCF10A-Er-Src	breast:	n/a	n/a
10	MXI1	chr3:28391585-28391649	GM12878	blood:	n/a	n/a
11	POLR2A	chr3:28388951-28391892	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr3:28389110-28391599	HepG2	liver:	n/a	n/a
13	POLR2A	chr3:28388762-28392516	K562	blood:	n/a	n/a
14	POLR2A	chr3:28389004-28391702	K562	blood:	n/a	n/a
15	POLR2A	chr3:28389792-28391617	K562	blood:	n/a	n/a
16	POLR2A	chr3:28387839-28396035	MCF10A-Er-Src	breast:	n/a	n/a
17	HCFC1	chr3:28388191-28391638	Hela-S3	cervix:	n/a	n/a
18	TAL1	chr3:28390059-28391590	K562	blood:	n/a	n/a
19	MAZ	chr3:28389127-28391603	IMR90	lung:	n/a	chr3:28389268-28389277
20	RCOR1	chr3:28389644-28391691	K562	blood:	n/a	n/a
21	IRF1	chr3:28388035-28391677	K562	blood:	n/a	chr3:28391536-28391549 chr3:28391382-28391398

No.	Distal block	Cell Line	Cell type
1	chr3:28360111..28361698-chr3:28390791..28393091,2	K562	blood:
2	chr3:28279814..28285757-chr3:28388127..28392208,14	K562	blood:
3	chr3:28390959..28393888-chr3:28439197..28440878,2	K562	blood:
4	chr3:28391232..28393248-chr3:28418194..28419782,2	K562	blood:
5	chr3:23957644..23960053-chr3:28390990..28393934,2	K562	blood:
6	chr3:28279814..28284603-chr3:28388127..28392296,9	K562	blood:
7	chr2:3621624..3624347-chr3:28389179..28391722,2	MCF-7	breast:

Variant related genes	Relation type
AZI2	TF binding region
ENSG00000174748	Chromatin interaction
ENSG00000171863	Chromatin interaction
ENSG00000187118	Chromatin interaction
ENSG00000197885	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3328565	chr3:27991169-28915035	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv876649	chr3:28126595-28718454	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	esv2500136	chr3:28391396-28393792	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:28387600-28391600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr3:28387600-28392200	Active TSS	Right Atrium	heart
3	chr3:28388000-28391600	Active TSS	Psoas Muscle	Psoas
4	chr3:28388000-28392000	Active TSS	NHLF	lung
5	chr3:28388200-28391800	Active TSS	HMEC	breast
6	chr3:28388200-28392000	Active TSS	GM12878-XiMat	blood
7	chr3:28388200-28392000	Active TSS	K562	blood
8	chr3:28388400-28391600	Active TSS	Stomach Smooth Muscle	stomach
9	chr3:28388400-28391800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr3:28388400-28392200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:28388600-28391600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr3:28389000-28391600	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr3:28389000-28391800	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr3:28389200-28391600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:28389200-28391600	Active TSS	NHDF-Ad	bronchial
16	chr3:28389200-28392200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:28389400-28391600	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr3:28389400-28391600	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr3:28389400-28391600	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr3:28389400-28391600	Active TSS	Brain Hippocampus Middle	brain
21	chr3:28389400-28391600	Active TSS	NH-A	brain
22	chr3:28389400-28391800	Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr3:28389600-28391600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:28389800-28391600	Active TSS	Fetal Brain Male	brain
25	chr3:28389800-28392000	Active TSS	Liver	Liver
26	chr3:28390000-28391600	Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr3:28390400-28391600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:28390800-28391600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
29	chr3:28390800-28391600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
30	chr3:28390800-28391800	Flanking Active TSS	Primary T cells from cord blood	blood
31	chr3:28390800-28391800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr3:28391000-28391600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
33	chr3:28391000-28391600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
34	chr3:28391000-28391600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
35	chr3:28391000-28391600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
36	chr3:28391000-28391600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
37	chr3:28391000-28391600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr3:28391000-28391600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
39	chr3:28391000-28391600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr3:28391000-28391800	Flanking Active TSS	Dnd41	blood
41	chr3:28391000-28391800	Flanking Active TSS	HSMMtube	muscle
42	chr3:28391000-28391800	Flanking Active TSS	HUVEC	blood vessel
43	chr3:28391000-28391800	Flanking Active TSS	Osteobl	bone
44	chr3:28391000-28392200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
45	chr3:28391000-28394400	Weak transcription	Spleen	Spleen
46	chr3:28391200-28391600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
47	chr3:28391200-28391600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
48	chr3:28391200-28391600	Flanking Active TSS	Duodenum Mucosa	Duodenum
49	chr3:28391200-28391600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
50	chr3:28391200-28393600	Weak transcription	Gastric	stomach

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