Variant report

Variant	rs565826236
Chromosome Location	chr3:52741492-52741493
allele	C/T
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	MEF2C	chr3:52741483-52742069	GM12878	blood:	n/a	chr3:52741652-52741673 chr3:52741811-52741826
2	NFIC	chr3:52741269-52742113	GM12878	blood:	n/a	n/a
3	ATF2	chr3:52741478-52741983	GM12878	blood:	n/a	n/a
4	ATF2	chr3:52741443-52742145	GM12878	blood:	n/a	n/a
5	SPI1	chr3:52741443-52741932	HL-60	blood:	n/a	chr3:52741681-52741694
6	FOXM1	chr3:52741492-52742131	GM12878	blood:	n/a	n/a
7	STAT5A	chr3:52741401-52742079	GM12878	blood:	n/a	n/a
8	EGR1	chr3:52741252-52741544	K562	blood:	n/a	n/a
9	SPI1	chr3:52741443-52741846	GM12891	blood:	n/a	chr3:52741681-52741694
10	POLR2A	chr3:52738509-52741957	GM12878	blood:	n/a	n/a
11	MXI1	chr3:52737444-52741872	SK-N-SH	brain:	n/a	n/a
12	PML	chr3:52741223-52742041	GM12878	blood:	n/a	n/a
13	SPI1	chr3:52741467-52741896	GM12891	blood:	n/a	chr3:52741681-52741694
14	RUNX3	chr3:52741360-52742165	GM12878	blood:	n/a	n/a
15	MEF2A	chr3:52741410-52742103	GM12878	blood:	n/a	chr3:52741652-52741673
16	NFIC	chr3:52741381-52742120	GM12878	blood:	n/a	n/a
17	POLR2A	chr3:52741251-52741948	GM12878	blood:	n/a	n/a
18	SPI1	chr3:52741492-52742095	GM12878	blood:	n/a	chr3:52741681-52741694
19	ELF1	chr3:52741265-52741752	GM12878	blood:	n/a	chr3:52741682-52741693
20	EGR1	chr3:52741272-52741509	K562	blood:	n/a	n/a
21	MAZ	chr3:52741420-52741991	GM12878	blood:	n/a	n/a
22	SPI1	chr3:52741491-52741948	HL-60	blood:	n/a	chr3:52741681-52741694
23	MTA3	chr3:52741227-52742130	GM12878	blood:	n/a	n/a
24	RUNX3	chr3:52741295-52742097	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:52718628..52724105-chr3:52738117..52743946,12	MCF-7	breast:
2	chr3:52567128..52569011-chr3:52738941..52741649,3	K562	blood:
3	chr3:52567315..52569798-chr3:52739141..52741499,3	MCF-7	breast:
4	chr3:52569513..52572297-chr3:52740518..52742042,2	K562	blood:

Variant related genes	Relation type
GLT8D1	TF binding region
ENSG00000163938	Chromatin interaction
ENSG00000212493	Chromatin interaction
ENSG00000168268	Chromatin interaction
ENSG00000168273	Chromatin interaction
ENSG00000163939	Chromatin interaction
ENSG00000252787	Chromatin interaction

Extended variants
information (count: 2 )
Associated
traits (count: 0)

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	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv508219	chr3:52741193-52803899	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52737800-52741600	Active TSS	Colonic Mucosa	Colon
2	chr3:52738000-52741600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:52738200-52741800	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr3:52738400-52741600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:52738400-52741800	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr3:52738800-52741600	Active TSS	A549	lung
7	chr3:52739000-52741600	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr3:52739000-52741600	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr3:52739000-52741600	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr3:52739000-52742600	Active TSS	GM12878-XiMat	blood
11	chr3:52739200-52741600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:52739400-52741600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr3:52740200-52741800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr3:52740200-52742200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr3:52740400-52741600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
16	chr3:52740400-52741800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr3:52740400-52741800	Flanking Active TSS	Brain Angular Gyrus	brain
18	chr3:52740400-52741800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
19	chr3:52740400-52742000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr3:52740600-52741600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:52740600-52741600	Flanking Active TSS	Fetal Stomach	stomach
22	chr3:52740600-52741600	Flanking Active TSS	Fetal Thymus	thymus
23	chr3:52740600-52741600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
24	chr3:52740600-52741800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:52740600-52742400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
26	chr3:52740800-52741600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr3:52740800-52741600	Flanking Active TSS	Fetal Lung	lung
28	chr3:52740800-52741600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
29	chr3:52740800-52741600	Flanking Active TSS	Stomach Smooth Muscle	stomach
30	chr3:52740800-52741600	Enhancers	Spleen	Spleen
31	chr3:52740800-52741800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr3:52740800-52741800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr3:52740800-52741800	Flanking Active TSS	Duodenum Mucosa	Duodenum
34	chr3:52740800-52741800	Flanking Active TSS	Thymus	Thymus
35	chr3:52740800-52741800	Flanking Active TSS	Dnd41	blood
36	chr3:52740800-52741800	Flanking Active TSS	HUVEC	blood vessel
37	chr3:52741000-52741600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr3:52741000-52741600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr3:52741000-52741600	Enhancers	Primary B cells from peripheral blood	blood
40	chr3:52741000-52741600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr3:52741000-52741600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr3:52741000-52741600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr3:52741000-52741600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr3:52741000-52741600	Enhancers	Esophagus	oesophagus
45	chr3:52741000-52741600	Enhancers	Placenta	Placenta
46	chr3:52741000-52741600	Enhancers	Placenta Amnion	Placenta Amnion
47	chr3:52741000-52741800	Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr3:52741000-52741800	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr3:52741000-52741800	Flanking Active TSS	Osteobl	bone
50	chr3:52741000-52742000	Enhancers	Primary monocytes fromperipheralblood	blood

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