Variant report

Variant	rs374725106
Chromosome Location	chr3:52741675-52741676
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	TBL1XR1	chr3:52741561-52741938	GM12878	blood:	n/a	n/a
3	NFIC	chr3:52741269-52742113	GM12878	blood:	n/a	n/a
4	GATA3	chr3:52741500-52741866	SH-SY5Y	brain:	n/a	n/a
5	ATF2	chr3:52741478-52741983	GM12878	blood:	n/a	n/a
6	ATF2	chr3:52741443-52742145	GM12878	blood:	n/a	n/a
7	SPI1	chr3:52741443-52741932	HL-60	blood:	n/a	chr3:52741681-52741694
8	SP1	chr3:52741606-52741993	H1-hESC	embryonic stem cell:	n/a	n/a
9	FOXM1	chr3:52741492-52742131	GM12878	blood:	n/a	n/a
10	STAT5A	chr3:52741401-52742079	GM12878	blood:	n/a	n/a
11	STAT5A	chr3:52741621-52742085	GM12878	blood:	n/a	n/a
12	POLR2A	chr3:52741617-52741980	GM12878	blood:	n/a	n/a
13	SPI1	chr3:52741443-52741846	GM12891	blood:	n/a	chr3:52741681-52741694
14	MTA3	chr3:52741524-52742141	GM12878	blood:	n/a	n/a
15	NFYB	chr3:52741662-52741835	GM12878	blood:	n/a	n/a
16	POLR2A	chr3:52738509-52741957	GM12878	blood:	n/a	n/a
17	MXI1	chr3:52737444-52741872	SK-N-SH	brain:	n/a	n/a
18	PML	chr3:52741223-52742041	GM12878	blood:	n/a	n/a
19	SPI1	chr3:52741467-52741896	GM12891	blood:	n/a	chr3:52741681-52741694
20	RUNX3	chr3:52741360-52742165	GM12878	blood:	n/a	n/a
21	POLR2A	chr3:52741530-52741884	GM12878	blood:	n/a	n/a
22	MXI1	chr3:52741569-52741983	GM12878	blood:	n/a	n/a
23	MEF2A	chr3:52741410-52742103	GM12878	blood:	n/a	chr3:52741652-52741673
24	NFIC	chr3:52741381-52742120	GM12878	blood:	n/a	n/a
25	POLR2A	chr3:52741251-52741948	GM12878	blood:	n/a	n/a
26	SPI1	chr3:52741556-52741799	GM12878	blood:	n/a	chr3:52741681-52741694
27	SPI1	chr3:52741492-52742095	GM12878	blood:	n/a	chr3:52741681-52741694
28	POLR2A	chr3:52741663-52741815	K562	blood:	n/a	n/a
29	ELF1	chr3:52741265-52741752	GM12878	blood:	n/a	chr3:52741682-52741693
30	SPI1	chr3:52741577-52741772	K562	blood:	n/a	chr3:52741681-52741694
31	MAZ	chr3:52741420-52741991	GM12878	blood:	n/a	n/a
32	EP300	chr3:52741610-52741970	GM12878	blood:	n/a	chr3:52741678-52741692 chr3:52741682-52741691
33	SPI1	chr3:52741491-52741948	HL-60	blood:	n/a	chr3:52741681-52741694
34	SPI1	chr3:52741516-52741837	GM12878	blood:	n/a	chr3:52741681-52741694
35	RCOR1	chr3:52741541-52742019	GM12878	blood:	n/a	n/a
36	BCL3	chr3:52741529-52741966	GM12878	blood:	n/a	n/a
37	MEF2A	chr3:52741580-52742102	GM12878	blood:	n/a	chr3:52741652-52741673
38	BCLAF1	chr3:52741495-52742117	GM12878	blood:	n/a	n/a
39	BHLHE40	chr3:52741636-52742038	GM12878	blood:	n/a	n/a
40	MTA3	chr3:52741227-52742130	GM12878	blood:	n/a	n/a
41	SPI1	chr3:52741560-52741790	K562	blood:	n/a	chr3:52741681-52741694
42	RUNX3	chr3:52741295-52742097	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52718628..52724105-chr3:52738117..52743946,12	MCF-7	breast:
2	chr3:52569513..52572297-chr3:52740518..52742042,2	K562	blood:

Variant related genes	Relation type
GLT8D1	TF binding region
ENSG00000163939	Chromatin interaction
ENSG00000163938	Chromatin interaction
ENSG00000168273	Chromatin interaction
ENSG00000212493	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:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52738200-52741800	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr3:52738400-52741800	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr3:52739000-52742600	Active TSS	GM12878-XiMat	blood
4	chr3:52740200-52741800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr3:52740200-52742200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr3:52740400-52741800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr3:52740400-52741800	Flanking Active TSS	Brain Angular Gyrus	brain
8	chr3:52740400-52741800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
9	chr3:52740400-52742000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr3:52740600-52741800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:52740600-52742400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
12	chr3:52740800-52741800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
13	chr3:52740800-52741800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:52740800-52741800	Flanking Active TSS	Duodenum Mucosa	Duodenum
15	chr3:52740800-52741800	Flanking Active TSS	Thymus	Thymus
16	chr3:52740800-52741800	Flanking Active TSS	Dnd41	blood
17	chr3:52740800-52741800	Flanking Active TSS	HUVEC	blood vessel
18	chr3:52741000-52741800	Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr3:52741000-52741800	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr3:52741000-52741800	Flanking Active TSS	Osteobl	bone
21	chr3:52741000-52742000	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr3:52741000-52742000	Enhancers	Primary neutrophils fromperipheralblood	blood
23	chr3:52741000-52742000	Enhancers	Primary B cells from cord blood	blood
24	chr3:52741000-52742000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr3:52741000-52742200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
26	chr3:52741000-52742400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr3:52741000-52742400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr3:52741000-52746400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:52741000-52748200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:52741000-52748200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr3:52741000-52748800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr3:52741000-52748800	Weak transcription	Lung	lung
33	chr3:52741200-52741800	Enhancers	Adipose Nuclei	Adipose
34	chr3:52741200-52741800	Enhancers	Brain Anterior Caudate	brain
35	chr3:52741200-52741800	Flanking Active TSS	Fetal Brain Female	brain
36	chr3:52741200-52742000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr3:52741200-52742000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr3:52741200-52742000	Weak transcription	Fetal Kidney	kidney
39	chr3:52741200-52742200	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr3:52741200-52742200	Enhancers	Colon Smooth Muscle	Colon
41	chr3:52741200-52742200	Enhancers	Fetal Brain Male	brain
42	chr3:52741200-52742400	Genic enhancers	Primary T cells fromperipheralblood	blood
43	chr3:52741200-52742400	Enhancers	Primary hematopoietic stem cells	blood
44	chr3:52741200-52748200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr3:52741400-52741800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr3:52741400-52741800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr3:52741400-52741800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr3:52741400-52741800	Active TSS	Brain Germinal Matrix	brain
49	chr3:52741400-52741800	Flanking Active TSS	HepG2	liver
50	chr3:52741400-52742000	Enhancers	Breast Myoepithelial Primary Cells	Breast

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