Variant report

Variant	rs539078521
Chromosome Location	chr1:210405547-210405548
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	FOS	chr1:210405312-210405580	MCF10A-Er-Src	breast:	n/a	chr1:210405560-210405569
2	TCF12	chr1:210405238-210406224	SK-N-SH	brain:	n/a	n/a
3	RAD21	chr1:210405344-210405552	SK-N-SH_RA	brain:	n/a	n/a
4	MAX	chr1:210405418-210406263	SK-N-SH	brain:	n/a	n/a
5	RAD21	chr1:210405448-210405790	SK-N-SH_RA	brain:	n/a	n/a
6	POLR2A	chr1:210405383-210405571	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr1:210405446-210405878	SK-N-SH	brain:	n/a	n/a
8	PBX3	chr1:210405387-210406376	SK-N-SH	brain:	n/a	n/a
9	MYC	chr1:210405314-210405803	MCF10A-Er-Src	breast:	n/a	n/a
10	EP300	chr1:210405319-210406323	SK-N-SH	brain:	n/a	chr1:210405510-210405524 chr1:210405976-210405985 chr1:210405975-210405991 chr1:210405979-210405988 chr1:210405511-210405525 chr1:210405561-210405570
11	REST	chr1:210405235-210408055	H1-neurons	neurons:	n/a	n/a
12	STAT3	chr1:210405304-210405624	MCF10A-Er-Src	breast:	n/a	n/a
13	EP300	chr1:210405323-210405817	SK-N-SH_RA	brain:	n/a	chr1:210405510-210405524 chr1:210405511-210405525 chr1:210405561-210405570
14	FOXP2	chr1:210405435-210405745	SK-N-MC	brain:	n/a	n/a
15	STAT3	chr1:210405175-210405567	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr1:210405299-210405899	SK-N-MC	brain:	n/a	n/a
17	TCF12	chr1:210405200-210408026	SK-N-SH	brain:	n/a	chr1:210407710-210407720

No.	Distal block	Cell Line	Cell type
1	chr1:210398376..210400495-chr1:210402941..210405832,2	K562	blood:
2	chr1:210404317..210408653-chr1:210545033..210548956,7	MCF-7	breast:
3	chr1:210404553..210406882-chr6:30538400..30541136,2	MCF-7	breast:

Variant related genes	Relation type
SERTAD4	TF binding region
ENSG00000204574	Chromatin interaction
ENSG00000200972	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv8769	chr1:210403509-210564588	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	esv3422029	chr1:210404854-210407702	Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv3334541	chr1:210405229-210407377	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210403800-210405600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr1:210403800-210405600	Enhancers	NHEK	skin
3	chr1:210404400-210405600	Bivalent Enhancer	Fetal Heart	heart
4	chr1:210405000-210405600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:210405000-210405600	Enhancers	Rectal Mucosa Donor 29	rectum
6	chr1:210405000-210405600	Bivalent Enhancer	Thymus	Thymus
7	chr1:210405000-210407400	Active TSS	Stomach Smooth Muscle	stomach
8	chr1:210405000-210407600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
9	chr1:210405200-210405600	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:210405200-210405600	Enhancers	Brain Cingulate Gyrus	brain
11	chr1:210405200-210405600	Enhancers	Duodenum Mucosa	Duodenum
12	chr1:210405200-210405600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr1:210405200-210405800	Enhancers	Placenta	Placenta
14	chr1:210405200-210405800	Flanking Active TSS	HUVEC	blood vessel
15	chr1:210405200-210406400	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr1:210405200-210406600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:210405200-210407600	Active TSS	NH-A	brain
18	chr1:210405400-210405600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:210405400-210405600	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:210405400-210405600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
21	chr1:210405400-210405600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
22	chr1:210405400-210405600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr1:210405400-210405600	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr1:210405400-210405600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:210405400-210405600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:210405400-210405600	Enhancers	Brain Hippocampus Middle	brain
27	chr1:210405400-210405600	Weak transcription	Left Ventricle	heart
28	chr1:210405400-210405600	Bivalent Enhancer	Osteobl	bone
29	chr1:210405400-210405800	Bivalent Enhancer	Fetal Thymus	thymus
30	chr1:210405400-210406000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:210405400-210406000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
32	chr1:210405400-210406400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:210405400-210406400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr1:210405400-210406400	Bivalent/Poised TSS	Brain Germinal Matrix	brain
35	chr1:210405400-210406600	Active TSS	Muscle Satellite Cultured Cells	--
36	chr1:210405400-210407600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr1:210405400-210407600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
38	chr1:210405400-210407600	Active TSS	Right Ventricle	heart
39	chr1:210405400-210407800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
40	chr1:210405400-210407800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
41	chr1:210405400-210407800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
42	chr1:210405400-210407800	Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr1:210405400-210407800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
44	chr1:210405400-210407800	Active TSS	Colon Smooth Muscle	Colon
45	chr1:210405400-210407800	Active TSS	Rectal Smooth Muscle	rectum
46	chr1:210405400-210408000	Bivalent Enhancer	Fetal Brain Male	brain
47	chr1:210405400-210408000	Active TSS	Pancreatic Islets	Pancreatic Islet

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