Variant report

Variant	rs539636569
Chromosome Location	chr4:3074998-3074999
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	REST	chr4:3074859-3075124	H1-hESC	embryonic stem cell:	n/a	chr4:3075044-3075053 chr4:3075037-3075050
2	MXI1	chr4:3074910-3076677	SK-N-SH	brain:	n/a	n/a
3	ZBTB7A	chr4:3074957-3075883	ECC-1	luminal epithelium:	n/a	chr4:3075182-3075189
4	REST	chr4:3074970-3075163	K562	blood:	n/a	chr4:3075044-3075053 chr4:3075037-3075050
5	ELF1	chr4:3074756-3075805	GM12878	blood:	n/a	n/a
6	POLR2A	chr4:3074789-3076732	HepG2	liver:	n/a	n/a
7	REST	chr4:3074879-3075181	H1-hESC	embryonic stem cell:	n/a	chr4:3075044-3075053 chr4:3075037-3075050
8	REST	chr4:3074802-3075249	ECC-1	luminal epithelium:	n/a	chr4:3075044-3075053 chr4:3075037-3075050
9	MAX	chr4:3074956-3076696	HepG2	liver:	n/a	n/a
10	ZBTB7A	chr4:3074865-3075845	ECC-1	luminal epithelium:	n/a	chr4:3075182-3075189
11	SIN3A	chr4:3074960-3075729	H1-hESC	embryonic stem cell:	n/a	chr4:3075375-3075388 chr4:3074993-3075004 chr4:3075326-3075335 chr4:3075418-3075429
12	CTCF	chr4:3074960-3075110	WI-38	lung:	n/a	n/a
13	REST	chr4:3074858-3075218	SK-N-SH	brain:	n/a	chr4:3075044-3075053 chr4:3075037-3075050

No.	Distal block	Cell Line	Cell type
1	chr4:3074016..3078502-chr4:3111809..3117809,7	MCF-7	breast:
2	chr4:3070733..3073155-chr4:3073597..3075559,3	K562	blood:
3	chr4:3068906..3071079-chr4:3073190..3075687,2	MCF-7	breast:
4	chr4:3074885..3077461-chr4:3292207..3294882,2	MCF-7	breast:
5	chr4:2964356..2966158-chr4:3074837..3077632,2	K562	blood:
6	chr4:2262471..2264332-chr4:3074788..3077577,2	MCF-7	breast:

Variant related genes	Relation type
HTT	TF binding region
ENSG00000159788	Chromatin interaction
ENSG00000123933	Chromatin interaction
ENSG00000197386	Chromatin interaction
ENSG00000087269	Chromatin interaction
ENSG00000125388	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv461163	chr4:2906285-3234980	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv593437	chr4:2906285-3234980	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
5	esv3326369	chr4:3074679-3077527	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3048200-3075200	Weak transcription	Right Atrium	heart
2	chr4:3058200-3075200	Weak transcription	Psoas Muscle	Psoas
3	chr4:3061600-3075000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr4:3062200-3075000	Weak transcription	Adipose Nuclei	Adipose
5	chr4:3063800-3075200	Weak transcription	Right Ventricle	heart
6	chr4:3064400-3075000	Weak transcription	Fetal Intestine Small	intestine
7	chr4:3064800-3075000	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr4:3068800-3075000	Weak transcription	Primary B cells from cord blood	blood
9	chr4:3069600-3075200	Weak transcription	Brain Hippocampus Middle	brain
10	chr4:3071800-3075000	Weak transcription	Fetal Muscle Leg	muscle
11	chr4:3072200-3075200	Enhancers	Liver	Liver
12	chr4:3072800-3075200	Weak transcription	Gastric	stomach
13	chr4:3073200-3075000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr4:3073400-3075000	Weak transcription	Osteobl	bone
15	chr4:3073600-3075000	Weak transcription	HSMM	muscle
16	chr4:3073600-3075200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr4:3073600-3075400	Weak transcription	HSMMtube	muscle
18	chr4:3073800-3075000	Weak transcription	NH-A	brain
19	chr4:3073800-3075200	Weak transcription	NHDF-Ad	bronchial
20	chr4:3074000-3075000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr4:3074000-3075200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr4:3074000-3075200	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr4:3074000-3075200	Enhancers	Pancreas	Pancrea
24	chr4:3074000-3075200	Weak transcription	NHLF	lung
25	chr4:3074200-3075000	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr4:3074600-3075000	Enhancers	Stomach Smooth Muscle	stomach
27	chr4:3074600-3075200	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr4:3074800-3075000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
29	chr4:3074800-3075000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr4:3074800-3075000	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr4:3074800-3075000	Enhancers	Primary hematopoietic stem cells	blood
32	chr4:3074800-3075000	Active TSS	Primary T helper cells fromperipheralblood	blood
33	chr4:3074800-3075000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr4:3074800-3075000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr4:3074800-3075000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr4:3074800-3075000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr4:3074800-3075000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr4:3074800-3075000	Enhancers	Brain Anterior Caudate	brain
39	chr4:3074800-3075000	Active TSS	Brain Inferior Temporal Lobe	brain
40	chr4:3074800-3075000	Enhancers	Fetal Muscle Trunk	muscle
41	chr4:3074800-3075000	Enhancers	Placenta Amnion	Placenta Amnion
42	chr4:3074800-3075000	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr4:3074800-3075000	Enhancers	Dnd41	blood
44	chr4:3074800-3075200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr4:3074800-3075200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr4:3074800-3075200	Enhancers	Primary B cells from peripheral blood	blood
47	chr4:3074800-3075200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr4:3074800-3075200	Enhancers	Brain Cingulate Gyrus	brain
49	chr4:3074800-3075200	Enhancers	Placenta	Placenta
50	chr4:3074800-3075200	Enhancers	Fetal Thymus	thymus

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