Variant report

Variant	rs59700988
Chromosome Location	chr4:79564026-79564027
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr4:79563980-79564549	ECC-1	luminal epithelium:	n/a	n/a
2	JUND	chr4:79564011-79564347	K562	blood:	n/a	n/a
3	TEAD4	chr4:79563928-79564454	K562	blood:	n/a	n/a
4	USF2	chr4:79563971-79564079	K562	blood:	n/a	n/a
5	CUX1	chr4:79564026-79564173	K562	blood:	n/a	n/a
6	RCOR1	chr4:79563983-79564434	K562	blood:	n/a	n/a
7	RCOR1	chr4:79563935-79564352	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:79555903..79561750-chr4:79563110..79566277,7	K562	blood:
2	chr4:79563120..79566472-chr4:79698388..79700680,4	K562	blood:
3	chr4:79557761..79562686-chr4:79563110..79568703,4	K562	blood:
4	chr4:79549184..79553600-chr4:79560172..79565329,6	K562	blood:
5	chr4:79563690..79568625-chr4:79568843..79572048,4	K562	blood:
6	chr4:79562196..79569044-chr4:79695847..79699797,11	MCF-7	breast:
7	chr4:79563449..79567560-chr4:79569303..79574487,6	K562	blood:
8	chr4:79562740..79566241-chr4:79702324..79704926,3	MCF-7	breast:

No data

Variant related genes	Relation type
LINC01094	TF binding region
ENSG00000200998	Chromatin interaction
ENSG00000238816	Chromatin interaction
ENSG00000138756	Chromatin interaction
ENSG00000251019	Chromatin interaction
ENSG00000260278	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10452151	1.00[AMR][1000 genomes]
rs55994157	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56071306	1.00[AMR][1000 genomes]
rs56098630	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57648305	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57649400	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59055207	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60681937	1.00[AMR][1000 genomes]
rs60950346	1.00[AMR][1000 genomes]
rs60998921	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61075598	1.00[AMR][1000 genomes]
rs61238857	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73828029	1.00[AMR][1000 genomes]
rs73828034	1.00[AMR][1000 genomes]
rs73828038	1.00[AMR][1000 genomes]
rs73828045	1.00[AMR][1000 genomes]
rs73828046	1.00[AMR][1000 genomes]
rs73828057	1.00[AMR][1000 genomes]
rs73828059	1.00[AMR][1000 genomes]
rs73828064	1.00[AMR][1000 genomes]
rs73828065	1.00[AMR][1000 genomes]
rs73828066	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73828067	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73828069	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73828070	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73828071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73828073	1.00[AMR][1000 genomes]
rs73828074	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73828075	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73828078	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73828079	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73828080	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73828081	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73828083	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73828092	1.00[AMR][1000 genomes]
rs73828098	1.00[AMR][1000 genomes]
rs73828100	1.00[AMR][1000 genomes]
rs73828102	1.00[AMR][1000 genomes]
rs73830206	1.00[AMR][1000 genomes]
rs73830208	1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79550400-79564200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:79551400-79578200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr4:79555800-79566400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr4:79557200-79568000	Enhancers	Primary B cells from cord blood	blood
5	chr4:79560200-79565200	Weak transcription	Primary T cells from cord blood	blood
6	chr4:79560200-79565400	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr4:79560200-79565600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr4:79560600-79564200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr4:79561000-79565400	Weak transcription	NHEK	skin
10	chr4:79561600-79565000	Enhancers	Placenta	Placenta
11	chr4:79561600-79568000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr4:79561800-79566800	Enhancers	K562	blood
13	chr4:79562000-79568000	Enhancers	Primary B cells from peripheral blood	blood
14	chr4:79562200-79564200	Weak transcription	NHDF-Ad	bronchial
15	chr4:79562400-79566400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr4:79562800-79567600	Enhancers	Primary hematopoietic stem cells	blood
17	chr4:79563000-79565000	Enhancers	Placenta Amnion	Placenta Amnion
18	chr4:79563000-79566000	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr4:79563200-79564400	Enhancers	Fetal Thymus	thymus
20	chr4:79563200-79568800	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr4:79563400-79564800	Flanking Active TSS	GM12878-XiMat	blood
22	chr4:79563400-79565000	Enhancers	Brain Anterior Caudate	brain
23	chr4:79563400-79567200	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr4:79563600-79564400	Enhancers	Rectal Mucosa Donor 29	rectum
25	chr4:79563600-79564800	Enhancers	HSMMtube	muscle
26	chr4:79563600-79565000	Enhancers	Brain Substantia Nigra	brain
27	chr4:79563800-79564200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr4:79563800-79566600	Enhancers	Hela-S3	cervix
29	chr4:79564000-79564200	Enhancers	NHLF	lung
30	chr4:79564000-79564400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr4:79564000-79564400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr4:79564000-79564400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr4:79564000-79564400	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr4:79564000-79564400	Enhancers	Brain Cingulate Gyrus	brain
35	chr4:79564000-79564400	Enhancers	Fetal Heart	heart
36	chr4:79564000-79564400	Enhancers	Spleen	Spleen
37	chr4:79564000-79564400	Enhancers	HMEC	breast
38	chr4:79564000-79564400	Enhancers	HSMM	muscle
39	chr4:79564000-79564600	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr4:79564000-79564600	Enhancers	Adipose Nuclei	Adipose
41	chr4:79564000-79564600	Enhancers	Duodenum Mucosa	Duodenum
42	chr4:79564000-79564600	Enhancers	Stomach Mucosa	stomach
43	chr4:79564000-79564800	Enhancers	Brain Hippocampus Middle	brain
44	chr4:79564000-79564800	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr4:79564000-79564800	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr4:79564000-79568000	Enhancers	Fetal Intestine Large	intestine

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