Variant report

Variant	rs7860710
Chromosome Location	chr9:94914429-94914430
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	POLR2A	chr9:94912692-94914690	U87	brain:	n/a	n/a
2	TCF12	chr9:94913949-94914850	SK-N-SH	brain:	n/a	chr9:94914360-94914368
3	ZNF217	chr9:94914069-94914812	MCF-7	breast:	n/a	n/a
4	MAX	chr9:94914173-94914728	MCF-7	breast:	n/a	n/a
5	GATA3	chr9:94914145-94914732	MCF-7	breast:	n/a	n/a
6	EP300	chr9:94914000-94914870	MCF-7	breast:	n/a	chr9:94914197-94914205
7	ESR1	chr9:94914277-94914632	ECC-1	luminal epithelium:	n/a	n/a
8	ESR1	chr9:94914166-94914672	T-47D	breast:	n/a	n/a
9	TEAD4	chr9:94914198-94914644	MCF-7	breast:	n/a	n/a
10	MYC	chr9:94914311-94914573	MCF-7	breast:	n/a	n/a
11	EP300	chr9:94914193-94914691	T-47D	breast:	n/a	chr9:94914197-94914205
12	EP300	chr9:94914225-94914717	T-47D	breast:	n/a	n/a
13	ESR1	chr9:94914089-94914742	ECC-1	luminal epithelium:	n/a	n/a
14	ESR1	chr9:94914262-94914602	ECC-1	luminal epithelium:	n/a	n/a
15	CEBPB	chr9:94914022-94914600	IMR90	lung:	n/a	chr9:94914193-94914210
16	GATA3	chr9:94914285-94914796	T-47D	breast:	n/a	n/a
17	TCF12	chr9:94914093-94914951	MCF-7	breast:	n/a	chr9:94914360-94914368
18	EP300	chr9:94914122-94915162	SK-N-SH	brain:	n/a	chr9:94914197-94914205
19	ESR1	chr9:94914261-94914598	T-47D	breast:	n/a	n/a
20	MAX	chr9:94914005-94914740	MCF-7	breast:	n/a	n/a
21	SIN3AK20	chr9:94914388-94914692	SK-N-SH	brain:	n/a	n/a
22	REST	chr9:94914247-94914700	MCF-7	breast:	n/a	chr9:94914305-94914318
23	GATA3	chr9:94914033-94914991	MCF-7	breast:	n/a	n/a
24	REST	chr9:94914326-94914682	SK-N-SH	brain:	n/a	n/a
25	POLR2A	chr9:94913620-94914637	U87	brain:	n/a	n/a
26	HDAC2	chr9:94914051-94914805	MCF-7	breast:	n/a	chr9:94914249-94914263
27	SIN3AK20	chr9:94913922-94914986	MCF-7	breast:	n/a	n/a
28	EP300	chr9:94914117-94914788	MCF-7	breast:	n/a	chr9:94914197-94914205
29	NR3C1	chr9:94914214-94914609	ECC-1	luminal epithelium:	n/a	chr9:94914468-94914494
30	NR2F2	chr9:94914036-94914837	MCF-7	breast:	n/a	n/a
31	STAT3	chr9:94914383-94914531	MCF10A-Er-Src	breast:	n/a	n/a
32	NFIC	chr9:94913964-94914796	SK-N-SH	brain:	n/a	n/a
33	POLR2A	chr9:94913811-94914626	U87	brain:	n/a	n/a
34	MXI1	chr9:94914202-94915125	SK-N-SH	brain:	n/a	n/a
35	PBX3	chr9:94914248-94914879	SK-N-SH	brain:	n/a	n/a
36	ESR1	chr9:94914262-94914707	ECC-1	luminal epithelium:	n/a	n/a
37	CEBPB	chr9:94914008-94914678	MCF-7	breast:	n/a	chr9:94914193-94914210
38	GATA2	chr9:94914082-94914842	SH-SY5Y	brain:	n/a	n/a
39	ELF1	chr9:94913984-94914709	MCF-7	breast:	n/a	n/a
40	ESR1	chr9:94914119-94914700	ECC-1	luminal epithelium:	n/a	n/a
41	EP300	chr9:94914309-94914751	SK-N-SH_RA	brain:	n/a	n/a
42	GATA3	chr9:94914383-94914786	SH-SY5Y	brain:	n/a	n/a
43	ESR1	chr9:94914095-94914639	ECC-1	luminal epithelium:	n/a	n/a
44	MAX	chr9:94914337-94914699	SK-N-SH	brain:	n/a	n/a
45	HA-E2F1	chr9:94913925-94914743	MCF-7	breast:	n/a	n/a
46	GATA3	chr9:94913935-94914867	MCF-7	breast:	n/a	n/a
47	ESR1	chr9:94914235-94914651	T-47D	breast:	n/a	n/a
48	FOXM1	chr9:94914093-94914910	MCF-7	breast:	n/a	n/a
49	NR2F2	chr9:94913942-94914913	MCF-7	breast:	n/a	n/a
50	EP300	chr9:94913989-94914898	SK-N-SH	brain:	n/a	chr9:94914197-94914205

No.	Distal block	Cell Line	Cell type
1	chr10:132897127..132897964-chr9:94913983..94914829,2	MCF-7	breast:
2	chr9:94903265..94904181-chr9:94913861..94914694,3	MCF-7	breast:
3	chr9:94907081..94909170-chr9:94913018..94916076,3	MCF-7	breast:
4	chr9:94912447..94914532-chr9:94951103..94952987,2	MCF-7	breast:
5	chr9:94909662..94911780-chr9:94913646..94915674,2	K562	blood:
6	chr9:94903732..94905881-chr9:94913415..94915626,3	MCF-7	breast:

Variant related genes	Relation type
LINC00475	TF binding region
ENSG00000225511	Chromatin interaction
ENSG00000238996	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11788037	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11793106	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11793157	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11794436	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11794519	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7846932	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7875826	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv1046733	chr9:94690622-95138564	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530947	chr9:94697309-95093377	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv917089	chr9:94857047-95099848	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv969760	chr9:94877924-94966209	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv893572	chr9:94891778-94944778	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv972779	chr9:94910607-94920083	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94910200-94914600	Weak transcription	Fetal Lung	lung
2	chr9:94910200-94923800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr9:94911200-94925600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr9:94912400-94915200	Enhancers	HSMM	muscle
5	chr9:94912400-94917600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr9:94913400-94915000	Enhancers	NHDF-Ad	bronchial
7	chr9:94913400-94916800	Enhancers	NH-A	brain
8	chr9:94913400-94917000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr9:94913600-94915000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr9:94913600-94915400	Enhancers	HSMMtube	muscle
11	chr9:94913600-94917800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr9:94913800-94914600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr9:94913800-94914600	Flanking Active TSS	Osteobl	bone
14	chr9:94913800-94915000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr9:94913800-94915000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr9:94913800-94915000	Enhancers	Brain Germinal Matrix	brain
17	chr9:94913800-94915000	Enhancers	Esophagus	oesophagus
18	chr9:94913800-94915000	Enhancers	Fetal Muscle Trunk	muscle
19	chr9:94913800-94915000	Enhancers	Fetal Muscle Leg	muscle
20	chr9:94913800-94915000	Enhancers	Ovary	ovary
21	chr9:94913800-94915000	Enhancers	Rectal Smooth Muscle	rectum
22	chr9:94913800-94915000	Enhancers	NHLF	lung
23	chr9:94913800-94915400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr9:94913800-94915400	Enhancers	Placenta Amnion	Placenta Amnion
25	chr9:94913800-94915400	Enhancers	HMEC	breast
26	chr9:94913800-94916400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr9:94913800-94916600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr9:94913800-94916600	Enhancers	Placenta	Placenta
29	chr9:94914000-94914600	Enhancers	Brain Substantia Nigra	brain
30	chr9:94914000-94914800	Enhancers	Brain Hippocampus Middle	brain
31	chr9:94914000-94914800	Enhancers	A549	lung
32	chr9:94914000-94915000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr9:94914000-94915000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr9:94914000-94915000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
35	chr9:94914000-94915000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr9:94914000-94915000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr9:94914000-94915000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr9:94914000-94915200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr9:94914000-94915200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr9:94914000-94915400	Enhancers	Stomach Smooth Muscle	stomach
41	chr9:94914000-94915400	Enhancers	NHEK	skin
42	chr9:94914000-94916800	Enhancers	Colon Smooth Muscle	Colon
43	chr9:94914200-94915000	Enhancers	Brain Angular Gyrus	brain
44	chr9:94914200-94915000	Enhancers	Fetal Brain Male	brain
45	chr9:94914200-94915000	Enhancers	Pancreas	Pancrea
46	chr9:94914200-94915000	Bivalent Enhancer	HepG2	liver
47	chr9:94914200-94915000	Enhancers	K562	blood
48	chr9:94914200-94915200	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr9:94914200-94916600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr9:94914400-94915000	Enhancers	Cortex derived primary cultured neurospheres	brain

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