Variant report

Variant	rs7980530
Chromosome Location	chr12:117096941-117096942
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	CEBPB	chr12:117096459-117096955	MCF-7	breast:	n/a	n/a
2	GATA3	chr12:117096450-117097016	MCF-7	breast:	n/a	n/a
3	MAX	chr12:117096586-117096967	HepG2	liver:	n/a	chr12:117096885-117096904 chr12:117096890-117096897
4	BHLHE40	chr12:117096337-117096942	HepG2	liver:	n/a	n/a
5	NR2F2	chr12:117096389-117096982	MCF-7	breast:	n/a	n/a
6	HDAC2	chr12:117096406-117096992	MCF-7	breast:	n/a	chr12:117096431-117096445
7	SP1	chr12:117096404-117096947	A549	lung:	n/a	n/a
8	SETDB1	chr12:117096747-117097055	U2OS	brain:	n/a	n/a
9	TCF12	chr12:117096142-117097002	SK-N-SH	brain:	n/a	chr12:117096710-117096720
10	EP300	chr12:117096503-117096995	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr12:117096364-117097116	PFSK-1	brain:	n/a	n/a
12	FOXA2	chr12:117096361-117097042	A549	lung:	n/a	n/a
13	FOXM1	chr12:117096424-117096959	MCF-7	breast:	n/a	n/a
14	NR2F2	chr12:117096463-117096955	MCF-7	breast:	n/a	n/a
15	TCF12	chr12:117096349-117096965	A549	lung:	n/a	chr12:117096710-117096720
16	MAX	chr12:117096632-117096975	MCF-7	breast:	n/a	chr12:117096885-117096904 chr12:117096890-117096897

No.	Distal block	Cell Line	Cell type
1	chr12:117088937..117090937-chr12:117094983..117097116,2	K562	blood:
2	chr12:117095945..117098090-chr12:117099384..117101804,2	K562	blood:
3	chr12:117094883..117097893-chr12:117100651..117103499,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257883	TF binding region
ENSG00000257883	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs58382373	0.84[AMR][1000 genomes]
rs60656302	0.84[AMR][1000 genomes]
rs7299368	0.84[AMR][1000 genomes]
rs73399267	0.84[AMR][1000 genomes]
rs73399270	0.84[AMR][1000 genomes]
rs7962169	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7962186	0.84[AMR][1000 genomes]

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	esv1794859	chr12:117087267-117103935	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv832523	chr12:117090343-117273810	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117093800-117100600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr12:117094200-117098000	Weak transcription	Lung	lung
3	chr12:117095600-117098600	Enhancers	Fetal Thymus	thymus
4	chr12:117095800-117097000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr12:117095800-117097000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr12:117095800-117097000	Enhancers	Fetal Lung	lung
7	chr12:117095800-117097000	Enhancers	Fetal Stomach	stomach
8	chr12:117095800-117098200	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr12:117095800-117098200	Enhancers	Placenta	Placenta
10	chr12:117095800-117098400	Enhancers	Fetal Brain Male	brain
11	chr12:117096000-117097000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr12:117096000-117097000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
13	chr12:117096000-117097000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr12:117096000-117097000	Flanking Active TSS	Liver	Liver
15	chr12:117096000-117097000	Enhancers	Esophagus	oesophagus
16	chr12:117096000-117097000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
17	chr12:117096000-117097000	Active TSS	HSMMtube	muscle
18	chr12:117096000-117097000	Flanking Active TSS	Osteobl	bone
19	chr12:117096200-117097000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr12:117096200-117097000	Flanking Active TSS	Adipose Nuclei	Adipose
21	chr12:117096200-117097000	Flanking Active TSS	Stomach Smooth Muscle	stomach
22	chr12:117096200-117097000	Flanking Active TSS	Hela-S3	cervix
23	chr12:117096200-117097800	Enhancers	Aorta	Aorta
24	chr12:117096200-117098200	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr12:117096400-117097000	Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr12:117096400-117097000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr12:117096400-117097000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
28	chr12:117096400-117100200	Weak transcription	Left Ventricle	heart
29	chr12:117096400-117100200	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr12:117096600-117097000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr12:117096600-117097000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr12:117096600-117097200	Enhancers	Fetal Muscle Trunk	muscle
33	chr12:117096600-117097400	Weak transcription	Gastric	stomach
34	chr12:117096600-117098000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr12:117096600-117098000	Enhancers	Fetal Muscle Leg	muscle
36	chr12:117096600-117099800	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr12:117096600-117100200	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr12:117096600-117100200	Weak transcription	Brain Germinal Matrix	brain
39	chr12:117096600-117103200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr12:117096800-117097000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr12:117096800-117097000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr12:117096800-117097000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr12:117096800-117097000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr12:117096800-117097000	Enhancers	Brain Angular Gyrus	brain
45	chr12:117096800-117097000	Enhancers	Brain Hippocampus Middle	brain
46	chr12:117096800-117097000	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr12:117096800-117097000	Enhancers	Duodenum Mucosa	Duodenum
48	chr12:117096800-117097000	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr12:117096800-117097000	Enhancers	Fetal Brain Female	brain
50	chr12:117096800-117097000	Flanking Active TSS	Pancreas	Pancrea

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