Variant report

Variant	rs12680907
Chromosome Location	chr8:99307463-99307464
allele	A/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	NR2F2	chr8:99305437-99307536	MCF-7	breast:	n/a	chr8:99305964-99305979
2	GATA3	chr8:99306480-99307635	MCF-7	breast:	n/a	n/a
3	POLR2A	chr8:99305305-99307543	MCF10A-Er-Src	breast:	n/a	n/a
4	GATA3	chr8:99305498-99307554	MCF-7	breast:	n/a	chr8:99305823-99305834 chr8:99306451-99306461
5	POLR2A	chr8:99305494-99307467	HepG2	liver:	n/a	n/a
6	SIN3AK20	chr8:99305460-99307664	MCF-7	breast:	n/a	n/a
7	MAX	chr8:99305559-99307509	MCF-7	breast:	n/a	n/a
8	GATA3	chr8:99306380-99307504	MCF-7	breast:	n/a	chr8:99306451-99306461

No.	Distal block	Cell Line	Cell type
1	chr6:24719766..24721631-chr8:99304778..99307612,2	MCF-7	breast:
2	chr8:99055062..99058733-chr8:99305548..99307498,3	MCF-7	breast:
3	chr8:99266294..99268249-chr8:99305433..99307936,2	MCF-7	breast:
4	chr6:26204334..26206803-chr8:99304596..99307549,2	MCF-7	breast:

Variant related genes	Relation type
NIPAL2	TF binding region
ENSG00000156482	Chromatin interaction
ENSG00000104361	Chromatin interaction
ENSG00000198518	Chromatin interaction
ENSG00000112308	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11787135	0.81[ASN][1000 genomes]
rs11988510	0.81[ASN][1000 genomes]
rs11990039	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12545495	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12545646	0.82[EUR][1000 genomes]
rs16896860	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16896886	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17288751	0.81[ASN][1000 genomes]
rs17360790	0.81[ASN][1000 genomes]
rs3923611	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4388427	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4552871	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4735549	0.81[ASN][1000 genomes]
rs4735550	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4735551	0.81[ASN][1000 genomes]
rs4735552	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4735555	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7813519	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032904	chr8:98756076-99476925	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv539687	chr8:98756076-99476925	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv831406	chr8:99290745-99482076	Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:99304800-99312400	Weak transcription	K562	blood
2	chr8:99306600-99307600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
3	chr8:99306800-99310600	Weak transcription	Pancreas	Pancrea
4	chr8:99306800-99312400	Weak transcription	Gastric	stomach
5	chr8:99306800-99312600	Weak transcription	Spleen	Spleen
6	chr8:99306800-99317000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr8:99306800-99317200	Weak transcription	Esophagus	oesophagus
8	chr8:99307000-99307600	Enhancers	Fetal Lung	lung
9	chr8:99307000-99307600	Enhancers	Placenta Amnion	Placenta Amnion
10	chr8:99307000-99307800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
11	chr8:99307000-99308400	Enhancers	Fetal Heart	heart
12	chr8:99307000-99308600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr8:99307000-99309400	Weak transcription	Aorta	Aorta
14	chr8:99307000-99309400	Weak transcription	Right Atrium	heart
15	chr8:99307000-99309400	Weak transcription	Right Ventricle	heart
16	chr8:99307000-99309400	Weak transcription	HSMMtube	muscle
17	chr8:99307000-99310600	Weak transcription	Left Ventricle	heart
18	chr8:99307000-99310600	Weak transcription	Psoas Muscle	Psoas
19	chr8:99307000-99311600	Weak transcription	Primary B cells from peripheral blood	blood
20	chr8:99307000-99311800	Weak transcription	Lung	lung
21	chr8:99307200-99307600	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr8:99307200-99307600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr8:99307200-99307600	Enhancers	Osteobl	bone
24	chr8:99307200-99308000	Enhancers	Fetal Intestine Small	intestine
25	chr8:99307200-99308200	Enhancers	Fetal Intestine Large	intestine
26	chr8:99307200-99309200	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr8:99307200-99309400	Weak transcription	HSMM	muscle
28	chr8:99307200-99312400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr8:99307400-99307600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr8:99307400-99307600	Enhancers	HMEC	breast
31	chr8:99307400-99307600	Enhancers	NHEK	skin
32	chr8:99307400-99307800	Enhancers	HepG2	liver
33	chr8:99307400-99308400	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr8:99307400-99309400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr8:99307400-99309400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr8:99307400-99309400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr8:99307400-99309400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr8:99307400-99309400	Weak transcription	Adipose Nuclei	Adipose
39	chr8:99307400-99309400	Weak transcription	NH-A	brain
40	chr8:99307400-99309400	Weak transcription	NHDF-Ad	bronchial
41	chr8:99307400-99309400	Weak transcription	NHLF	lung
42	chr8:99307400-99309600	Weak transcription	Stomach Mucosa	stomach
43	chr8:99307400-99312600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr8:99307400-99312800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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