Variant report

Variant	rs1560000
Chromosome Location	chr12:106493147-106493148
allele	C/G
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	chr12:106492612-106493232	MCF-7	breast:	n/a	n/a
2	EP300	chr12:106492193-106493174	HepG2	liver:	n/a	chr12:106492690-106492704 chr12:106492858-106492868 chr12:106492683-106492692
3	MYBL2	chr12:106492262-106493183	HepG2	liver:	n/a	n/a
4	NR2F2	chr12:106492270-106493243	HepG2	liver:	n/a	n/a
5	TCF12	chr12:106492371-106493248	A549	lung:	n/a	chr12:106492891-106492900
6	TEAD4	chr12:106492372-106493162	HepG2	liver:	n/a	n/a
7	FOXA2	chr12:106492290-106493328	HepG2	liver:	n/a	chr12:106492855-106492867
8	NFIC	chr12:106492282-106493149	HepG2	liver:	n/a	chr12:106492342-106492370
9	NR2F2	chr12:106492243-106493215	HepG2	liver:	n/a	n/a
10	FOXA1	chr12:106492307-106493169	HepG2	liver:	n/a	chr12:106492855-106492867 chr12:106492853-106492868
11	FOXA1	chr12:106492271-106493197	HepG2	liver:	n/a	chr12:106492855-106492867 chr12:106492853-106492868
12	ARID3A	chr12:106492366-106493193	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:106492655..106494743-chr12:106531247..106533400,2	MCF-7	breast:
2	chr12:106491668..106493233-chr12:106494081..106496361,2	MCF-7	breast:
3	chr12:106325602..106327976-chr12:106491240..106494183,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257438	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10861555	0.83[ASN][1000 genomes]
rs10861556	0.80[ASN][1000 genomes]
rs11112867	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs11112868	0.83[ASN][1000 genomes]
rs11112869	0.84[ASN][1000 genomes]
rs11112870	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11112872	0.89[CHB][hapmap]
rs12371401	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1427785	0.92[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1427786	0.94[CHB][hapmap];0.82[ASN][1000 genomes]
rs2434082	0.94[ASN][1000 genomes]
rs2436597	0.85[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs2436598	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2468198	0.94[ASN][1000 genomes]
rs2468199	0.83[ASN][1000 genomes]
rs2468200	0.86[ASN][1000 genomes]
rs2569973	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2956406	0.94[ASN][1000 genomes]
rs7131912	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7132167	0.89[CEU][hapmap]
rs7964234	0.83[ASN][1000 genomes]
rs958422	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs967872	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.83[EUR][1000 genomes];0.84[ASN][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	nsv832509	chr12:106363888-106516221	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106458800-106500200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr12:106461800-106499600	Weak transcription	Fetal Intestine Large	intestine
3	chr12:106469000-106499400	Weak transcription	Fetal Intestine Small	intestine
4	chr12:106485200-106500400	Weak transcription	HMEC	breast
5	chr12:106485400-106500800	Weak transcription	Lung	lung
6	chr12:106485600-106496200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:106485600-106500600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr12:106485800-106495000	Strong transcription	HSMMtube	muscle
9	chr12:106486200-106493400	Enhancers	Brain Substantia Nigra	brain
10	chr12:106487400-106499400	Weak transcription	Brain Germinal Matrix	brain
11	chr12:106487600-106500200	Weak transcription	NHLF	lung
12	chr12:106488600-106495600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr12:106489600-106494600	Weak transcription	Fetal Muscle Trunk	muscle
14	chr12:106490000-106496800	Weak transcription	Aorta	Aorta
15	chr12:106490200-106493400	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr12:106490200-106493400	Enhancers	Brain Hippocampus Middle	brain
17	chr12:106490400-106493400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr12:106490400-106494200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr12:106490600-106493200	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr12:106490600-106493400	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr12:106490600-106494600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr12:106490600-106498200	Weak transcription	Pancreas	Pancrea
23	chr12:106490800-106493400	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr12:106490800-106493400	Enhancers	Brain Cingulate Gyrus	brain
25	chr12:106490800-106494800	Weak transcription	Fetal Stomach	stomach
26	chr12:106490800-106499600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr12:106491000-106493400	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr12:106491000-106493400	Enhancers	Fetal Heart	heart
29	chr12:106491000-106493600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr12:106491000-106495000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr12:106491000-106496600	Weak transcription	Stomach Smooth Muscle	stomach
32	chr12:106491000-106499600	Weak transcription	Fetal Kidney	kidney
33	chr12:106491200-106493600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr12:106491200-106494400	Weak transcription	Adipose Nuclei	Adipose
35	chr12:106491200-106494600	Weak transcription	Gastric	stomach
36	chr12:106491200-106499800	Strong transcription	HSMM	muscle
37	chr12:106491200-106500000	Weak transcription	Fetal Lung	lung
38	chr12:106491200-106500800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr12:106491400-106493400	Enhancers	H1 Cell Line	embryonic stem cell
40	chr12:106491400-106495400	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr12:106491400-106496600	Weak transcription	NHDF-Ad	bronchial
42	chr12:106491400-106499600	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr12:106491600-106493400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:106491600-106493600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr12:106491600-106493600	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr12:106491600-106495200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr12:106491600-106495600	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr12:106491600-106496000	Weak transcription	NH-A	brain
49	chr12:106491600-106497200	Strong transcription	Osteobl	bone
50	chr12:106491600-106497600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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