Variant report

Variant	rs66767092
Chromosome Location	chr12:66523675-66523676
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:66523647-66524135	GM12891	blood:	n/a	n/a
2	MTA3	chr12:66523668-66525489	GM12878	blood:	n/a	n/a
3	POLR2A	chr12:66523654-66524916	GM12892	blood:	n/a	n/a
4	MXI1	chr12:66523620-66525402	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr12:66523641-66525025	GM12892	blood:	n/a	n/a
6	HCFC1	chr12:66523520-66525391	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr12:66523633-66524960	GM12878	blood:	n/a	n/a
8	PML	chr12:66523608-66525036	GM12878	blood:	n/a	n/a
9	POLR2A	chr12:66523620-66524988	GM12892	blood:	n/a	n/a
10	POLR2A	chr12:66523650-66526889	K562	blood:	n/a	n/a
11	POLR2A	chr12:66523664-66524871	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr12:66523618-66524842	IMR90	lung:	n/a	n/a
13	GABPA	chr12:66523584-66525368	MCF-7	breast:	n/a	n/a
14	POLR2A	chr12:66523552-66525187	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr12:66523519-66525661	GM12891	blood:	n/a	n/a
16	POLR2A	chr12:66523486-66525451	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr12:66523638-66525378	PANC-1	pancreas:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:66523453..66525027-chr12:66562451..66564555,2	K562	blood:
2	chr1:145096186..145098889-chr12:66522673..66525529,2	MCF-7	breast:
3	chr12:66523081..66526604-chr12:66560988..66564576,8	MCF-7	breast:
4	chr12:66523095..66527368-chr12:66532414..66535159,4	MCF-7	breast:
5	chr12:66523311..66525203-chr12:66696051..66697589,2	MCF-7	breast:
6	chr12:66521057..66526734-chr12:66560807..66565257,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000239335	TF binding region
ENSG00000223380	Chromatin interaction
ENSG00000155957	Chromatin interaction
ENSG00000127311	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10459263	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10506475	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10506479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10878379	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10878380	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10878384	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10878387	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10878388	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11176040	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11176041	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11176042	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11176044	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11176046	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11176047	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11176048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11176050	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11176051	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11176058	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11176059	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11176061	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11176062	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1168758	0.81[EUR][1000 genomes]
rs1168772	0.81[EUR][1000 genomes]
rs12230221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12230240	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12230800	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12426813	0.90[EUR][1000 genomes]
rs12578364	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12578752	0.93[EUR][1000 genomes]
rs12578754	0.90[EUR][1000 genomes]
rs12578801	1.00[AMR][1000 genomes]
rs12578994	0.93[EUR][1000 genomes]
rs12581033	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12581836	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12582384	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12814331	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12814606	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12821415	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12822410	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12823414	0.85[EUR][1000 genomes]
rs12823732	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12825992	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1370129	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17245364	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17825943	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1921080	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2870786	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2904498	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34406211	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34552143	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35085853	0.84[EUR][1000 genomes]
rs35131575	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35187440	0.93[EUR][1000 genomes]
rs35447479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35971570	0.93[EUR][1000 genomes]
rs36073795	0.93[EUR][1000 genomes]
rs4281516	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57825508	0.88[ASN][1000 genomes]
rs59112451	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60102429	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71450848	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73315943	0.90[EUR][1000 genomes]
rs737614	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052503	chr12:66293898-67269495	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv541515	chr12:66293898-67269495	Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1049537	chr12:66403269-66606174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv899214	chr12:66516692-66556960	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66509000-66523800	Weak transcription	Pancreas	Pancrea
2	chr12:66513600-66523800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:66514400-66523800	Weak transcription	Spleen	Spleen
4	chr12:66516000-66524000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr12:66516600-66523800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:66519000-66523800	Weak transcription	Aorta	Aorta
7	chr12:66521400-66523800	Weak transcription	Esophagus	oesophagus
8	chr12:66522600-66523800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr12:66522600-66526000	Active TSS	GM12878-XiMat	blood
10	chr12:66523000-66524000	Flanking Active TSS	Dnd41	blood
11	chr12:66523000-66524200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr12:66523000-66525200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr12:66523000-66525800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr12:66523000-66526000	Active TSS	A549	lung
15	chr12:66523000-66526400	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr12:66523200-66525200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr12:66523200-66525400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr12:66523400-66523800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:66523400-66523800	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr12:66523400-66523800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr12:66523400-66523800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr12:66523400-66523800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr12:66523400-66523800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
24	chr12:66523400-66523800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr12:66523400-66523800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
26	chr12:66523400-66523800	Enhancers	Small Intestine	intestine
27	chr12:66523400-66523800	Flanking Active TSS	Stomach Mucosa	stomach
28	chr12:66523400-66523800	Flanking Active TSS	Hela-S3	cervix
29	chr12:66523400-66523800	Flanking Active TSS	HepG2	liver
30	chr12:66523400-66523800	Flanking Active TSS	HMEC	breast
31	chr12:66523400-66523800	Flanking Active TSS	HSMM	muscle
32	chr12:66523400-66523800	Flanking Active TSS	HUVEC	blood vessel
33	chr12:66523400-66523800	Flanking Active TSS	NHEK	skin
34	chr12:66523400-66524000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr12:66523400-66524000	Flanking Active TSS	Primary hematopoietic stem cells	blood
36	chr12:66523400-66524000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
37	chr12:66523400-66524000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr12:66523400-66524000	Flanking Active TSS	Brain Cingulate Gyrus	brain
39	chr12:66523400-66524000	Flanking Active TSS	Brain Germinal Matrix	brain
40	chr12:66523400-66524000	Flanking Active TSS	Brain Substantia Nigra	brain
41	chr12:66523400-66524000	Flanking Active TSS	Duodenum Mucosa	Duodenum
42	chr12:66523400-66524000	Flanking Active TSS	Fetal Brain Male	brain
43	chr12:66523400-66524000	Flanking Active TSS	Fetal Brain Female	brain
44	chr12:66523400-66524000	Flanking Active TSS	Fetal Heart	heart
45	chr12:66523400-66524000	Flanking Active TSS	Fetal Thymus	thymus
46	chr12:66523400-66524000	Flanking Active TSS	Osteobl	bone
47	chr12:66523400-66524200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr12:66523400-66524200	Flanking Active TSS	Primary B cells from cord blood	blood
49	chr12:66523400-66524200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
50	chr12:66523400-66524200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood

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