Variant report

Variant	rs560586465
Chromosome Location	chr12:57113360-57113361
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:33)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:33 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:57113131-57113437	U87	brain:	n/a	n/a
2	POLR2A	chr12:57111849-57115834	K562	blood:	n/a	n/a
3	POLR2A	chr12:57113259-57113718	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr12:57112899-57113514	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr12:57109223-57113587	K562	blood:	n/a	n/a
6	POLR2A	chr12:57113138-57113802	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr12:57109373-57115069	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr12:57109486-57115298	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr12:57111326-57114042	GM12892	blood:	n/a	n/a
10	POLR2A	chr12:57109177-57115890	PFSK-1	brain:	n/a	n/a
11	POLR2A	chr12:57112257-57114921	A549	lung:	n/a	n/a
12	POLR2A	chr12:57112732-57113502	U87	brain:	n/a	n/a
13	POLR2A	chr12:57112532-57115744	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr12:57113205-57113899	GM12892	blood:	n/a	n/a
15	POLR2A	chr12:57109283-57116293	GM12878	blood:	n/a	n/a
16	POLR2A	chr12:57113204-57113365	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr12:57112634-57115751	K562	blood:	n/a	n/a
18	POLR2A	chr12:57109094-57117058	SK-N-MC	brain:	n/a	n/a
19	POLR2A	chr12:57112836-57113480	MCF-7	breast:	n/a	n/a
20	POLR2A	chr12:57112794-57113369	GM12891	blood:	n/a	n/a
21	POLR2A	chr12:57111836-57114109	K562	blood:	n/a	n/a
22	POLR2A	chr12:57113232-57113641	GM12891	blood:	n/a	n/a
23	POLR2A	chr12:57112650-57113668	HepG2	liver:	n/a	n/a
24	POLR2A	chr12:57112872-57115428	HL-60	blood:	n/a	n/a
25	POLR2A	chr12:57109356-57117115	GM12878	blood:	n/a	n/a
26	POLR2A	chr12:57113084-57113637	GM12878	blood:	n/a	n/a
27	POLR2A	chr12:57113284-57113661	ECC-1	luminal epithelium:	n/a	n/a
28	POLR2A	chr12:57113022-57113562	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr12:57113348-57114064	GM12891	blood:	n/a	n/a
30	POLR2A	chr12:57113250-57113647	K562	blood:	n/a	n/a
31	POLR2A	chr12:57112598-57113727	HL-60	blood:	n/a	n/a
32	POLR2A	chr12:57112599-57115857	GM12878	blood:	n/a	n/a
33	POLR2A	chr12:57109233-57116354	PANC-1	pancreas:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57075341..57085478-chr12:57112447..57121011,58	MCF-7	breast:
2	chr12:57112436..57114253-chr12:57144608..57146371,2	K562	blood:
3	chr12:56510526..56513327-chr12:57111291..57113363,2	K562	blood:
4	chr12:57113156..57115169-chr12:57146013..57147663,2	K562	blood:
5	chr12:57111474..57114081-chr12:57143216..57146135,2	MCF-7	breast:
6	chr12:57074578..57085543-chr12:57108746..57121559,55	K562	blood:
7	chr12:57076604..57085974-chr12:57112559..57120474,46	MCF-7	breast:
8	chr12:57112603..57114130-chr12:57504633..57506166,2	K562	blood:
9	chr12:57078475..57085183-chr12:57112918..57121559,38	K562	blood:
10	chr12:57022951..57032187-chr12:57113330..57121462,17	K562	blood:

No data

Variant related genes	Relation type
NACA	TF binding region
ENSG00000139641	Chromatin interaction
ENSG00000198056	Chromatin interaction
ENSG00000166888	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000110958	Chromatin interaction
ENSG00000025423	Chromatin interaction
ENSG00000076108	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers 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 miRNA target site	181 gene(s)	inside rSNPs	diseases
2	esv3378333	chr12:57109685-57113883	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
3	esv3367526	chr12:57109835-57113733	Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Enhancers	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
4	esv3356085	chr12:57110085-57113583	Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
5	esv20867	chr12:57110564-57115506	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
6	nsv559018	chr12:57112637-57114012	Genic enhancers Strong transcription Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	11 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	chr12:57104000-57114600	Weak transcription	Fetal Brain Male	brain
2	chr12:57104600-57115000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr12:57107400-57113800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:57108400-57115400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr12:57108600-57117200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr12:57109200-57116200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr12:57109400-57114800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr12:57109600-57115400	Genic enhancers	Duodenum Smooth Muscle	Duodenum
9	chr12:57109600-57116000	Genic enhancers	Fetal Muscle Leg	muscle
10	chr12:57109600-57117000	Genic enhancers	Primary T cells fromperipheralblood	blood
11	chr12:57109600-57117000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
12	chr12:57109600-57117800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr12:57109800-57113600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr12:57109800-57113600	Genic enhancers	Fetal Muscle Trunk	muscle
15	chr12:57109800-57114400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr12:57109800-57114600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
17	chr12:57109800-57115800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr12:57109800-57117200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr12:57110200-57115400	Strong transcription	Muscle Satellite Cultured Cells	--
20	chr12:57110200-57115800	Genic enhancers	Placenta	Placenta
21	chr12:57110200-57116800	Genic enhancers	Fetal Stomach	stomach
22	chr12:57110400-57116800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr12:57110400-57117600	Genic enhancers	Primary B cells from peripheral blood	blood
24	chr12:57110600-57113800	Genic enhancers	Monocytes-CD14+_RO01746	blood
25	chr12:57110800-57114600	Weak transcription	Ovary	ovary
26	chr12:57111000-57113800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr12:57111200-57113800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:57111200-57114800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr12:57111200-57114800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr12:57111200-57114800	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr12:57111400-57114800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr12:57112000-57114000	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr12:57112000-57114200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr12:57112000-57115400	Genic enhancers	A549	lung
35	chr12:57112000-57115600	Genic enhancers	Lung	lung
36	chr12:57112000-57116000	Genic enhancers	Fetal Intestine Small	intestine
37	chr12:57112200-57113400	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr12:57112200-57115800	Enhancers	Fetal Heart	heart
39	chr12:57112200-57117000	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
40	chr12:57112200-57117200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr12:57112400-57114200	Genic enhancers	Brain Substantia Nigra	brain
42	chr12:57112400-57114400	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr12:57112400-57114600	Genic enhancers	Fetal Lung	lung
44	chr12:57112400-57114800	Genic enhancers	Psoas Muscle	Psoas
45	chr12:57112400-57114800	Enhancers	Right Atrium	heart
46	chr12:57112400-57114800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
47	chr12:57112400-57115000	Genic enhancers	Brain Hippocampus Middle	brain
48	chr12:57112400-57115000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
49	chr12:57112400-57115800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr12:57112400-57116800	Genic enhancers	Primary monocytes fromperipheralblood	blood

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