Variant report

Variant	nsv560067
Chromosome Location	chr12:106641085-106641886
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:270)
CpG islands
(count:122)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:270 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BHLHE40	chr12:106641572-106641918	GM12878	blood:	n/a	chr12:106641740-106641756
2	BHLHE40	chr12:106641682-106641768	K562	blood:	n/a	chr12:106641740-106641756
3	BHLHE40	chr12:106641655-106641899	HepG2	liver:	n/a	chr12:106641740-106641756
4	BHLHE40	chr12:106641123-106641230	GM12878	blood:	n/a	n/a
5	CCNT2	chr12:106641692-106641893	K562	blood:	n/a	n/a
6	CEBPD	chr12:106641712-106642110	HepG2	liver:	n/a	n/a
7	CEBPD	chr12:106641748-106642031	HepG2	liver:	n/a	n/a
8	CHD1	chr12:106639633-106643296	IMR90	lung:	n/a	chr12:106641025-106641035
9	CHD2	chr12:106641803-106641805	HepG2	liver:	n/a	n/a
10	CHD2	chr12:106641823-106641890	Hela-S3	cervix:	n/a	n/a
11	CHD2	chr12:106641149-106641203	GM12878	blood:	n/a	n/a
12	CREB1	chr12:106641338-106642036	A549	lung:	n/a	n/a
13	CTCF	chr12:106641200-106641350	GM12869	blood:	n/a	n/a
14	CTCF	chr12:106641180-106641330	HBMEC	blood vessel:	n/a	n/a
15	CTCF	chr12:106641200-106641350	GM12866	blood:	n/a	n/a
16	CTCF	chr12:106641180-106641330	AoAF	blood vessel:	n/a	n/a
17	CTCF	chr12:106641080-106641230	HCM	heart:	n/a	n/a
18	CTCF	chr12:106641180-106641330	HMF	breast:	n/a	n/a
19	CTCF	chr12:106641225-106641338	Pancreas_OC	pancreas:	n/a	n/a
20	CTCF	chr12:106641160-106641310	NHDF-neo	bronchial:	n/a	n/a
21	CTCF	chr12:106641266-106641292	MCF-7	breast:	n/a	n/a
22	CTCF	chr12:106641151-106641318	GM12878	blood:	n/a	n/a
23	CTCF	chr12:106640980-106641130	GM12873	blood:	n/a	chr12:106641027-106641040
24	CTCF	chr12:106641140-106641290	GM12864	blood:	n/a	n/a
25	CTCF	chr12:106641200-106641350	GM12873	blood:	n/a	n/a
26	CTCF	chr12:106641000-106641150	WI-38	lung:	n/a	chr12:106641027-106641040
27	CTCF	chr12:106641160-106641310	HAc	cerebellar:	n/a	n/a
28	CTCF	chr12:106640940-106641090	SAEC	small airway:	n/a	chr12:106641027-106641040
29	CTCF	chr12:106641160-106641310	GM12873	blood:	n/a	n/a
30	CTCF	chr12:106641200-106641350	NHDF-neo	bronchial:	n/a	n/a
31	CTCF	chr12:106641151-106641404	IMR90	lung:	n/a	n/a
32	CTCF	chr12:106641200-106641350	GM12864	blood:	n/a	n/a
33	CTCF	chr12:106641100-106641250	GM12866	blood:	n/a	n/a
34	CTCF	chr12:106641140-106641290	SAEC	small airway:	n/a	n/a
35	CTCF	chr12:106641160-106641310	WERI-Rb-1	eye:	n/a	n/a
36	CTCF	chr12:106641200-106641350	BJ	skin:	n/a	n/a
37	CTCF	chr12:106641240-106641390	HFF	foreskin:	n/a	n/a
38	CTCF	chr12:106641250-106641280	LNCaP	prostate:	n/a	n/a
39	CTCF	chr12:106641100-106641250	GM12873	blood:	n/a	n/a
40	CTCF	chr12:106641100-106641250	HEK293	kidney:	n/a	n/a
41	CTCF	chr12:106641120-106641270	HPAF	blood vessel:	n/a	n/a
42	CTCF	chr12:106641160-106641310	SK-N-SH_RA	brain:	n/a	n/a
43	CTCF	chr12:106641160-106641310	HA-sp	spinal cord:	n/a	n/a
44	CTCF	chr12:106641020-106641170	BJ	skin:	n/a	chr12:106641027-106641040
45	CTCF	chr12:106641188-106641345	Kidney_OC	kidney:	n/a	n/a
46	CTCF	chr12:106641248-106641265	MCF-7	breast:	n/a	n/a
47	CTCF	chr12:106641264-106641298	GM19238	blood:	n/a	n/a
48	CTCF	chr12:106641177-106641187	Kidney_OC	kidney:	n/a	n/a
49	CTCF	chr12:106641207-106641265	GM12891	blood:	n/a	n/a
50	CTCF	chr12:106641140-106641290	HBMEC	blood vessel:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:106641486-106641536	SKMC	muscle:	n/a
2	chr12:106641134-106641184	SAEC	small airway:	n/a
3	chr12:106641486-106641536	AG04450	lung:	fetal
4	chr12:106641134-106641184	AG09309	skin:	n/a
5	chr12:106641134-106641184	PrEC	prostate:	n/a
6	chr12:106641486-106641536	HCT-116	colon:	n/a
7	chr12:106641486-106641536	NHDF-neo	bronchial:	n/a
8	chr12:106641486-106641536	SK-N-MC	brain:	n/a
9	chr12:106641134-106641184	U87	brain:	n/a
10	chr12:106641134-106641184	HCT-116	colon:	n/a
11	chr12:106641134-106641184	SK-N-MC	brain:	n/a
12	chr12:106641134-106641184	PFSK-1	brain:	n/a
13	chr12:106641134-106641184	HMEC	breast:	n/a
14	chr12:106641486-106641536	PANC-1	pancreas:	n/a
15	chr12:106641486-106641536	HRPEpiC	eye:	n/a
16	chr12:106641134-106641184	HUVEC	blood vessel:	n/a
17	chr12:106641486-106641536	AoSMC	blood vessel:	n/a
18	chr12:106641134-106641184	HAEpiC	amniotic membrane:	n/a
19	chr12:106641486-106641536	SK-N-SH	brain:	n/a
20	chr12:106641134-106641184	A549	lung:	n/a
21	chr12:106641134-106641184	HNPCEpiC	eye:	n/a
22	chr12:106641486-106641536	PrEC	prostate:	n/a
23	chr12:106641134-106641184	Jurkat	blood:	n/a
24	chr12:106641134-106641184	GM06990	blood:	n/a
25	chr12:106641134-106641184	NHDF-neo	bronchial:	n/a
26	chr12:106641486-106641536	PFSK-1	brain:	n/a
27	chr12:106641134-106641184	GM12891	blood:	n/a
28	chr12:106641134-106641184	T-47D	breast:	n/a
29	chr12:106641486-106641536	BE2_C	brain:	n/a
30	chr12:106641486-106641536	HEEpiC	esophagus:	n/a
31	chr12:106641486-106641536	U87	brain:	n/a
32	chr12:106641134-106641184	ovcar-3	ovarian:	n/a
33	chr12:106641134-106641184	AG10803	skin:	n/a
34	chr12:106641134-106641184	H1-hESC	embryonic stem cell:	embryo
35	chr12:106641486-106641536	AG10803	skin:	n/a
36	chr12:106641134-106641184	MCF-7	breast:	n/a
37	chr12:106641134-106641184	LNCaP	prostate:	n/a
38	chr12:106641134-106641184	BE2_C	brain:	n/a
39	chr12:106641134-106641184	GM12878	blood:	n/a
40	chr12:106641134-106641184	Hela-S3	cervix:	n/a
41	chr12:106641486-106641536	IMR90	lung:	fetal
42	chr12:106641134-106641184	AG04449	skin:	fetal
43	chr12:106641486-106641536	GM12878	blood:	n/a
44	chr12:106641134-106641184	HRPEpiC	eye:	n/a
45	chr12:106641134-106641184	HCF	heart:	n/a
46	chr12:106641486-106641536	AG04449	skin:	fetal
47	chr12:106641134-106641184	HRCEpiC	kidney:	n/a
48	chr12:106641486-106641536	HUVEC	blood vessel:	n/a
49	chr12:106641486-106641536	LNCaP	prostate:	n/a
50	chr12:106641486-106641536	K562	blood:	n/a

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:106634944..106646449-chr12:106667585..106679535,27	MCF-7	breast:
2	chr12:106640021..106643402-chr12:106749618..106753030,5	MCF-7	breast:
3	chr12:106639673..106643649-chr12:106748400..106753718,9	MCF-7	breast:
4	chr12:106641570..106642137-chr12:106697112..106697741,2	MCF-7	breast:
5	chr12:106531582..106534564-chr12:106638638..106642825,4	MCF-7	breast:
6	chr12:106639346..106644112-chr12:106694122..106698214,13	MCF-7	breast:
7	chr12:105500524..105503114-chr12:106640734..106642263,2	MCF-7	breast:
8	chr12:106640861..106643735-chr12:106674267..106678317,3	MCF-7	breast:
9	chr12:106641882..106643930-chr12:106685440..106687264,2	MCF-7	breast:
10	chr12:106640063..106644049-chr12:106694395..106698756,11	MCF-7	breast:
11	chr12:106639693..106641308-chr12:106715072..106718036,2	MCF-7	breast:
12	chr12:106640559..106643459-chr12:107485293..107487296,2	K562	blood:

No data

Variant related genes	Relation type
CKAP4	TF binding region
ENSG00000258355	TF binding region
CKAP4	CpG island
ENSG00000258355	CpG island
ENSG00000008405	chromatin interactions
ENSG00000238609	chromatin interactions
ENSG00000074590	chromatin interactions
ENSG00000257548	chromatin interactions
ENSG00000257999	chromatin interactions
ENSG00000013503	chromatin interactions
ENSG00000166046	chromatin interactions
ENSG00000136051	chromatin interactions
ENSG00000136026	chromatin interactions

Extended variants
information (count: 17 )
Associated
traits (count: 66 )

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs368446858	chr12:106641101-106641102	Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription	TF binding region Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
2	rs201998196	chr12:106641117-106641118	Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription	TF binding region Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
3	rs200990380	chr12:106641198-106641199	Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription	TF binding region Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
4	rs188646596	chr12:106641204-106641205	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
5	rs181386764	chr12:106641250-106641251	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
6	rs545073070	chr12:106641268-106641269	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
7	rs374143471	chr12:106641290-106641291	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
8	rs61942134	chr12:106641297-106641298	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
9	rs575354598	chr12:106641334-106641335	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
10	rs544179575	chr12:106641343-106641344	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
11	rs572619681	chr12:106641347-106641348	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
12	rs371991101	chr12:106641363-106641364	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
13	rs576389141	chr12:106641377-106641378	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
14	rs561280299	chr12:106641484-106641485	Active TSS Weak transcription Enhancers Bivalent/Poised TSS	TF binding region Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
15	rs368519473	chr12:106641490-106641491	Active TSS Weak transcription Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
16	rs111475395	chr12:106641668-106641669	Active TSS Weak transcription Bivalent/Poised TSS	TF binding region Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
17	rs574774303	chr12:106641729-106641730	Active TSS Weak transcription Bivalent/Poised TSS	TF binding region Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:66)

Disease	PMID	Source
Esophageal cancer	21851588	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Ewing''s sarcoma	21437220	CNVD
Testicular germ cell tumor	18059402	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Medulloblastoma	21979893	CNVD
Malaria	21533027	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
Basal cell lymphoma	17053054	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Autism	22495311	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Breast cancer	21949216	CNVD
Carcinoma ex pleomorphic adenoma	18828159	CNVD
Acute myeloid leukemia	16864856	CNVD
Cancer	21637783	CNVD
Glioblastoma multiforme	21080181	CNVD
Renal cell carcinoma	19461508	CNVD
Burkitt''s lymphoma	18698080	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Adenoid cystic carcinoma	17372589	CNVD
Lung cancer	18438408	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
small cell lung cancer	20016488	CNVD
Melanoma	18172304	CNVD
Glioblastoma multiforme	21390271	CNVD
Cancer	20164919	CNVD
Breast cancer	22032731	CNVD
Cancer	16751803	CNVD
Biliary cancer	20360734	CNVD
Breast cancer	20360734	CNVD
Coronary artery disease	20360734	CNVD
Crohn''s disease	20360734	CNVD
Hypertension	20360734	CNVD
Rheumatoid arthritis	20360734	CNVD
Type 1 diabetes	20360734	CNVD
Type 2 diabetes	20360734	CNVD
Wilms tumour	21544195	CNVD
Ovarian cancer	21720365	CNVD
Colorectal cancer	16272173	CNVD
lymphocytic leukemia	21291569	CNVD
Hepatocellular carcinoma	16750200	CNVD
Breast cancer	17603634	CNVD
Breast cancer	16397240	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Sudden cardiac death	19188705	CNVD
Breast cancer	17133270	CNVD
Chronic lymphocytic leukemia	21049055	CNVD
Neurocytoma	17123091	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Breast cancer	21509527	CNVD
Breast cancer	21364760	CNVD
Multiple myeloma	16616336	CNVD
Myelofibrosis	22110671	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:170 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106638800-106641200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
2	chr12:106639000-106641200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
3	chr12:106639200-106642400	Active TSS	HSMM	muscle
4	chr12:106639200-106642400	Active TSS	NHLF	lung
5	chr12:106639200-106642800	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr12:106639400-106642600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr12:106639600-106641200	Flanking Active TSS	Colonic Mucosa	Colon
8	chr12:106639600-106642600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr12:106639800-106642600	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr12:106639800-106643000	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr12:106640000-106641200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
12	chr12:106640000-106641400	Active TSS	Fetal Kidney	kidney
13	chr12:106640000-106642200	Active TSS	Lung	lung
14	chr12:106640000-106642400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr12:106640000-106642400	Active TSS	Muscle Satellite Cultured Cells	--
16	chr12:106640000-106642400	Active TSS	Esophagus	oesophagus
17	chr12:106640000-106642600	Active TSS	Left Ventricle	heart
18	chr12:106640000-106642600	Active TSS	NHDF-Ad	bronchial
19	chr12:106640000-106642800	Active TSS	Brain Anterior Caudate	brain
20	chr12:106640000-106643000	Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr12:106640000-106643000	Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr12:106640200-106641200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
23	chr12:106640200-106642200	Active TSS	GM12878-XiMat	blood
24	chr12:106640200-106642400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr12:106640200-106642400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr12:106640200-106642400	Active TSS	A549	lung
27	chr12:106640200-106642400	Active TSS	Osteobl	bone
28	chr12:106640200-106642600	Active TSS	Ovary	ovary
29	chr12:106640200-106642600	Active TSS	Placenta Amnion	Placenta Amnion
30	chr12:106640200-106642600	Active TSS	HMEC	breast
31	chr12:106640200-106642800	Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr12:106640200-106642800	Active TSS	Right Ventricle	heart
33	chr12:106640200-106643000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr12:106640400-106641200	Flanking Active TSS	Primary T cells from cord blood	blood
35	chr12:106640400-106641200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
36	chr12:106640400-106641200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
37	chr12:106640400-106641400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
38	chr12:106640400-106641400	Flanking Active TSS	Placenta	Placenta
39	chr12:106640400-106642400	Active TSS	Gastric	stomach
40	chr12:106640400-106642400	Active TSS	Sigmoid Colon	Sigmoid Colon
41	chr12:106640400-106642600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr12:106640400-106642600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:106640400-106642600	Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr12:106640400-106642800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr12:106640400-106642800	Active TSS	Fetal Brain Female	brain
46	chr12:106640400-106643000	Active TSS	ES-I3 Cell Line	embryonic stem cell
47	chr12:106640400-106643000	Active TSS	H9 Cell Line	embryonic stem cell
48	chr12:106640600-106641200	Flanking Active TSS	Primary hematopoietic stem cells	blood
49	chr12:106640600-106641200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr12:106640600-106641200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood

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