Variant report

Variant	nsv558098
Chromosome Location	chr12:31743365-31744089
allele	n/a
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	ARID3A	chr12:31743401-31743530	K562	blood:	n/a	n/a
2	ATF1	chr12:31743345-31743636	K562	blood:	n/a	n/a
3	ATF3	chr12:31743379-31743631	K562	blood:	n/a	chr12:31743593-31743602
4	BCL3	chr12:31744072-31744796	A549	lung:	n/a	chr12:31744265-31744278
5	BCLAF1	chr12:31742479-31743737	GM12878	blood:	n/a	chr12:31743162-31743175 chr12:31743617-31743630 chr12:31743242-31743255 chr12:31743078-31743091 chr12:31742784-31742797 chr12:31743616-31743625
6	BHLHE40	chr12:31744028-31744155	K562	blood:	n/a	chr12:31744029-31744045
7	BHLHE40	chr12:31742555-31744782	HepG2	liver:	n/a	chr12:31743218-31743231 chr12:31743220-31743229 chr12:31743219-31743228 chr12:31743220-31743229 chr12:31744029-31744045
8	BHLHE40	chr12:31742707-31743593	GM12878	blood:	n/a	chr12:31743218-31743231 chr12:31743220-31743229 chr12:31743219-31743228 chr12:31743220-31743229
9	BHLHE40	chr12:31743956-31744258	GM12878	blood:	n/a	chr12:31744029-31744045
10	BHLHE40	chr12:31742679-31743687	K562	blood:	n/a	chr12:31743218-31743231 chr12:31743220-31743229 chr12:31743219-31743228 chr12:31743220-31743229
11	BHLHE40	chr12:31743014-31743621	A549	lung:	n/a	chr12:31743218-31743231 chr12:31743220-31743229 chr12:31743219-31743228 chr12:31743220-31743229
12	BRCA1	chr12:31743983-31744080	GM12878	blood:	n/a	n/a
13	BRCA1	chr12:31743911-31744094	HepG2	liver:	n/a	n/a
14	CCNT2	chr12:31742878-31744401	K562	blood:	n/a	chr12:31744156-31744165
15	CEBPB	chr12:31743920-31743953	Hela-S3	cervix:	n/a	n/a
16	CEBPD	chr12:31743823-31744195	HepG2	liver:	n/a	n/a
17	CHD1	chr12:31743874-31743925	GM12878	blood:	n/a	n/a
18	CHD1	chr12:31742929-31743758	H1-hESC	embryonic stem cell:	n/a	chr12:31743165-31743175
19	CHD2	chr12:31743849-31744542	HepG2	liver:	n/a	n/a
20	CHD2	chr12:31742748-31743543	HepG2	liver:	n/a	chr12:31743165-31743175
21	CHD2	chr12:31742588-31744661	Hela-S3	cervix:	n/a	chr12:31743165-31743175
22	CHD2	chr12:31743820-31744189	GM12878	blood:	n/a	n/a
23	CHD2	chr12:31743873-31744683	K562	blood:	n/a	n/a
24	CREB1	chr12:31743784-31744935	GM12878	blood:	n/a	n/a
25	CREB1	chr12:31742538-31744807	HepG2	liver:	n/a	n/a
26	CREB1	chr12:31742669-31744279	A549	lung:	n/a	n/a
27	CREB1	chr12:31742576-31743752	H1-hESC	embryonic stem cell:	n/a	n/a
28	CREB1	chr12:31742467-31743757	GM12878	blood:	n/a	n/a
29	CREB1	chr12:31743274-31743810	H1-hESC	embryonic stem cell:	n/a	n/a
30	CTCF	chr12:31743432-31743634	GM19240	blood:	n/a	n/a
31	CTCF	chr12:31743420-31743570	SAEC	small airway:	n/a	n/a
32	CTCF	chr12:31743420-31743570	HPAF	blood vessel:	n/a	n/a
33	CTCF	chr12:31743463-31743604	Gliobla	brain:	n/a	n/a
34	CTCF	chr12:31743360-31743510	HUVEC	blood vessel:	n/a	n/a
35	CTCF	chr12:31743480-31743630	GM12878	blood:	n/a	n/a
36	CTCF	chr12:31743420-31743570	HMEC	breast:	n/a	n/a
37	CTCF	chr12:31743400-31743550	GM12866	blood:	n/a	n/a
38	CTCF	chr12:31743498-31743557	Lung_OC	lung:	n/a	n/a
39	CTCF	chr12:31743500-31743650	A549	lung:	n/a	n/a
40	CTCF	chr12:31743540-31743690	HRE	kidney:	n/a	n/a
41	CTCF	chr12:31743463-31743651	GM10266	blood:	n/a	n/a
42	CTCF	chr12:31743440-31743590	HEEpiC	esophagus:	n/a	n/a
43	CTCF	chr12:31743500-31743650	GM12873	blood:	n/a	n/a
44	CTCF	chr12:31743460-31743610	SK-N-SH_RA	brain:	n/a	n/a
45	CTCF	chr12:31743440-31743590	GM06990	blood:	n/a	n/a
46	CTCF	chr12:31743440-31743590	HRPEpiC	eye:	n/a	n/a
47	CTCF	chr12:31743360-31743510	GM12875	blood:	n/a	n/a
48	CTCF	chr12:31743420-31743570	BJ	skin:	n/a	n/a
49	CTCF	chr12:31743440-31743590	BE2_C	brain:	n/a	n/a
50	CTCF	chr12:31743460-31743610	AoAF	blood vessel:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:31743882-31743932	HEK293	kidney:	embryo
2	chr12:31743882-31743932	HEK293	kidney:	embryo
3	chr12:31744043-31744093	AG09319	gingival:	n/a
4	chr12:31743882-31743932	AG09319	gingival:	n/a
5	chr12:31743857-31743907	AG09319	gingival:	n/a
6	chr12:31744043-31744093	AG04450	lung:	fetal
7	chr12:31743882-31743932	NH-A	brain:	n/a
8	chr12:31744043-31744093	IMR90	lung:	fetal
9	chr12:31743367-31743417	T-47D	breast:	n/a
10	chr12:31743882-31743932	SKMC	muscle:	n/a
11	chr12:31743449-31743499	HNPCEpiC	eye:	n/a
12	chr12:31743857-31743907	GM12892	blood:	n/a
13	chr12:31743367-31743417	HPAEpiC	pulmonary alveolar:	n/a
14	chr12:31743367-31743417	HL-60	blood:	n/a
15	chr12:31743882-31743932	MCF-7	breast:	n/a
16	chr12:31744043-31744093	Hepatocyte	liver:	n/a
17	chr12:31744043-31744093	SAEC	small airway:	n/a
18	chr12:31744043-31744093	ovcar-3	ovarian:	n/a
19	chr12:31743367-31743417	HRPEpiC	eye:	n/a
20	chr12:31743882-31743932	HPAEpiC	pulmonary alveolar:	n/a
21	chr12:31743367-31743417	AG09309	skin:	n/a
22	chr12:31744043-31744093	PrEC	prostate:	n/a
23	chr12:31743367-31743417	BJ	skin:	n/a
24	chr12:31743367-31743417	U87	brain:	n/a
25	chr12:31743857-31743907	AoSMC	blood vessel:	n/a
26	chr12:31743449-31743499	NHDF-neo	bronchial:	n/a
27	chr12:31743882-31743932	MCF10A-Er-Src	breast:	n/a
28	chr12:31743367-31743417	SAEC	small airway:	n/a
29	chr12:31743367-31743417	HEK293	kidney:	embryo
30	chr12:31743857-31743907	GM12878	blood:	n/a
31	chr12:31743449-31743499	HCF	heart:	n/a
32	chr12:31743449-31743499	AG04450	lung:	fetal
33	chr12:31743449-31743499	SKMC	muscle:	n/a
34	chr12:31743857-31743907	Hela-S3	cervix:	n/a
35	chr12:31743857-31743907	HepG2	liver:	n/a
36	chr12:31743367-31743417	PANC-1	pancreas:	n/a
37	chr12:31744043-31744093	HCM	heart:	n/a
38	chr12:31744043-31744093	NB4	blood:	n/a
39	chr12:31743367-31743417	SK-N-SH_RA	brain:	n/a
40	chr12:31743449-31743499	HCT-116	colon:	n/a
41	chr12:31744043-31744093	K562	blood:	n/a
42	chr12:31743857-31743907	NH-A	brain:	n/a
43	chr12:31743857-31743907	HNPCEpiC	eye:	n/a
44	chr12:31743882-31743932	GM19239	blood:	n/a
45	chr12:31743367-31743417	NH-A	brain:	n/a
46	chr12:31743882-31743932	ECC-1	luminal epithelium:	n/a
47	chr12:31743857-31743907	A549	lung:	n/a
48	chr12:31744043-31744093	HIPEpiC	eye:	n/a
49	chr12:31743882-31743932	HNPCEpiC	eye:	n/a
50	chr12:31743857-31743907	HRPEpiC	eye:	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:31477472..31480749-chr12:31741860..31744200,4	MCF-7	breast:
2	chr12:31741307..31745552-chr12:31748528..31751513,3	MCF-7	breast:
3	chr12:31477521..31479099-chr12:31743621..31745412,2	K562	blood:
4	chr12:31645308..31649621-chr12:31742506..31745309,6	MCF-7	breast:
5	chr12:31743215..31744081-chr19:1875675..1876438,2	Hela-S3	cervix:

Variant related genes	Relation type
DENND5B-AS1	TF binding region
DENND5B	TF binding region
DENND5B-AS1	CpG island
DENND5B	CpG island
ENSG00000261526	chromatin interactions
ENSG00000170456	chromatin interactions
ENSG00000139146	chromatin interactions
ENSG00000231788	chromatin interactions

Extended variants
information (count: 21 )
Associated
traits (count: 58 )

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs12825651	chr12:31743365-31743366	Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
2	rs112357978	chr12:31743382-31743383	Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
3	rs12825684	chr12:31743416-31743417	Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
4	rs538895742	chr12:31743423-31743424	Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
5	rs558701542	chr12:31743459-31743460	Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
6	rs572436877	chr12:31743520-31743521	Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
7	rs541291271	chr12:31743577-31743578	Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
8	rs369687591	chr12:31743592-31743593	Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
9	rs560114046	chr12:31743594-31743595	Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
10	rs370134978	chr12:31743596-31743597	Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
11	rs573509610	chr12:31743600-31743601	Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
12	rs542715497	chr12:31743755-31743756	Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
13	rs562484243	chr12:31743774-31743775	Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
14	rs531413019	chr12:31743803-31743804	Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
15	rs551636732	chr12:31743908-31743909	Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
16	rs565039447	chr12:31743923-31743924	Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
17	rs527606169	chr12:31743965-31743966	Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
18	rs547330530	chr12:31743969-31743970	Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
19	rs567663004	chr12:31743990-31743991	Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
20	rs536294217	chr12:31744047-31744048	Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
21	rs550148221	chr12:31744072-31744073	Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:58)

Disease	PMID	Source
Chronic lymphocytic leukemia	21546498	CNVD
Myxofibrosarcoma	16751306	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Wilms tumour	21544195	CNVD
Squamous cell cancer	21044232	CNVD
Acute myeloid leukemia	16864856	CNVD
T-cell acute lymphoblastic leukemia	20065082	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	21080181	CNVD
Endometrial cancer	22040021	CNVD
Colorectal cancer	20709793	CNVD
Breast cancer	21264507	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Cancer	16751803	CNVD
Testicular cancer	18059402	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Seminomas	18059402	CNVD
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
Testicular germ cell tumor	18059402	CNVD
Medulloblastoma	21979893	CNVD
Malaria	21533027	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
Basal cell lymphoma	17053054	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
Ewing''s sarcoma	17952124	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Breast cancer	21858162	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Myelodysplastic syndrome	21251322	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Autism	22495311	CNVD
Cancer	20164919	CNVD
Neurodevelopmental disorder	22521361	CNVD
Breast cancer	21509527	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Cancer	21129771	CNVD
Hepatocellular carcinoma	16750200	CNVD
Breast cancer	17899364	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Breast cancer	17133270	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Lung cancer	18438408	CNVD
Myelofibrosis	22110671	CNVD
microdeletion syndrome	16199537	CNVD
Chordoma	18071362	CNVD
Cancer	20164920	CNVD
Ovarian cancer	21720365	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:140 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31741400-31745000	Active TSS	Ovary	ovary
2	chr12:31741600-31744200	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr12:31741600-31744800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr12:31741600-31745000	Active TSS	Fetal Kidney	kidney
5	chr12:31741800-31743600	Active TSS	Right Atrium	heart
6	chr12:31741800-31744400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:31741800-31744400	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr12:31741800-31744400	Active TSS	GM12878-XiMat	blood
9	chr12:31741800-31744800	Active TSS	Brain Cingulate Gyrus	brain
10	chr12:31741800-31745000	Active TSS	Rectal Smooth Muscle	rectum
11	chr12:31742000-31744200	Active TSS	Primary hematopoietic stem cells short term culture	blood
12	chr12:31742000-31744200	Active TSS	Cortex derived primary cultured neurospheres	brain
13	chr12:31742000-31744400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr12:31742000-31744400	Active TSS	Fetal Intestine Small	intestine
15	chr12:31742000-31744400	Active TSS	HSMM	muscle
16	chr12:31742000-31744400	Active TSS	HSMMtube	muscle
17	chr12:31742000-31744600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr12:31742000-31744600	Active TSS	Brain Anterior Caudate	brain
19	chr12:31742000-31744600	Active TSS	Brain Germinal Matrix	brain
20	chr12:31742000-31744600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr12:31742000-31744600	Active TSS	Fetal Intestine Large	intestine
22	chr12:31742000-31744800	Active TSS	NHDF-Ad	bronchial
23	chr12:31742000-31745000	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr12:31742000-31745000	Active TSS	Right Ventricle	heart
25	chr12:31742200-31744200	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr12:31742200-31744200	Active TSS	Skeletal Muscle Female	skeletal muscle
27	chr12:31742200-31744200	Active TSS	NHLF	lung
28	chr12:31742200-31744400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr12:31742200-31744400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:31742200-31744400	Active TSS	Brain Angular Gyrus	brain
31	chr12:31742200-31744400	Active TSS	Brain Hippocampus Middle	brain
32	chr12:31742200-31744400	Active TSS	Duodenum Mucosa	Duodenum
33	chr12:31742200-31744400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
34	chr12:31742200-31744400	Active TSS	HepG2	liver
35	chr12:31742200-31744600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr12:31742200-31744600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr12:31742200-31744800	Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr12:31742200-31744800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr12:31742200-31744800	Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr12:31742200-31744800	Active TSS	NHEK	skin
41	chr12:31742200-31745000	Active TSS	Colon Smooth Muscle	Colon
42	chr12:31742200-31745000	Active TSS	Fetal Brain Female	brain
43	chr12:31742400-31744200	Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr12:31742400-31744200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
45	chr12:31742400-31744200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr12:31742400-31744200	Active TSS	Fetal Muscle Trunk	muscle
47	chr12:31742400-31744200	Active TSS	Placenta	Placenta
48	chr12:31742400-31744200	Active TSS	HMEC	breast
49	chr12:31742400-31744400	Active TSS	HUES64 Cell Line	embryonic stem cell
50	chr12:31742400-31744400	Active TSS	Fetal Lung	lung

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