Variant report

Variant	nsv1009161
Chromosome Location	chr2:52297892-52480182
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	chr2:52467445-52467547	K562	blood:	n/a	n/a
2	BACH1	chr2:52362395-52362744	H1-hESC	embryonic stem cell:	n/a	n/a
3	BACH1	chr2:52362389-52362723	K562	blood:	n/a	n/a
4	BATF	chr2:52304385-52304596	GM12878	blood:	n/a	n/a
5	BRCA1	chr2:52412674-52412755	GM12878	blood:	n/a	n/a
6	CBX3	chr2:52309795-52311146	HCT-116	colon:	n/a	n/a
7	CBX3	chr2:52310166-52311117	HCT-116	colon:	n/a	n/a
8	CEBPB	chr2:52331040-52331249	HepG2	liver:	n/a	chr2:52331137-52331148
9	CEBPB	chr2:52424527-52424851	IMR90	lung:	n/a	chr2:52424680-52424691
10	CEBPB	chr2:52324256-52324506	K562	blood:	n/a	chr2:52324407-52324416 chr2:52324407-52324416 chr2:52324407-52324416
11	CEBPB	chr2:52317536-52317835	HepG2	liver:	n/a	chr2:52317668-52317679
12	CEBPB	chr2:52324224-52324581	IMR90	lung:	n/a	chr2:52324407-52324416 chr2:52324407-52324416 chr2:52324407-52324416
13	CEBPB	chr2:52317611-52317713	H1-hESC	embryonic stem cell:	n/a	chr2:52317668-52317679
14	CEBPB	chr2:52309821-52310890	HCT-116	colon:	n/a	n/a
15	CEBPB	chr2:52447440-52447956	ECC-1	luminal epithelium:	n/a	n/a
16	CEBPB	chr2:52424578-52424825	A549	lung:	n/a	chr2:52424680-52424691
17	CEBPB	chr2:52323284-52323495	A549	lung:	n/a	chr2:52323383-52323394 chr2:52323383-52323396 chr2:52323383-52323396
18	CEBPB	chr2:52344262-52344853	HCT-116	colon:	n/a	n/a
19	CEBPB	chr2:52324253-52324595	H1-hESC	embryonic stem cell:	n/a	chr2:52324407-52324416 chr2:52324407-52324416 chr2:52324407-52324416
20	CEBPB	chr2:52362409-52362746	Hela-S3	cervix:	n/a	n/a
21	CEBPB	chr2:52344400-52344790	IMR90	lung:	n/a	n/a
22	CEBPB	chr2:52324229-52324587	HepG2	liver:	n/a	chr2:52324407-52324416 chr2:52324407-52324416 chr2:52324407-52324416
23	CEBPB	chr2:52317584-52317773	A549	lung:	n/a	chr2:52317668-52317679
24	CEBPB	chr2:52475213-52475267	H1-hESC	embryonic stem cell:	n/a	n/a
25	CEBPB	chr2:52324223-52324560	A549	lung:	n/a	chr2:52324407-52324416 chr2:52324407-52324416 chr2:52324407-52324416
26	CEBPB	chr2:52306793-52307085	HepG2	liver:	n/a	chr2:52306925-52306936 chr2:52306927-52306936
27	CEBPB	chr2:52475235-52475401	A549	lung:	n/a	chr2:52475269-52475280
28	CEBPB	chr2:52344349-52344906	HCT-116	colon:	n/a	n/a
29	CEBPB	chr2:52324251-52324554	ECC-1	luminal epithelium:	n/a	chr2:52324407-52324416 chr2:52324407-52324416 chr2:52324407-52324416
30	CEBPB	chr2:52309741-52310995	HCT-116	colon:	n/a	n/a
31	CEBPB	chr2:52311668-52312445	HCT-116	colon:	n/a	n/a
32	CEBPB	chr2:52324255-52324571	A549	lung:	n/a	chr2:52324407-52324416 chr2:52324407-52324416 chr2:52324407-52324416
33	CEBPB	chr2:52475176-52475438	HepG2	liver:	n/a	chr2:52475269-52475280
34	CEBPB	chr2:52344406-52344788	Hela-S3	cervix:	n/a	n/a
35	CEBPB	chr2:52424565-52424782	Hela-S3	cervix:	n/a	chr2:52424680-52424691
36	CEBPB	chr2:52447446-52447926	ECC-1	luminal epithelium:	n/a	n/a
37	CEBPB	chr2:52357130-52357365	HepG2	liver:	n/a	chr2:52357259-52357270
38	CEBPB	chr2:52324312-52324599	MCF-7	breast:	n/a	chr2:52324407-52324416 chr2:52324407-52324416 chr2:52324407-52324416
39	CEBPB	chr2:52317588-52317783	IMR90	lung:	n/a	chr2:52317668-52317679
40	CEBPB	chr2:52324213-52324590	Hela-S3	cervix:	n/a	chr2:52324407-52324416 chr2:52324407-52324416 chr2:52324407-52324416
41	CEBPB	chr2:52424571-52424862	HepG2	liver:	n/a	chr2:52424680-52424691
42	CEBPB	chr2:52437849-52438049	IMR90	lung:	n/a	n/a
43	CEBPB	chr2:52434940-52435407	HepG2	liver:	n/a	n/a
44	CEBPB	chr2:52306763-52307073	IMR90	lung:	n/a	chr2:52306925-52306936 chr2:52306927-52306936
45	CTCF	chr2:52313220-52313370	HPAF	blood vessel:	n/a	n/a
46	CTCF	chr2:52372300-52372450	HCFaa	heart:	n/a	chr2:52372370-52372391
47	CTCF	chr2:52371789-52371831	GM20000	blood:	n/a	n/a
48	CTCF	chr2:52456953-52457031	LNCaP	prostate:	n/a	n/a
49	CTCF	chr2:52456934-52457008	MCF-7	breast:	n/a	n/a
50	CTCF	chr2:52474540-52474690	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:52444137..52446093-chr2:52447228..52448981,2	K562	blood:
2	chr2:52444137..52446093-chr2:52447228..52448981,2	K562	blood:
3	chr2:52344101..52346354-chr2:52360940..52363061,2	MCF-7	breast:
4	chr2:52344101..52346354-chr2:52360940..52363061,2	MCF-7	breast:
5	chr2:52476747..52479271-chr2:52487226..52489997,2	K562	blood:
6	chr2:52357469..52360071-chr20:52739539..52742222,2	MCF-7	breast:
7	chr2:52367783..52370728-chr2:52370744..52372935,2	K562	blood:
8	chr2:52321532..52323280-chr2:52325089..52327796,2	K562	blood:
9	chr2:52335533..52337278-chr2:52346386..52348387,2	K562	blood:
10	chr2:52321532..52323280-chr2:52325089..52327796,2	K562	blood:
11	chr2:52335533..52337278-chr2:52346386..52348387,2	K562	blood:
12	chr2:52367783..52370728-chr2:52370744..52372935,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CHAC2-10	chr2:52453760-52453813	NONHSAT070667
2	lnc-CHAC2-11	chr2:52304140-52304335	NONHSAT070666
3	lnc-CHAC2-11	chr2:52298493-52298559	NONHSAT070666
4	lnc-CHAC2-10	chr2:52470105-52470654	NONHSAT070667
5	lnc-CHAC2-11	chr2:52302622-52302775	NONHSAT070666

Variant related genes	Relation type
ZNF863P	TF binding region

Extended variants
information (count: 2627 )
Associated
traits (count: 85 )

Variant overlapped rSNPs/rCNVs (count:2627 , 50 per page) page: 1 2 3 4 5 6 7 ... 53

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs75289810	chr2:52298249-52298250	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs181773163	chr2:52298264-52298265	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs535357914	chr2:52298387-52298388	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs550778315	chr2:52298389-52298390	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs531952960	chr2:52298488-52298489	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs568940847	chr2:52298505-52298506	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
7	rs539185749	chr2:52298549-52298550	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
8	rs557425048	chr2:52298588-52298589	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs17042464	chr2:52298624-52298625	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs533561468	chr2:52298633-52298634	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs549934683	chr2:52298669-52298670	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs148876877	chr2:52298677-52298678	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs185977528	chr2:52298686-52298687	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs542145247	chr2:52298713-52298714	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs111940780	chr2:52298723-52298724	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs10206604	chr2:52298729-52298730	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs546372595	chr2:52298768-52298769	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs564580512	chr2:52298807-52298808	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs528560606	chr2:52298830-52298831	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs140872283	chr2:52298834-52298835	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs188436534	chr2:52298848-52298849	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs10206799	chr2:52298898-52298899	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs550590049	chr2:52298902-52298903	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs542688309	chr2:52298904-52298905	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs145027848	chr2:52298909-52298910	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs569098209	chr2:52298945-52298946	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs532961162	chr2:52298999-52299000	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs138808367	chr2:52299003-52299004	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs17042470	chr2:52299005-52299006	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs76673378	chr2:52299033-52299034	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs200341448	chr2:52299043-52299044	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs555377337	chr2:52299069-52299070	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs11437540	chr2:52299072-52299073	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs368739989	chr2:52299081-52299082	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs201238870	chr2:52299082-52299083	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs368451491	chr2:52299128-52299129	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs181252802	chr2:52299167-52299168	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs557374614	chr2:52299215-52299216	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs184922345	chr2:52299225-52299226	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs191049750	chr2:52299236-52299237	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs558354048	chr2:52299262-52299263	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs56792068	chr2:52299273-52299274	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs573401413	chr2:52299285-52299286	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs540354385	chr2:52299291-52299292	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs562151576	chr2:52299343-52299344	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs545189703	chr2:52299398-52299399	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs544546038	chr2:52299413-52299414	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs72884395	chr2:52299415-52299416	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs577334688	chr2:52299438-52299439	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs377751630	chr2:52299462-52299463	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:85)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Lynch syndrome	18415027	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Ovarian neoplasms	16753589	CNVD
Glioblastoma multiforme	17387387	CNVD
Neuroblastoma	17533364	CNVD
Neuroblastoma	18923191	CNVD
Endometrial cancer	22040021	CNVD
Adrenal tumor	17535989	CNVD
Breast cancer	21264507	CNVD
Basal cell lymphoma	17053054	CNVD
Medulloblastoma	17522785	CNVD
Cancer	23418310	CNVD
Breast cancer	17603634	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Ependymoma	16718352	CNVD
lymphocytic leukemia	21291569	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Follicular lymphoma	20505157	CNVD
Autism	17483303	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Medulloblastoma	20607354	CNVD
Leukemia	18628472	CNVD
Autism	22495311	CNVD
Autism	18522746	CNVD
Breast cancer	21785460	CNVD
Lung cancer	18438408	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Neuroblastoma	21508638	CNVD
Neurodevelopmental disorder	22521361	CNVD
small cell lung cancer	20016488	CNVD
Melanoma	18172304	CNVD
Cancer	16751803	CNVD
Colorectal cancer	16272173	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Williams Syndrome	20824207	CNVD
Breast cancer	16272173	CNVD
Lung cancer	17297452	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Ovarian cancer	21720365	CNVD
abnormal development	18461090	CNVD
Schizophrenia	20433910	CNVD
Autism	21701786	CNVD
Attention deficit hyperactivity disorder	21324949	CNVD
Austim spectrum disorder	21302340	CNVD
Schizophrenia	20587603	CNVD
Schizophrenia	20553308	CNVD
Autism	22241247	CNVD
Myelofibrosis	22110671	CNVD
Lung adenocarcinoma	17086460	CNVD
Retinoblastoma	22278416	CNVD
Cancer	21183584	CNVD
Breast cancer	16397240	CNVD
Acute lymphoblastic leukemia	18768390	CNVD
Mental retardation	19521722	CNVD
Schizophrenia	18990708	CNVD
Schizophrenia	18940311	CNVD
Schizophrenia	19348701	CNVD
Schizophrenia	18945720	CNVD
Schizophrenia	19571808	CNVD
Prostate cancer	16573809	CNVD
Neuroticism	17667963	CNVD
Schizophrenia	19443537	CNVD
Schizophrenia	19546859	CNVD
Autism	17322880	CNVD
Lung cancer	17086460	CNVD
Chronic lymphocytic leukemia	17053054	CNVD
Hereditary non-polyposis colorectal cancer	19566914	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Schizophrenia	23813976	CNVD
Bipolar disorder	19114987	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:52298200-52298400	Enhancers	Brain Germinal Matrix	brain
2	chr2:52298400-52300200	Weak transcription	Brain Germinal Matrix	brain
3	chr2:52299400-52300200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr2:52299800-52300200	Enhancers	Pancreatic Islets	Pancreatic Islet
5	chr2:52300200-52300600	Enhancers	Brain Germinal Matrix	brain
6	chr2:52300200-52301800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr2:52300600-52300800	Weak transcription	Brain Germinal Matrix	brain
8	chr2:52300800-52302600	Enhancers	Brain Germinal Matrix	brain
9	chr2:52301400-52301800	Enhancers	Fetal Muscle Leg	muscle
10	chr2:52301400-52302400	Enhancers	Fetal Kidney	kidney
11	chr2:52301800-52302000	Enhancers	Pancreatic Islets	Pancreatic Islet
12	chr2:52306200-52306400	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr2:52306400-52310000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr2:52307200-52308200	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr2:52307600-52308000	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr2:52307600-52308200	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr2:52307800-52308200	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr2:52310000-52310200	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr2:52310200-52310600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr2:52310600-52311000	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr2:52334400-52335000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:52335000-52336000	Enhancers	HMEC	breast
23	chr2:52335600-52336000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:52339000-52341000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:52339000-52341400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:52339400-52340600	Enhancers	Osteobl	bone
27	chr2:52340400-52341600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr2:52340600-52344400	Weak transcription	Osteobl	bone
29	chr2:52341400-52344200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr2:52341600-52344000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr2:52342600-52343000	Enhancers	Pancreatic Islets	Pancreatic Islet
32	chr2:52342600-52343200	Enhancers	NHDF-Ad	bronchial
33	chr2:52342800-52343000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr2:52343200-52344200	Weak transcription	NHDF-Ad	bronchial
35	chr2:52343200-52347200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr2:52344000-52344600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr2:52344200-52344400	Enhancers	NHDF-Ad	bronchial
38	chr2:52344200-52344600	Enhancers	Adipose Nuclei	Adipose
39	chr2:52344200-52345200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr2:52344400-52345000	Enhancers	Osteobl	bone
41	chr2:52344600-52346400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr2:52345000-52355000	Weak transcription	Osteobl	bone
43	chr2:52347200-52350600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr2:52347400-52347800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr2:52350600-52354400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr2:52352800-52353000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr2:52353200-52354200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr2:52353600-52355800	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr2:52354200-52355000	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr2:52354200-52355600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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