Variant report

Variant	esv3448810
Chromosome Location	chr1:246672297-246672842
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:44)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:44 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BHLHE40	chr1:246672265-246672773	HepG2	liver:	n/a	n/a
2	CTCF	chr1:246672245-246672467	MCF-7	breast:	n/a	n/a
3	CTCF	chr1:246672180-246672330	GM12864	blood:	n/a	n/a
4	CTCF	chr1:246672260-246672410	HepG2	liver:	n/a	n/a
5	CTCF	chr1:246672280-246672430	GM12874	blood:	n/a	n/a
6	CTCF	chr1:246672380-246672530	GM12864	blood:	n/a	n/a
7	CTCF	chr1:246672243-246672427	HepG2	liver:	n/a	n/a
8	CTCF	chr1:246672260-246672410	Hela-S3	cervix:	n/a	n/a
9	CTCF	chr1:246672339-246672358	GM13976	blood:	n/a	n/a
10	CTCF	chr1:246672245-246672470	MCF-7	breast:	n/a	n/a
11	CTCF	chr1:246672261-246672457	MCF-7	breast:	n/a	n/a
12	CTCF	chr1:246672232-246672495	MCF-7	breast:	n/a	n/a
13	CTCF	chr1:246672260-246672410	SAEC	small airway:	n/a	n/a
14	CTCF	chr1:246672280-246672430	SK-N-SH_RA	brain:	n/a	n/a
15	CTCF	chr1:246672316-246672442	GM12891	blood:	n/a	n/a
16	CTCF	chr1:246672300-246672363	NHEK	skin:	n/a	n/a
17	CTCF	chr1:246672340-246672490	MCF-7	breast:	n/a	n/a
18	CTCF	chr1:246672323-246672371	GM19238	blood:	n/a	n/a
19	CTCF	chr1:246672240-246672390	WERI-Rb-1	eye:	n/a	n/a
20	CTCF	chr1:246672260-246672410	GM12868	blood:	n/a	n/a
21	CTCF	chr1:246672254-246672361	Fibrobl	skin:	n/a	n/a
22	CTCF	chr1:246672260-246672410	GM12870	blood:	n/a	n/a
23	CTCF	chr1:246672272-246672433	Hela-S3	cervix:	n/a	n/a
24	CTCF	chr1:246672280-246672430	GM12875	blood:	n/a	n/a
25	CTCF	chr1:246672200-246672350	A549	lung:	n/a	n/a
26	CTCF	chr1:246672188-246672554	MCF-7	breast:	n/a	n/a
27	CTCF	chr1:246672260-246672410	HRE	kidney:	n/a	n/a
28	CTCF	chr1:246672292-246672389	GM12892	blood:	n/a	n/a
29	CTCF	chr1:246672300-246672450	GM12874	blood:	n/a	n/a
30	CTCF	chr1:246672331-246672407	Gliobla	brain:	n/a	n/a
31	CTCF	chr1:246672400-246672550	SAEC	small airway:	n/a	n/a
32	CTCF	chr1:246672280-246672430	HBMEC	blood vessel:	n/a	n/a
33	CTCF	chr1:246672022-246672662	A549	lung:	n/a	n/a
34	CTCF	chr1:246672660-246672810	HepG2	liver:	n/a	n/a
35	CTCF	chr1:246672221-246672478	MCF-7	breast:	n/a	n/a
36	CTCF	chr1:246672193-246672542	MCF-7	breast:	n/a	n/a
37	CTCF	chr1:246672317-246672374	HepG2	liver:	n/a	n/a
38	CTCF	chr1:246672460-246672610	Hela-S3	cervix:	n/a	n/a
39	CTCF	chr1:246672267-246672428	A549	lung:	n/a	n/a
40	CTCF	chr1:246672240-246672390	MCF-7	breast:	n/a	n/a
41	MAX	chr1:246672398-246672420	HepG2	liver:	n/a	n/a
42	MAZ	chr1:246672389-246672535	Hela-S3	cervix:	n/a	n/a
43	RAD21	chr1:246672235-246672424	HepG2	liver:	n/a	n/a
44	RAD21	chr1:246672280-246672420	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:246672116..246673896-chr1:246728925..246730470,2	MCF-7	breast:
2	chr1:246671783..246672632-chr1:246690944..246691587,2	MCF-7	breast:
3	chr1:246669150..246672151-chr1:246672470..246677945,5	K562	blood:

No data

Variant related genes	Relation type
SMYD3	TF binding region
ENSG00000162852	chromatin interactions
ENSG00000162851	chromatin interactions
ENSG00000185420	chromatin interactions

Extended variants
information (count: 31 )
Associated
traits (count: 84 )

Variant overlapped rSNPs/rCNVs (count:31 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs61839848	chr1:246672307-246672308	Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs550954101	chr1:246672336-246672337	Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
3	rs4081311	chr1:246672337-246672338	Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs187311735	chr1:246672351-246672352	Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
5	rs546865189	chr1:246672383-246672384	Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
6	rs566689830	chr1:246672399-246672400	Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
7	rs538808396	chr1:246672400-246672401	Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
8	rs551393512	chr1:246672418-246672419	Weak transcription ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
9	rs192209789	chr1:246672455-246672456	Weak transcription ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
10	rs537548527	chr1:246672464-246672465	Weak transcription ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
11	rs554288509	chr1:246672465-246672466	Weak transcription ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
12	rs574363024	chr1:246672471-246672472	Weak transcription ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
13	rs376988540	chr1:246672488-246672489	Weak transcription ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
14	rs4040219	chr1:246672503-246672504	Weak transcription ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	4 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs576772111	chr1:246672508-246672509	Weak transcription ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
16	rs142527672	chr1:246672586-246672587	Weak transcription ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
17	rs559973760	chr1:246672641-246672642	Weak transcription Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
18	rs371480596	chr1:246672688-246672689	Weak transcription Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
19	rs573479984	chr1:246672698-246672699	Weak transcription Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
20	rs545584763	chr1:246672712-246672713	Weak transcription Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
21	rs114039624	chr1:246672719-246672720	Weak transcription Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
22	rs530980969	chr1:246672720-246672721	Weak transcription Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
23	rs544716223	chr1:246672721-246672722	Weak transcription Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
24	rs75525164	chr1:246672739-246672740	Weak transcription Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
25	rs530092384	chr1:246672748-246672749	Weak transcription Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
26	rs546708204	chr1:246672757-246672758	Weak transcription Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
27	rs78148537	chr1:246672776-246672777	Weak transcription Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
28	rs2152887	chr1:246672790-246672791	Weak transcription Enhancers	TF binding region Chromatin interactive region	4 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs115562670	chr1:246672797-246672798	Weak transcription Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
30	rs567907794	chr1:246672809-246672810	Weak transcription Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
31	rs535231818	chr1:246672813-246672814	Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:84)

Disease	PMID	Source
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Melanoma	18172304	CNVD
Rett syndrome	21593744	CNVD
Medulloblastoma	21979893	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	17133270	CNVD
Non-small cell lung cancer	21044232	CNVD
Cervical cancer	21063398	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	20632083	CNVD
Endometrial cancer	22040021	CNVD
Ewing''s sarcoma	21437220	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	21080181	CNVD
Hepatocellular carcinoma	22174799	CNVD
Medulloblastoma	21292688	CNVD
Phyllodes tumor	17334353	CNVD
Breast cancer	21264507	CNVD
Liposarcoma	21253554	CNVD
Multiple myeloma	21628407	CNVD
Cancer	16751803	CNVD
Prostate cancer	16705090	CNVD
Neuroblastoma	19435921	CNVD
Breast cancer	17850661	CNVD
Breast cancer	16461572	CNVD
Intracranial tumor	16823260	CNVD
Medulloblastoma	18056178	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Colorectal cancer	16272173	CNVD
Neuroblastoma	21899760	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Breast cancer	16608533	CNVD
Ewing''s sarcoma	22429812	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17001317	CNVD
Acute myeloid leukemia	20729466	CNVD
Testicular germ cell tumor	18059402	CNVD
Neuroblastoma	18923191	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Breast cancer	21509527	CNVD
Urothelial carcinoma	21177765	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Hepatocellular carcinoma	18803288	CNVD
Urothelial tumor	18831757	CNVD
Lung cancer	18438408	CNVD
Medulloblastoma	16783165	CNVD
Basal cell lymphoma	17170743	CNVD
Basal cell lymphoma	17053054	CNVD
Congenital abnormalities	21549014	CNVD
Developmental delay	21549014	CNVD
Mental retardation	21549014	CNVD
small cell lung cancer	20016488	CNVD
Cancer	20164920	CNVD
Cancer	17060936	CNVD
abnormal development	18461090	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Non-small cell lung cancer	21829676	CNVD
Multiple myeloma	16616336	CNVD
Ovarian cancer	21720365	CNVD
Glioblastoma multiforme	22291905	CNVD
Myelofibrosis	22110671	CNVD
Disease	21936942	CNVD
laryngomalacia	21936942	CNVD
GLUT3 deficiency syndrome	20509907	CNVD
Developmental delay	21373258	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Developmental delay	19490664	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Cutaneous malignant melanoma	18794153	CNVD
Astrocytoma	17934521	CNVD
Neurocytoma	17123091	CNVD
Central neurocytomas	17123091	CNVD
Breast cancer	20409316	CNVD
Fibroblasts	17951408	CNVD
Lung cancer	17951408	CNVD
Schizophrenia	20967226	CNVD
Schizophrenia	19805367	CNVD

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246671200-246675000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:246671200-246676000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:246672200-246672400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:246672200-246672400	Enhancers	Esophagus	oesophagus
5	chr1:246672200-246672400	Enhancers	Fetal Stomach	stomach
6	chr1:246672200-246672400	Enhancers	Stomach Smooth Muscle	stomach
7	chr1:246672200-246672400	Flanking Active TSS	HepG2	liver
8	chr1:246672200-246672600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:246672400-246672600	Enhancers	HepG2	liver
10	chr1:246672600-246674400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:246672600-246675400	Weak transcription	HepG2	liver

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