Variant report

Variant	esv2756968
Chromosome Location	chr3:221081-236759
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:62)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F6	chr3:234230-234592	H1-hESC	embryonic stem cell:	n/a	n/a
2	E2F6	chr3:234185-234722	H1-hESC	embryonic stem cell:	n/a	n/a
3	JUN	chr3:230115-230134	H1-hESC	embryonic stem cell:	n/a	n/a
4	JUND	chr3:233799-233803	H1-hESC	embryonic stem cell:	n/a	n/a
5	MAFF	chr3:233681-233933	HepG2	liver:	n/a	n/a
6	MAFK	chr3:233657-233979	HepG2	liver:	n/a	n/a
7	MAFK	chr3:233700-233956	IMR90	lung:	n/a	n/a
8	MAFK	chr3:233667-233976	HepG2	liver:	n/a	n/a
9	MAX	chr3:222580-222751	NB4	blood:	n/a	chr3:222641-222651
10	POLR2A	chr3:234420-234532	A549	lung:	n/a	n/a
11	POLR2A	chr3:223375-223500	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr3:223208-223399	MCF10A-Er-Src	breast:	n/a	n/a
13	STAT3	chr3:228023-228177	MCF10A-Er-Src	breast:	n/a	n/a
14	WRNIP1	chr3:222633-222725	GM12878	blood:	n/a	n/a

(count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:236078-236128	CMK	blood:	n/a
2	chr3:236078-236128	CMK	blood:	n/a
3	chr3:236078-236128	H1-hESC	embryonic stem cell:	embryo
4	chr3:236078-236128	SAEC	small airway:	n/a
5	chr3:236078-236128	HCF	heart:	n/a
6	chr3:236078-236128	Caco-2	colon:	n/a
7	chr3:236078-236128	PrEC	prostate:	n/a
8	chr3:236078-236128	HL-60	blood:	n/a
9	chr3:236078-236128	Hela-S3	cervix:	n/a
10	chr3:236078-236128	GM06990	blood:	n/a
11	chr3:236078-236128	HEEpiC	esophagus:	n/a
12	chr3:236078-236128	GM12878	blood:	n/a
13	chr3:236078-236128	AG10803	skin:	n/a
14	chr3:236078-236128	NHBE	bronchial:	n/a
15	chr3:236078-236128	PANC-1	pancreas:	n/a
16	chr3:236078-236128	HEK293	kidney:	embryo
17	chr3:236078-236128	AG09309	skin:	n/a
18	chr3:236078-236128	HMEC	breast:	n/a
19	chr3:236078-236128	AG04450	lung:	fetal
20	chr3:236078-236128	IMR90	lung:	fetal
21	chr3:236078-236128	SK-N-MC	brain:	n/a
22	chr3:236078-236128	AoSMC	blood vessel:	n/a
23	chr3:236078-236128	SK-N-SH_RA	brain:	n/a
24	chr3:236078-236128	HPAEpiC	pulmonary alveolar:	n/a
25	chr3:236078-236128	HCPEpiC	choroid plexus:	n/a
26	chr3:236078-236128	HCT-116	colon:	n/a
27	chr3:236078-236128	AG04449	skin:	fetal
28	chr3:236078-236128	HIPEpiC	eye:	n/a
29	chr3:236078-236128	BE2_C	brain:	n/a
30	chr3:236078-236128	HRCEpiC	kidney:	n/a
31	chr3:236078-236128	HNPCEpiC	eye:	n/a
32	chr3:236078-236128	HRPEpiC	eye:	n/a
33	chr3:236078-236128	ovcar-3	ovarian:	n/a
34	chr3:236078-236128	NB4	blood:	n/a
35	chr3:236078-236128	NHDF-neo	bronchial:	n/a
36	chr3:236078-236128	LNCaP	prostate:	n/a
37	chr3:236078-236128	HCM	heart:	n/a
38	chr3:236078-236128	NH-A	brain:	n/a
39	chr3:236078-236128	ECC-1	luminal epithelium:	n/a
40	chr3:236078-236128	AG09319	gingival:	n/a
41	chr3:236078-236128	K562	blood:	n/a
42	chr3:236078-236128	U87	brain:	n/a
43	chr3:236078-236128	GM12892	blood:	n/a
44	chr3:236078-236128	Hepatocyte	liver:	n/a
45	chr3:236078-236128	GM19239	blood:	n/a
46	chr3:236078-236128	T-47D	breast:	n/a
47	chr3:236078-236128	PFSK-1	brain:	n/a
48	chr3:236078-236128	ProgFib	skin:	n/a
49	chr3:236078-236128	NT2-D1	testis:	n/a
50	chr3:236078-236128	SK-N-SH	brain:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:217250..219144-chr3:222760..225297,2	MCF-7	breast:

No data

Variant related genes	Relation type
CHL1	TF binding region
CHL1	CpG island

Extended variants
information (count: 228 )
Associated
traits (count: 84 )

Variant overlapped rSNPs/rCNVs (count:228 , 50 per page) page: 1 2 3 4 5

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs370191847	chr3:225266-225267	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs3946790	chr3:225296-225297	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs563441225	chr3:225298-225299	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs181529959	chr3:225321-225322	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs141665501	chr3:225346-225347	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs564078510	chr3:225355-225356	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs2839803	chr3:225361-225362	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs561494290	chr3:225368-225369	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs186229595	chr3:225369-225370	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs546935843	chr3:225372-225373	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs145237184	chr3:225402-225403	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs529120525	chr3:225421-225422	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs73086725	chr3:225429-225430	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs79058949	chr3:225460-225461	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs570455725	chr3:225470-225471	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs2173496	chr3:225473-225474	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs534272811	chr3:225517-225518	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs552220617	chr3:225535-225536	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs570535067	chr3:225545-225546	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs189340578	chr3:225585-225586	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs137903269	chr3:225590-225591	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs141633818	chr3:225595-225596	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs9846093	chr3:226603-226604	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs190204611	chr3:226629-226630	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs182825543	chr3:226635-226636	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs56935729	chr3:226646-226647	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs544794685	chr3:226650-226651	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs33973117	chr3:226652-226653	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs528582709	chr3:226694-226695	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs547033647	chr3:226700-226701	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs568376356	chr3:226717-226718	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs529257239	chr3:226719-226720	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs373336464	chr3:226729-226730	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs58544565	chr3:226733-226734	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs74619414	chr3:226808-226809	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs9819270	chr3:226861-226862	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs187430698	chr3:226888-226889	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs59080621	chr3:226899-226900	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs145493379	chr3:226913-226914	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs565828779	chr3:233612-233613	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs527394707	chr3:233653-233654	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs536499007	chr3:233676-233677	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
43	rs554808861	chr3:233678-233679	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
44	rs569827349	chr3:233687-233688	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
45	rs191197208	chr3:233713-233714	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
46	rs147742006	chr3:233736-233737	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
47	rs368812162	chr3:233744-233745	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
48	rs73814162	chr3:233747-233748	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
49	rs577995689	chr3:233758-233759	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
50	rs545063805	chr3:233818-233819	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:84)

Disease	PMID	Source
Cancer	20164920	CNVD
Lung cancer	16618734	CNVD
Autism	18349135	CNVD
Breast cancer	20409316	CNVD
Myelofibrosis	22110671	CNVD
Autism	22241247	CNVD
Intellectual disability	22045946	CNVD
Squamous cell cancer	19607727	CNVD
Gastric adenocarcinoma	19115996	CNVD
sporadic birth defects	19047251	CNVD
Mental retardation	17124404	CNVD
abnormal development	18461090	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Sudden cardiac death	19188705	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Ovarian cancer	21720365	CNVD
Neuroblastoma	18923191	CNVD
Papillary thyroid carcinoma	21436994	CNVD
Biliary cancer	19435499	CNVD
Medulloblastoma	21979893	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Breast cancer	17603634	CNVD
Neuroblastoma	17327916	CNVD
Glioblastoma multiforme	21080181	CNVD
Colorectal cancer	21297112	CNVD
Lynch syndrome	18415027	CNVD
Renal cell carcinoma	18592004	CNVD
Acute myeloid leukemia	20729466	CNVD
Urothelial carcinoma	18382360	CNVD
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Insulin resistance	16721378	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Oral cancer	19627613	CNVD
Renal cell carcinoma	19461508	CNVD
Epithelial cancer	22065749	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Acute myeloid leukemia	16864856	CNVD
Liposarcoma	21253554	CNVD
Basal cell lymphoma	21115979	CNVD
Endometrial cancer	22040021	CNVD
Pancreatic endocrine tumor	20981439	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Oral cancer	21386901	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	21364760	CNVD
Schizophrenia	20967226	CNVD
Autism	22543975	CNVD
Attention deficit hyperactivity disorder	19546859	CNVD
lymphocytic leukemia	21291569	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Non-syndromic sensorineural hearing loss	17289997	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Tetralogy of Fallot	22912587	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Autism	20685689	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD
Melanoma	20877625	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Multiple myeloma	17550852	CNVD
Prostate cancer	18632612	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:225200-225600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:226600-227000	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr3:233600-233800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:233600-234400	Enhancers	Primary B cells from peripheral blood	blood
5	chr3:233800-235000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:234200-234800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
7	chr3:234600-234800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
8	chr3:235000-235200	Enhancers	Fetal Brain Female	brain
9	chr3:235000-236000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr3:235200-236000	Weak transcription	Fetal Brain Female	brain
11	chr3:235400-236600	Enhancers	Fetal Brain Male	brain
12	chr3:235800-236000	Enhancers	Adipose Nuclei	Adipose
13	chr3:235800-236400	Enhancers	Spleen	Spleen
14	chr3:235800-237000	Enhancers	Ovary	ovary
15	chr3:236000-236200	Flanking Active TSS	Adipose Nuclei	Adipose
16	chr3:236000-236400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr3:236000-236600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:236000-236800	Enhancers	Fetal Brain Female	brain
19	chr3:236200-236400	Enhancers	Brain Cingulate Gyrus	brain
20	chr3:236200-236400	Enhancers	Brain Substantia Nigra	brain
21	chr3:236200-237800	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr3:236400-237000	Enhancers	Brain Germinal Matrix	brain
23	chr3:236400-237400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr3:236400-238200	Weak transcription	Spleen	Spleen
25	chr3:236600-237200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr3:236600-237200	Flanking Active TSS	Fetal Brain Male	brain

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