Variant report

Variant	esv17057
Chromosome Location	chr4:92946774-92966992
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	BATF	chr4:92956979-92957141	GM12878	blood:	n/a	chr4:92957060-92957071
2	BATF	chr4:92956941-92957201	GM12878	blood:	n/a	chr4:92957060-92957071
3	BHLHE40	chr4:92956890-92957081	GM12878	blood:	n/a	n/a
4	CREB1	chr4:92956973-92957308	GM12878	blood:	n/a	n/a
5	CTCF	chr4:92948094-92948176	Spleen_OC	spleen:	n/a	n/a
6	CTCF	chr4:92963292-92963417	Lung_OC	lung:	n/a	n/a
7	CTCF	chr4:92957011-92957067	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr4:92960060-92960088	Pancreas_OC	pancreas:	n/a	n/a
9	CTCF	chr4:92959669-92959688	Lung_OC	lung:	n/a	n/a
10	CTCF	chr4:92949282-92949339	GM20000	blood:	n/a	n/a
11	CUX1	chr4:92956967-92957048	GM12878	blood:	n/a	n/a
12	EBF1	chr4:92963887-92964116	GM12878	blood:	n/a	n/a
13	EBF1	chr4:92956984-92957057	GM12878	blood:	n/a	n/a
14	EBF1	chr4:92963873-92964154	GM12878	blood:	n/a	n/a
15	GATA2	chr4:92959823-92960044	K562	blood:	n/a	n/a
16	POLR2A	chr4:92959262-92959372	HUVEC	blood vessel:	n/a	n/a
17	RAD21	chr4:92956955-92957178	H1-hESC	embryonic stem cell:	n/a	n/a
18	RUNX3	chr4:92956830-92957158	GM12878	blood:	n/a	n/a
19	SPI1	chr4:92956842-92957133	GM12891	blood:	n/a	n/a
20	SPI1	chr4:92956831-92957139	GM12878	blood:	n/a	n/a
21	SPI1	chr4:92956746-92957232	GM12891	blood:	n/a	n/a
22	SPI1	chr4:92956840-92957059	GM12878	blood:	n/a	n/a
23	STAT3	chr4:92956060-92956220	MCF10A-Er-Src	breast:	n/a	n/a
24	STAT3	chr4:92954984-92955182	MCF10A-Er-Src	breast:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GRID2-2	chr4:92947431-92947539	NONHSAT097424
2	lnc-GRID2-2	chr4:92951738-92951863	NONHSAT097424

Variant related genes	Relation type
ENSG00000256889	TF binding region

Extended variants
information (count: 542 )
Associated
traits (count: 87 )

Variant overlapped rSNPs/rCNVs (count:542 , 50 per page) page: 1 2 3 4 5 6 7 ... 11

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs377751754	chr4:92946791-92946792	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs34675149	chr4:92946794-92946795	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs138751150	chr4:92946821-92946822	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs563389459	chr4:92946827-92946828	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs531991212	chr4:92946843-92946844	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs181919794	chr4:92946869-92946870	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs186567552	chr4:92946903-92946904	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs190579085	chr4:92946954-92946955	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs547942318	chr4:92946967-92946968	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs112361032	chr4:92946968-92946969	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs140377301	chr4:92946973-92946974	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs182092063	chr4:92947016-92947017	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs551263976	chr4:92947022-92947023	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs571199995	chr4:92947049-92947050	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs551441343	chr4:92947123-92947124	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs556391093	chr4:92947127-92947128	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs150355834	chr4:92947136-92947137	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs553434305	chr4:92947142-92947143	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs566858912	chr4:92947151-92947152	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs535963367	chr4:92947168-92947169	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs555551815	chr4:92947199-92947200	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs574579454	chr4:92947222-92947223	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs186243112	chr4:92947244-92947245	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs556729518	chr4:92947265-92947266	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs576753570	chr4:92947294-92947295	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs545095076	chr4:92947310-92947311	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs558938523	chr4:92947322-92947323	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs117167889	chr4:92947386-92947387	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs554166123	chr4:92947403-92947404	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs541908952	chr4:92947409-92947410	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs561586253	chr4:92947412-92947413	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs191455042	chr4:92947423-92947424	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs550938682	chr4:92947429-92947430	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs564650762	chr4:92947445-92947446	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
35	rs533704806	chr4:92947481-92947482	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
36	rs138010357	chr4:92947483-92947484	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
37	rs149380215	chr4:92947494-92947495	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
38	rs572762573	chr4:92947501-92947502	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
39	rs144728918	chr4:92947503-92947504	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
40	rs182357585	chr4:92947525-92947526	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
41	rs186065834	chr4:92947545-92947546	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs556770386	chr4:92947546-92947547	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs576592621	chr4:92947614-92947615	Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs189870432	chr4:92947617-92947618	Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs552801819	chr4:92947666-92947667	Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs572802528	chr4:92947682-92947683	Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs541499426	chr4:92947694-92947695	Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs183176173	chr4:92947699-92947700	Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs575270056	chr4:92947710-92947711	Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs544310917	chr4:92947738-92947739	Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:87)

Disease	PMID	Source
Acute lymphoblastic leukemia	22237106	CNVD
Glioblastoma multiforme	21080181	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Chordoma	21602918	CNVD
HIV/AIDS	22032296	CNVD
Medulloblastoma	21979893	CNVD
Neuroblastoma	18923191	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Breast cancer	21858162	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Gastric cancer	21586687	CNVD
lymphocytic leukemia	21291569	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Melanoma	18172304	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Breast cancer	17603634	CNVD
Hepatocellular carcinoma	16750200	CNVD
Myxofibrosarcoma	16751306	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Parkinson disease	18923514	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Cancer	21183584	CNVD
Breast cancer	16272173	CNVD
Colorectal cancer	19359472	CNVD
Malignant mesothelioma	18160781	CNVD
Medulloblastoma	18056178	CNVD
Multiple myeloma	17077331	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Oral squamous cell carcinoma	17134496	CNVD
4q-syndrome	17576883	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Colorectal cancer	20709793	CNVD
Muscular dystrophy	21149563	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Hepatocellular carcinoma	22174799	CNVD
Liposarcoma	21253554	CNVD
Oligodendroglial tumors	17285580	CNVD
Cervical cancer	21062161	CNVD
Metanephric adenoma	20802469	CNVD
Breast cancer	16608533	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Lung cancer	19208797	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	21785460	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Myelodysplastic syndrome	21251322	CNVD
Lung cancer	18438408	CNVD
Chronic lymphocytic leukemia	18922857	CNVD
Cancer	22429812	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Autism	18414403	CNVD
primary effusion lymphomas	17116491	CNVD
Mental retardation	20522426	CNVD
delayed speech	20522426	CNVD
growth disorder	20522426	CNVD
Olfactory neuroblastoma	18408657	CNVD
small cell lung cancer	20016488	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Breast cancer	17133270	CNVD
Colorectal cancer	20459617	CNVD
Acute monocytic leukemia	16498392	CNVD
Multiple myeloma	16616336	CNVD
Esophageal adenocarcinoma	18820669	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Myelofibrosis	22110671	CNVD
Parkinson disease	20877625	CNVD
Hirschsprung''s Disease	21712996	CNVD
Congenital anomalies of the kidney and urinary tract	20505237	CNVD
Breast cancer	17393978	CNVD
Ovarian cancer	21720365	CNVD
Obesity	20622171	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Cancer	20164920	CNVD
Cancer	20164919	CNVD
Esophageal cancer	21851588	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD
Cancer	19907438	CNVD

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:92936800-92949200	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr4:92947600-92948000	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr4:92947600-92948000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr4:92947600-92948000	Active TSS	H9 Cell Line	embryonic stem cell
5	chr4:92949200-92949600	Active TSS	Duodenum Mucosa	Duodenum
6	chr4:92949200-92949600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
7	chr4:92949600-92950000	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr4:92949600-92950600	Enhancers	Duodenum Mucosa	Duodenum
9	chr4:92950000-92950200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
10	chr4:92950200-92951600	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr4:92950600-92951600	Weak transcription	Duodenum Mucosa	Duodenum
12	chr4:92951600-92952600	Enhancers	Duodenum Mucosa	Duodenum
13	chr4:92952600-92953400	Weak transcription	Duodenum Mucosa	Duodenum
14	chr4:92953400-92953800	Enhancers	Duodenum Mucosa	Duodenum
15	chr4:92955400-92955600	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr4:92955600-92956200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr4:92956000-92957400	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr4:92956200-92957200	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr4:92956200-92957600	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr4:92956400-92957600	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr4:92956600-92957800	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr4:92957800-92959400	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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