Variant report

Variant	esv275373
Chromosome Location	chr3:178887218-178892336
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	CEBPB	chr3:178887903-178887906	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr3:178887991-178888046	GM13976	blood:	n/a	n/a
3	CUX1	chr3:178888014-178888102	GM12878	blood:	n/a	n/a
4	RUNX3	chr3:178892169-178892532	GM12878	blood:	n/a	n/a
5	SETDB1	chr3:178889178-178889731	U2OS	brain:	n/a	n/a
6	SPI1	chr3:178891934-178892572	GM12878	blood:	n/a	chr3:178892292-178892301
7	SPI1	chr3:178892139-178892394	GM12891	blood:	n/a	chr3:178892292-178892301
8	SPI1	chr3:178892192-178892436	GM12878	blood:	n/a	chr3:178892292-178892301
9	SPI1	chr3:178892192-178892374	GM12878	blood:	n/a	chr3:178892292-178892301
10	SPI1	chr3:178892138-178892425	GM12891	blood:	n/a	chr3:178892292-178892301
11	SRF	chr3:178891228-178891355	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:178888452..178890564-chr3:178897631..178899148,2	MCF-7	breast:
2	chr3:178889061..178891401-chr3:178905876..178907714,2	MCF-7	breast:
3	chr3:178864911..178866513-chr3:178885186..178888175,2	MCF-7	breast:
4	chr3:178883467..178885785-chr3:178891482..178893959,2	K562	blood:
5	chr3:178865398..178868537-chr3:178888868..178891938,3	MCF-7	breast:
6	chr3:178882042..178883552-chr3:178887353..178888877,2	K562	blood:
7	chr3:178891781..178894758-chr3:178901909..178904636,2	MCF-7	breast:
8	chr3:178884535..178886468-chr3:178887552..178889136,2	K562	blood:
9	chr3:178892192..178894702-chr3:178896410..178899147,2	K562	blood:

Variant related genes	Relation type
ENSG00000201957	TF binding region
ENSG00000121879	chromatin interactions
ENSG00000229102	chromatin interactions

Extended variants
information (count: 206 )
Associated
traits (count: 80 )

Variant overlapped rSNPs/rCNVs (count:206 , 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	rs542680875	chr3:178887314-178887315	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs559495257	chr3:178887321-178887322	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs527848823	chr3:178887341-178887342	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs147899484	chr3:178887346-178887347	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs371447475	chr3:178887352-178887353	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs564719847	chr3:178887372-178887373	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs533657714	chr3:178887383-178887384	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs188087286	chr3:178887393-178887394	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs570002283	chr3:178887429-178887430	Weak transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs141615029	chr3:178887446-178887447	Weak transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs554500400	chr3:178887457-178887458	Weak transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs549023937	chr3:178887500-178887501	Weak transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs565825649	chr3:178887545-178887546	Weak transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs78163832	chr3:178887632-178887633	Weak transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs540373813	chr3:178887640-178887641	Weak transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs377546508	chr3:178887651-178887652	Weak transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs9838411	chr3:178887687-178887688	Weak transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
18	rs181920870	chr3:178887697-178887698	Weak transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs79060419	chr3:178887717-178887718	Weak transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs556996688	chr3:178887803-178887804	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs573534837	chr3:178887845-178887846	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs542268153	chr3:178887848-178887849	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs9862294	chr3:178887849-178887850	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs574634103	chr3:178887855-178887856	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs545155313	chr3:178887856-178887857	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs564656606	chr3:178887857-178887858	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs533380370	chr3:178887859-178887860	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs200251651	chr3:178887861-178887862	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs201635701	chr3:178887862-178887863	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs2699903	chr3:178887863-178887864	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
31	rs562589708	chr3:178887864-178887865	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
32	rs66994875	chr3:178887872-178887873	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
33	rs187070470	chr3:178887883-178887884	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs55780144	chr3:178887887-178887888	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs113050063	chr3:178887914-178887915	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs79847525	chr3:178887926-178887927	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
37	rs375023579	chr3:178887986-178887987	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
38	rs548960849	chr3:178887998-178887999	Enhancers Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
39	rs565764406	chr3:178888032-178888033	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
40	rs181491628	chr3:178888042-178888043	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
41	rs551475831	chr3:178888087-178888088	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
42	rs545770956	chr3:178888088-178888089	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
43	rs74833247	chr3:178888145-178888146	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
44	rs536858874	chr3:178888156-178888157	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs557180694	chr3:178888177-178888178	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs186919052	chr3:178888179-178888180	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs190438176	chr3:178888180-178888181	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs552985331	chr3:178888187-178888188	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs572913530	chr3:178888197-178888198	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs182601399	chr3:178888223-178888224	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:80)

Disease	PMID	Source
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Medulloblastoma	21979893	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Breast cancer	22032731	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
Cervical Cancer	21857958	CNVD
Melanoma	21693616	CNVD
Lung cancer	21426551	CNVD
Cancer	21637783	CNVD
Cervical cancer	21063398	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Oral cancer	21386901	CNVD
Renal cell carcinoma	19461508	CNVD
Cancer	22065749	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Basal cell lymphoma	21115979	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myelodysplastic syndrome	21251322	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Breast cancer	16608533	CNVD
Acute myeloid leukemia	20729466	CNVD
Non-small cell lung cancer	19010865	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Prostate cancer	16573809	CNVD
Breast cancer	21785460	CNVD
Breast cancer	17133270	CNVD
epilepsy	18472482	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Myxofibrosarcoma	16751306	CNVD
Parkinson disease	21907011	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Breast cancer	21364760	CNVD
Anaplastic thyroid cancer	17989125	CNVD
Lung adenocarcinoma	19525976	CNVD
Lung cancer	19525976	CNVD
Ovarian cancer	18208621	CNVD
Thyroid cancer	17317825	CNVD
Thyroid cancer	17989125	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Non-small cell lung cancer	21829676	CNVD
Ovarian neoplasms	16753589	CNVD
Breast cancer	21806811	CNVD
Hirschsprung''s Disease	21712996	CNVD
Cancer	16751803	CNVD
abnormal development	18461090	CNVD
lymphocytic leukemia	21291569	CNVD
Autism	19653912	CNVD
Endometrial cancer	19261849	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Esophageal squamous carcinoma	17470683	CNVD
Breast cancer	21509527	CNVD
Myelofibrosis	22110671	CNVD
Prostate cancer	17217626	CNVD
Adenocarcinoma	19607727	CNVD
Squamous cell cancer	19607727	CNVD
Neurodevelopmental disorder	22521361	CNVD
small cell lung cancer	20016488	CNVD
Cancer	20164920	CNVD
Acute lymphoblastic leukemia	18458336	CNVD
Prostate cancer	18632612	CNVD
Autism	20685689	CNVD
Human papillomavirus	17975027	CNVD
Adenocarcinoma	18757405	CNVD
Lung cancer	18757405	CNVD
Squamous cell cancer	18757405	CNVD
small cell lung cancer	18757405	CNVD

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:178867800-178900200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:178868000-178892400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr3:178868600-178893000	Weak transcription	Aorta	Aorta
4	chr3:178869200-178898000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr3:178870800-178896400	Weak transcription	K562	blood
6	chr3:178874800-178888600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr3:178877400-178897800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:178879200-178891800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr3:178879400-178892000	Weak transcription	Lung	lung
10	chr3:178879400-178896400	Weak transcription	Right Atrium	heart
11	chr3:178879600-178896400	Weak transcription	Left Ventricle	heart
12	chr3:178880400-178887800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr3:178883400-178887800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:178883600-178892400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr3:178883600-178893600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr3:178883800-178905800	Weak transcription	Fetal Kidney	kidney
17	chr3:178884800-178887800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:178884800-178888400	Weak transcription	Fetal Lung	lung
19	chr3:178885800-178887800	Weak transcription	Adipose Nuclei	Adipose
20	chr3:178886600-178887400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:178886800-178887400	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr3:178886800-178888600	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr3:178886800-178891800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr3:178887200-178888000	ZNF genes & repeats	Fetal Brain Male	brain
25	chr3:178887200-178892400	Weak transcription	HUVEC	blood vessel
26	chr3:178887200-178912000	Weak transcription	Thymus	Thymus
27	chr3:178887800-178888000	Enhancers	H1 Cell Line	embryonic stem cell
28	chr3:178887800-178888000	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr3:178887800-178888000	Enhancers	Adipose Nuclei	Adipose
30	chr3:178887800-178888200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:178888000-178889600	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr3:178888000-178898800	Weak transcription	Fetal Brain Male	brain
33	chr3:178888400-178888800	ZNF genes & repeats	Fetal Lung	lung
34	chr3:178888600-178888800	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr3:178888800-178889800	Weak transcription	Fetal Lung	lung
36	chr3:178888800-178896800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr3:178889200-178891600	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr3:178889800-178890800	ZNF genes & repeats	Fetal Lung	lung
39	chr3:178890000-178890400	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr3:178890800-178896600	Weak transcription	Fetal Lung	lung
41	chr3:178891400-178893400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr3:178891600-178892400	Enhancers	Primary T cells fromperipheralblood	blood
43	chr3:178891600-178894000	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr3:178891800-178892200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr3:178891800-178893000	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr3:178891800-178893400	Enhancers	Primary B cells from peripheral blood	blood
47	chr3:178891800-178893400	Enhancers	GM12878-XiMat	blood
48	chr3:178891800-178894200	Enhancers	Primary B cells from cord blood	blood
49	chr3:178891800-178894400	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr3:178891800-178894600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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