Variant report

Variant	esv3504892
Chromosome Location	chr3:42837523-42841746
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	BACH1	chr3:42838053-42838294	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAFK	chr3:42838158-42838283	HepG2	liver:	n/a	n/a
3	MAFK	chr3:42838056-42838338	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr3:42840875-42841890	HepG2	liver:	n/a	n/a
5	POLR2A	chr3:42840854-42841324	K562	blood:	n/a	n/a
6	POLR2A	chr3:42837920-42838052	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr3:42836985-42838378	K562	blood:	n/a	n/a
8	POLR2A	chr3:42840834-42841169	K562	blood:	n/a	n/a
9	POLR2A	chr3:42841353-42841404	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr3:42836861-42838374	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr3:42837860-42838350	HepG2	liver:	n/a	n/a
12	POLR2A	chr3:42841500-42841615	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr3:42840808-42841275	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr3:42840849-42841520	K562	blood:	n/a	n/a
15	POLR2A	chr3:42838190-42838248	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr3:42837575-42837630	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr3:42837466-42837655	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr3:42840954-42841076	HepG2	liver:	n/a	n/a
19	POLR2A	chr3:42837965-42838078	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr3:42837543-42837554	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr3:42837886-42838464	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr3:42837563-42837644	HepG2	liver:	n/a	n/a
23	POLR2A	chr3:42838156-42838349	HepG2	liver:	n/a	n/a
24	POLR2A	chr3:42838110-42838126	HepG2	liver:	n/a	n/a
25	POLR2A	chr3:42837558-42837565	HepG2	liver:	n/a	n/a
26	POLR2A	chr3:42837143-42837725	HepG2	liver:	n/a	n/a
27	SETDB1	chr3:42837499-42838255	U2OS	brain:	n/a	n/a
28	SIN3A	chr3:42838069-42838090	H1-hESC	embryonic stem cell:	n/a	n/a
29	STAT3	chr3:42837923-42837934	MCF10A-Er-Src	breast:	n/a	n/a
30	TBL1XR1	chr3:42838106-42838140	K562	blood:	n/a	n/a
31	TCF7L2	chr3:42837063-42837715	HEK293	kidney:	n/a	chr3:42837248-42837264 chr3:42837248-42837264 chr3:42837252-42837261 chr3:42837249-42837263 chr3:42837546-42837555 chr3:42837250-42837260
32	ZNF384	chr3:42838014-42838052	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:42830549..42834930-chr3:42834971..42839390,5	K562	blood:
2	chr3:42601326..42604045-chr3:42837393..42838978,2	K562	blood:
3	chr3:42631172..42633792-chr3:42841692..42844503,2	K562	blood:
4	chr3:42840530..42842881-chr6:27858992..27861024,2	MCF-7	breast:
5	chr3:42824804..42827092-chr3:42834818..42838109,3	K562	blood:
6	chr3:42833054..42839463-chr3:42839853..42848908,22	MCF-7	breast:

Variant related genes	Relation type
ACKR2	TF binding region
ENSG00000197153	chromatin interactions
ENSG00000144648	chromatin interactions
ENSG00000181061	chromatin interactions
ENSG00000233224	chromatin interactions
ENSG00000008324	chromatin interactions

Extended variants
information (count: 81 )
Associated
traits (count: 89 )

Variant overlapped rSNPs/rCNVs (count:81 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs564138868	chr3:42837523-42837524	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs535995283	chr3:42837599-42837600	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs533124391	chr3:42837600-42837601	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs139690938	chr3:42837625-42837626	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs145604583	chr3:42837658-42837659	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs191501325	chr3:42837684-42837685	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs544451924	chr3:42837691-42837692	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs183110297	chr3:42837694-42837695	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs562784619	chr3:42837743-42837744	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs567246576	chr3:42837787-42837788	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs368258688	chr3:42837811-42837812	Weak transcription Enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs548176056	chr3:42837868-42837869	Weak transcription Enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs369668261	chr3:42837882-42837883	Weak transcription Enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs568067399	chr3:42837909-42837910	Weak transcription Enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs149809350	chr3:42837910-42837911	Weak transcription Enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs143969215	chr3:42837927-42837928	Weak transcription Enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs200319751	chr3:42837938-42837939	Weak transcription Enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs67866715	chr3:42837939-42837940	Weak transcription Enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs60899296	chr3:42837940-42837941	Weak transcription Enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs10719438	chr3:42837948-42837949	Weak transcription Enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs371755253	chr3:42837949-42837950	Weak transcription Enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs556024983	chr3:42837971-42837972	Weak transcription Enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs569762115	chr3:42838002-42838003	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs535493379	chr3:42838018-42838019	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs73077214	chr3:42838020-42838021	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs542073078	chr3:42838059-42838060	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs572032931	chr3:42838179-42838180	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs34336220	chr3:42838213-42838214	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs113018903	chr3:42838344-42838345	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs374981004	chr3:42838374-42838375	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
31	rs188234935	chr3:42838414-42838415	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
32	rs558012665	chr3:42838530-42838531	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
33	rs543596103	chr3:42838531-42838532	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs573613125	chr3:42838546-42838547	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs562888935	chr3:42838547-42838548	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs531696391	chr3:42838651-42838652	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
37	rs541881598	chr3:42838653-42838654	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
38	rs561761912	chr3:42838655-42838656	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
39	rs28516936	chr3:42838746-42838747	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
40	rs536463650	chr3:42839117-42839118	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
41	rs557559118	chr3:42839317-42839318	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
42	rs539669342	chr3:42839334-42839335	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs527656671	chr3:42839923-42839924	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs532630050	chr3:42840789-42840790	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs77006856	chr3:42840810-42840811	Weak transcription Enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
46	rs547810626	chr3:42840836-42840837	Weak transcription Enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
47	rs370239541	chr3:42840845-42840846	Weak transcription Enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
48	rs527825187	chr3:42840849-42840850	Weak transcription Enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
49	rs552394138	chr3:42840858-42840859	Weak transcription Enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
50	rs564465082	chr3:42840874-42840875	Weak transcription Enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:89)

Disease	PMID	Source
Glioblastoma multiforme	21080181	CNVD
Neuroblastoma	18923191	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
Oral squamous cell carcinoma	17134496	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
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Esophageal cancer	20955586	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Breast cancer	17133270	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Melanoma	20688739	CNVD
Acute myeloid leukemia	21251322	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21183584	CNVD
Wilms tumour	17204608	CNVD
Biliary cancer	19435499	CNVD
Non-small cell lung cancer	20864512	CNVD
Non-small cell lung cancer	21829676	CNVD
Kartagener syndrome	16639409	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Breast cancer	21509527	CNVD
Melanoma	21693616	CNVD
Myelofibrosis	22110671	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Breast cancer	20409316	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Breast cancer	21364760	CNVD
abnormal development	18461090	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:238 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42814800-42840800	Weak transcription	Spleen	Spleen
2	chr3:42815200-42842000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr3:42815200-42842200	Weak transcription	Aorta	Aorta
4	chr3:42815200-42842400	Weak transcription	Psoas Muscle	Psoas
5	chr3:42815400-42844000	Weak transcription	NHDF-Ad	bronchial
6	chr3:42815600-42841800	Weak transcription	Thymus	Thymus
7	chr3:42815600-42842000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr3:42815600-42842000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr3:42816200-42837600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr3:42822000-42841200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr3:42822400-42843400	Weak transcription	Small Intestine	intestine
12	chr3:42822800-42841600	Weak transcription	Brain Substantia Nigra	brain
13	chr3:42822800-42842800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:42822800-42844000	Weak transcription	Fetal Kidney	kidney
15	chr3:42822800-42844200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr3:42823000-42842800	Weak transcription	Fetal Brain Male	brain
17	chr3:42825200-42843800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr3:42825600-42841000	Weak transcription	Gastric	stomach
19	chr3:42826800-42838400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:42827600-42844600	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr3:42828000-42840800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr3:42828400-42841000	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr3:42828600-42844000	Weak transcription	NH-A	brain
24	chr3:42829800-42838200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:42830000-42840800	Weak transcription	Primary B cells from peripheral blood	blood
26	chr3:42830200-42841000	Weak transcription	Stomach Mucosa	stomach
27	chr3:42830400-42844000	Weak transcription	NHEK	skin
28	chr3:42830800-42841800	Weak transcription	Fetal Thymus	thymus
29	chr3:42832600-42838400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:42832800-42842000	Weak transcription	Fetal Heart	heart
31	chr3:42832800-42843800	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr3:42834400-42838000	Strong transcription	K562	blood
33	chr3:42835200-42842200	Weak transcription	Fetal Lung	lung
34	chr3:42835400-42838000	Weak transcription	Fetal Muscle Leg	muscle
35	chr3:42835400-42841000	Weak transcription	Pancreas	Pancrea
36	chr3:42835400-42841200	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr3:42835400-42841200	Weak transcription	Rectal Smooth Muscle	rectum
38	chr3:42835400-42841800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr3:42835400-42842400	Weak transcription	Right Ventricle	heart
40	chr3:42835400-42842600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr3:42835400-42843400	Weak transcription	Colonic Mucosa	Colon
42	chr3:42835400-42843400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr3:42835400-42843400	Weak transcription	HSMMtube	muscle
44	chr3:42835400-42844000	Weak transcription	Osteobl	bone
45	chr3:42835400-42844200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr3:42835400-42844200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr3:42835400-42844200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr3:42835400-42844200	Weak transcription	Fetal Stomach	stomach
49	chr3:42835400-42844200	Weak transcription	A549	lung
50	chr3:42835400-42844200	Weak transcription	HUVEC	blood vessel

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