Variant report

Variant	esv3325883
Chromosome Location	chr3:99684162-99687960
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	chr3:99686723-99686915	Hela-S3	cervix:	n/a	n/a
2	CEBPB	chr3:99683854-99684216	IMR90	lung:	n/a	n/a
3	CEBPB	chr3:99686640-99686999	IMR90	lung:	n/a	n/a
4	E2F4	chr3:99684899-99684995	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr3:99683897-99684237	MCF10A-Er-Src	breast:	n/a	chr3:99684063-99684071
6	FOS	chr3:99683861-99684299	MCF10A-Er-Src	breast:	n/a	chr3:99684063-99684071
7	FOS	chr3:99683884-99684263	MCF10A-Er-Src	breast:	n/a	chr3:99684063-99684071
8	FOS	chr3:99687954-99688299	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr3:99683861-99684263	MCF10A-Er-Src	breast:	n/a	chr3:99684063-99684071
10	FOS	chr3:99686657-99687046	MCF10A-Er-Src	breast:	n/a	n/a
11	FOS	chr3:99686646-99687001	MCF10A-Er-Src	breast:	n/a	n/a
12	FOS	chr3:99686659-99687005	MCF10A-Er-Src	breast:	n/a	n/a
13	FOS	chr3:99685062-99685074	MCF10A-Er-Src	breast:	n/a	n/a
14	FOS	chr3:99686631-99687043	MCF10A-Er-Src	breast:	n/a	n/a
15	GATA3	chr3:99686545-99687188	SK-N-SH	brain:	n/a	n/a
16	GATA3	chr3:99686528-99687225	SK-N-SH	brain:	n/a	n/a
17	GATA3	chr3:99686612-99686985	MCF-7	breast:	n/a	n/a
18	GATA3	chr3:99686626-99686981	T-47D	breast:	n/a	n/a
19	GATA3	chr3:99686504-99687112	MCF-7	breast:	n/a	n/a
20	JUND	chr3:99686771-99686841	K562	blood:	n/a	n/a
21	MAFK	chr3:99683930-99684241	HepG2	liver:	n/a	n/a
22	MAFK	chr3:99683956-99684225	IMR90	lung:	n/a	n/a
23	MYC	chr3:99683967-99684327	MCF10A-Er-Src	breast:	n/a	n/a
24	MYC	chr3:99683923-99684337	MCF10A-Er-Src	breast:	n/a	n/a
25	MYC	chr3:99686724-99687005	MCF10A-Er-Src	breast:	n/a	n/a
26	MYC	chr3:99686660-99687060	MCF10A-Er-Src	breast:	n/a	n/a
27	POLR2A	chr3:99684701-99684719	MCF-7	breast:	n/a	n/a
28	POLR2A	chr3:99683833-99684327	MCF10A-Er-Src	breast:	n/a	n/a
29	POLR2A	chr3:99686880-99686892	MCF10A-Er-Src	breast:	n/a	n/a
30	POLR2A	chr3:99686351-99686982	H1-neurons	neurons:	n/a	n/a
31	POLR2A	chr3:99686581-99687020	MCF10A-Er-Src	breast:	n/a	n/a
32	POLR2A	chr3:99686485-99686965	H1-neurons	neurons:	n/a	n/a
33	STAT3	chr3:99683916-99684235	MCF10A-Er-Src	breast:	n/a	n/a
34	STAT3	chr3:99683881-99684172	MCF10A-Er-Src	breast:	n/a	n/a
35	STAT3	chr3:99683903-99684212	MCF10A-Er-Src	breast:	n/a	n/a
36	STAT3	chr3:99686840-99686910	MCF10A-Er-Src	breast:	n/a	n/a
37	STAT3	chr3:99686595-99686960	MCF10A-Er-Src	breast:	n/a	n/a
38	STAT3	chr3:99686710-99686974	MCF10A-Er-Src	breast:	n/a	n/a
39	USF2	chr3:99684275-99684295	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:99686804..99688799-chr3:99690706..99692750,2	MCF-7	breast:
2	chr3:99683725..99685720-chr3:99687425..99689237,2	MCF-7	breast:
3	chr3:99684840..99686543-chr3:99978018..99980934,2	MCF-7	breast:
4	chr3:99686155..99688649-chr3:99689841..99691929,2	MCF-7	breast:
5	chr3:99683941..99686099-chr3:99690442..99692720,2	MCF-7	breast:
6	chr3:99683725..99685720-chr3:99687425..99689237,2	MCF-7	breast:
7	chr3:99592456..99594885-chr3:99685238..99688172,2	MCF-7	breast:

Variant related genes	Relation type
MIR3921	TF binding region
ENSG00000036054	chromatin interactions

Extended variants
information (count: 135 )
Associated
traits (count: 52 )

Variant overlapped rSNPs/rCNVs (count:135 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs76406835	chr3:99684173-99684174	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs549916421	chr3:99684205-99684206	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs148435031	chr3:99684221-99684222	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs141658014	chr3:99684266-99684267	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs547365746	chr3:99684274-99684275	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs566124228	chr3:99684316-99684317	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs536625535	chr3:99684319-99684320	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs555136391	chr3:99684321-99684322	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs576572170	chr3:99684329-99684330	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs537269297	chr3:99684341-99684342	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs559061700	chr3:99684362-99684363	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs200985339	chr3:99684373-99684374	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs368333208	chr3:99684382-99684383	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs551378741	chr3:99684474-99684475	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
15	rs577479520	chr3:99684523-99684524	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
16	rs541753416	chr3:99684541-99684542	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
17	rs559617623	chr3:99684595-99684596	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
18	rs571739349	chr3:99684621-99684622	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
19	rs200868525	chr3:99684662-99684663	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
20	rs566452652	chr3:99684686-99684687	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
21	rs190132562	chr3:99684688-99684689	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
22	rs150512364	chr3:99684695-99684696	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
23	rs531386889	chr3:99684698-99684699	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
24	rs533925383	chr3:99684728-99684729	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
25	rs77854514	chr3:99684749-99684750	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
26	rs565127610	chr3:99684754-99684755	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
27	rs532203854	chr3:99684756-99684757	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
28	rs547740084	chr3:99684776-99684777	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
29	rs139458654	chr3:99684791-99684792	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
30	rs555149789	chr3:99684806-99684807	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
31	rs6805884	chr3:99684808-99684809	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
32	rs74921744	chr3:99684916-99684917	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
33	rs570166272	chr3:99684949-99684950	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs182665444	chr3:99685036-99685037	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs558776336	chr3:99685116-99685117	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs140862778	chr3:99685147-99685148	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs146629095	chr3:99685185-99685186	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs74890908	chr3:99685243-99685244	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs534886493	chr3:99685253-99685254	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs187575731	chr3:99685254-99685255	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs574762468	chr3:99685260-99685261	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs538448716	chr3:99685297-99685298	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs373315273	chr3:99685329-99685330	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs542216333	chr3:99685345-99685346	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs554100387	chr3:99685358-99685359	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs140147334	chr3:99685359-99685360	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs377730434	chr3:99685390-99685391	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs556746514	chr3:99685392-99685393	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs578254754	chr3:99685456-99685457	Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs74560952	chr3:99685458-99685459	Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:52)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Renal cell carcinoma	21668985	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Hirschsprung''s Disease	21712996	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21183584	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Prostate cancer	21965145	CNVD
Cancer	21129771	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Cervical cancer	21062161	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Bipolar disorder	18458673	CNVD
Breast cancer	22032731	CNVD
Neurodevelopmental disorder	22521361	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
microdeletion syndrome	22180640	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
Myelofibrosis	22110671	CNVD
Epilepsy	21858020	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
small cell lung cancer	20016488	CNVD

Chromatin state (count:134 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99657600-99686600	Weak transcription	Primary B cells from cord blood	blood
2	chr3:99671600-99684200	Weak transcription	NHEK	skin
3	chr3:99671600-99688200	Weak transcription	Primary T cells from cord blood	blood
4	chr3:99677400-99696600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr3:99677600-99684400	Weak transcription	Fetal Stomach	stomach
6	chr3:99677600-99684400	Weak transcription	Pancreas	Pancrea
7	chr3:99677600-99684600	Weak transcription	Lung	lung
8	chr3:99677600-99692600	Weak transcription	Fetal Lung	lung
9	chr3:99678800-99691800	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr3:99679400-99684400	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr3:99679600-99688200	Weak transcription	GM12878-XiMat	blood
12	chr3:99679600-99697000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr3:99680000-99684400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr3:99680200-99684200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr3:99680200-99684400	Weak transcription	Duodenum Mucosa	Duodenum
16	chr3:99680600-99685600	Weak transcription	Adipose Nuclei	Adipose
17	chr3:99681000-99684800	Weak transcription	Fetal Muscle Leg	muscle
18	chr3:99681000-99685800	Weak transcription	Fetal Heart	heart
19	chr3:99681200-99684200	Weak transcription	Ovary	ovary
20	chr3:99681200-99684200	Weak transcription	Small Intestine	intestine
21	chr3:99681200-99684800	Weak transcription	Right Atrium	heart
22	chr3:99681200-99685600	Weak transcription	Gastric	stomach
23	chr3:99682000-99684600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:99682000-99685000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr3:99682200-99684200	Weak transcription	HSMM	muscle
26	chr3:99682200-99684600	Weak transcription	Colon Smooth Muscle	Colon
27	chr3:99682400-99684200	Weak transcription	HSMMtube	muscle
28	chr3:99682400-99685600	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr3:99683000-99684600	Enhancers	HepG2	liver
30	chr3:99683000-99687200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:99683200-99684400	Enhancers	Stomach Mucosa	stomach
32	chr3:99683200-99685000	Enhancers	Muscle Satellite Cultured Cells	--
33	chr3:99683200-99685600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr3:99683200-99685600	Enhancers	Fetal Intestine Large	intestine
35	chr3:99683200-99685800	Enhancers	Left Ventricle	heart
36	chr3:99683200-99686000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr3:99683200-99686400	Enhancers	Fetal Intestine Small	intestine
38	chr3:99683400-99684400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:99683400-99684400	Weak transcription	Psoas Muscle	Psoas
40	chr3:99683400-99684600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:99683400-99684800	Enhancers	Osteobl	bone
42	chr3:99683400-99685000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:99683400-99685000	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr3:99683400-99685400	Enhancers	Aorta	Aorta
45	chr3:99683400-99685400	Enhancers	HMEC	breast
46	chr3:99683400-99687000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr3:99683400-99687200	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr3:99683600-99684400	Weak transcription	Right Ventricle	heart
49	chr3:99683600-99685000	Enhancers	Hela-S3	cervix
50	chr3:99683600-99685200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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