Variant report

Variant	esv3358022
Chromosome Location	chr3:99628309-99630115
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:99629219..99631187-chr3:99636036..99638648,2	MCF-7	breast:
2	chr3:99626736..99629187-chr3:99773539..99775564,2	MCF-7	breast:
3	chr3:99624361..99628142-chr3:99629982..99633873,3	MCF-7	breast:
4	chr3:99622083..99624890-chr3:99625118..99628705,4	MCF-7	breast:
5	chr3:99594614..99596231-chr3:99626754..99629032,2	MCF-7	breast:
6	chr3:99628880..99629497-chr3:99663053..99663668,2	MCF-7	breast:
7	chr3:99627181..99629035-chr3:99632871..99635218,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168386	chromatin interactions

Extended variants
information (count: 47 )
Associated
traits (count: 52 )

Variant overlapped rSNPs/rCNVs (count:47 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs34518627	chr3:99628352-99628353	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs114702587	chr3:99628392-99628393	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs146061113	chr3:99628407-99628408	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs566814639	chr3:99628458-99628459	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs527845538	chr3:99628513-99628514	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs140003823	chr3:99628520-99628521	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs567574849	chr3:99628562-99628563	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs185911152	chr3:99628589-99628590	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs550347125	chr3:99628606-99628607	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs568821934	chr3:99628636-99628637	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs539189352	chr3:99628641-99628642	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs111599877	chr3:99628669-99628670	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs191754961	chr3:99628674-99628675	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs573082146	chr3:99628721-99628722	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs553958868	chr3:99628770-99628771	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs533924558	chr3:99628775-99628776	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs183275568	chr3:99628782-99628783	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs574022519	chr3:99628867-99628868	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs188101012	chr3:99628896-99628897	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs556309465	chr3:99628998-99628999	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs577942247	chr3:99629011-99629012	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs143526524	chr3:99629086-99629087	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
23	rs62283532	chr3:99629092-99629093	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
24	rs527882567	chr3:99629112-99629113	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
25	rs374235717	chr3:99629211-99629212	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
26	rs115963161	chr3:99629239-99629240	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
27	rs561137425	chr3:99629246-99629247	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
28	rs536315196	chr3:99629256-99629257	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
29	rs74606664	chr3:99629303-99629304	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
30	rs550429299	chr3:99629398-99629399	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
31	rs568785711	chr3:99629435-99629436	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
32	rs532909683	chr3:99629469-99629470	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
33	rs190961167	chr3:99629590-99629591	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
34	rs367810026	chr3:99629636-99629637	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
35	rs577030088	chr3:99629711-99629712	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
36	rs533862428	chr3:99629740-99629741	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
37	rs148884037	chr3:99629770-99629771	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
38	rs567445065	chr3:99629774-99629775	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
39	rs537771485	chr3:99629784-99629785	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
40	rs555150114	chr3:99629824-99629825	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs76686852	chr3:99629933-99629934	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs577968425	chr3:99629963-99629964	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs142608314	chr3:99629999-99630000	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs150974543	chr3:99630013-99630014	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs182343867	chr3:99630069-99630070	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs535590632	chr3:99630093-99630094	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs558963550	chr3:99630104-99630105	Enhancers Weak transcription	n/a	n/a	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:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99600800-99638600	Weak transcription	Left Ventricle	heart
2	chr3:99604600-99648200	Weak transcription	Primary T cells from cord blood	blood
3	chr3:99616000-99631200	Weak transcription	Primary B cells from cord blood	blood
4	chr3:99619600-99644400	Weak transcription	Right Ventricle	heart
5	chr3:99620000-99629800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr3:99620000-99638600	Weak transcription	Small Intestine	intestine
7	chr3:99620800-99628400	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr3:99620800-99628600	Weak transcription	Colon Smooth Muscle	Colon
9	chr3:99621200-99638600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr3:99621400-99628600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr3:99621400-99628600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr3:99621400-99629800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr3:99621600-99628600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:99623000-99628600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:99623000-99628600	Weak transcription	HUVEC	blood vessel
16	chr3:99623000-99629600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:99623200-99628400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:99623200-99629400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr3:99624200-99628800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:99624800-99628600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:99624800-99628600	Weak transcription	NHDF-Ad	bronchial
22	chr3:99625000-99632800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr3:99625000-99639400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:99626200-99630000	Enhancers	HepG2	liver
25	chr3:99626600-99629000	Enhancers	Liver	Liver
26	chr3:99626800-99628600	Enhancers	A549	lung
27	chr3:99626800-99629800	Weak transcription	Fetal Muscle Leg	muscle
28	chr3:99626800-99631200	Enhancers	NHEK	skin
29	chr3:99627200-99628600	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr3:99627200-99630000	Enhancers	Hela-S3	cervix
31	chr3:99627200-99630600	Enhancers	Stomach Mucosa	stomach
32	chr3:99627200-99638600	Weak transcription	K562	blood
33	chr3:99627400-99628800	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr3:99627400-99629200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr3:99627800-99631200	Enhancers	HMEC	breast
36	chr3:99628000-99629800	Enhancers	Placenta Amnion	Placenta Amnion
37	chr3:99628000-99630600	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr3:99628000-99631200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr3:99628200-99628800	Enhancers	Psoas Muscle	Psoas
40	chr3:99628200-99629000	Enhancers	HSMM	muscle
41	chr3:99628200-99629400	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr3:99628200-99629600	Weak transcription	HSMMtube	muscle
43	chr3:99628200-99629800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr3:99628200-99630400	Weak transcription	Fetal Kidney	kidney
45	chr3:99628200-99630600	Enhancers	Osteobl	bone
46	chr3:99628400-99630600	Enhancers	NH-A	brain
47	chr3:99628400-99630800	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr3:99628400-99630800	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr3:99628400-99631400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr3:99628600-99628800	Enhancers	ES-WA7 Cell Line	embryonic stem cell

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