Variant report

Variant	esv3324373
Chromosome Location	chr3:120031312-120034110
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:120032416..120034924-chr3:120037587..120040555,3	MCF-7	breast:

Extended variants
information (count: 98 )
Associated
traits (count: 57 )

Variant overlapped rSNPs/rCNVs (count:98 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs372081593	chr3:120031363-120031364	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs555880670	chr3:120031372-120031373	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs572561294	chr3:120031398-120031399	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs73856469	chr3:120031409-120031410	Weak transcription Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs190075621	chr3:120031410-120031411	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs369279182	chr3:120031414-120031415	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs536003495	chr3:120031417-120031418	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs576883193	chr3:120031439-120031440	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs143927679	chr3:120031468-120031469	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs374887570	chr3:120031497-120031498	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs6808344	chr3:120031522-120031523	Weak transcription Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs182007075	chr3:120031556-120031557	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs787191	chr3:120031585-120031586	Weak transcription Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs561883031	chr3:120031586-120031587	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs527512392	chr3:120031607-120031608	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs565951260	chr3:120031610-120031611	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs547641814	chr3:120031623-120031624	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs787192	chr3:120031653-120031654	Weak transcription Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs533142180	chr3:120031691-120031692	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs150636399	chr3:120031749-120031750	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs186242689	chr3:120031757-120031758	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs189823380	chr3:120031792-120031793	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs549224924	chr3:120031793-120031794	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs564662435	chr3:120031827-120031828	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs534931359	chr3:120031891-120031892	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs558666675	chr3:120031924-120031925	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs558471688	chr3:120031926-120031927	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs572435719	chr3:120031936-120031937	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs139713385	chr3:120031951-120031952	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs539435201	chr3:120031957-120031958	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs4676695	chr3:120031964-120031965	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs532932462	chr3:120032066-120032067	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs541878107	chr3:120032138-120032139	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs561654474	chr3:120032186-120032187	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs555207569	chr3:120032195-120032196	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs572184492	chr3:120032197-120032198	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs540862623	chr3:120032209-120032210	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs564031055	chr3:120032243-120032244	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs180905763	chr3:120032282-120032283	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs549671612	chr3:120032319-120032320	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs563665191	chr3:120032329-120032330	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs575217466	chr3:120032331-120032332	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs543985444	chr3:120032360-120032361	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs548490986	chr3:120032424-120032425	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
45	rs529292797	chr3:120032460-120032461	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
46	rs787193	chr3:120032474-120032475	Weak transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs34035570	chr3:120032493-120032494	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
48	rs397702356	chr3:120032494-120032495	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
49	rs112327843	chr3:120032495-120032496	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
50	rs545121689	chr3:120032547-120032548	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:57)

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
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
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
Acute lymphoblastic leukemia	21339820	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Breast cancer	16608533	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Developmental delay	22180640	CNVD
Multiple myeloma	17550852	CNVD
Basal cell lymphoma	21115979	CNVD
Ovarian cancer	22174824	CNVD
lymphocytic leukemia	21291569	CNVD
small cell lung cancer	20016488	CNVD
Cancer	20164920	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Glioblastoma multiforme	22286061	CNVD
Neurodevelopmental disorder	22521361	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120024400-120032600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:120024400-120049200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:120024600-120032600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:120025400-120040600	Weak transcription	Fetal Lung	lung
5	chr3:120026600-120042400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:120026600-120060800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:120026800-120032400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:120026800-120032600	Weak transcription	Pancreas	Pancrea
9	chr3:120026800-120049200	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr3:120026800-120067200	Weak transcription	Aorta	Aorta
11	chr3:120028200-120031400	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr3:120029600-120032600	Weak transcription	Primary T cells from cord blood	blood
13	chr3:120030000-120042600	Weak transcription	HMEC	breast
14	chr3:120030400-120032600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr3:120030600-120034200	Weak transcription	Adipose Nuclei	Adipose
16	chr3:120031000-120041200	Weak transcription	Fetal Stomach	stomach
17	chr3:120031000-120042400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr3:120031000-120055600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr3:120031200-120033800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr3:120031400-120031800	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr3:120031400-120032000	Enhancers	GM12878-XiMat	blood
22	chr3:120031400-120040600	Weak transcription	Ovary	ovary
23	chr3:120031400-120042400	Weak transcription	A549	lung
24	chr3:120031600-120032600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr3:120031600-120034600	Weak transcription	Fetal Muscle Leg	muscle
26	chr3:120031800-120033800	Weak transcription	Esophagus	oesophagus
27	chr3:120031800-120034400	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr3:120032200-120034200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr3:120032400-120033200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr3:120032400-120047600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr3:120032600-120032800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr3:120032600-120032800	Flanking Bivalent TSS/Enh	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr3:120032600-120032800	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr3:120032600-120032800	ZNF genes & repeats	Rectal Smooth Muscle	rectum
35	chr3:120032600-120033000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr3:120032600-120033000	Enhancers	Brain Hippocampus Middle	brain
37	chr3:120032600-120033200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr3:120032600-120033200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr3:120032600-120033200	Strong transcription	Primary T cells from cord blood	blood
40	chr3:120032600-120033200	Enhancers	Gastric	stomach
41	chr3:120032600-120033200	Genic enhancers	Pancreas	Pancrea
42	chr3:120032600-120033200	ZNF genes & repeats	Spleen	Spleen
43	chr3:120032600-120033200	ZNF genes & repeats	Dnd41	blood
44	chr3:120032600-120033600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr3:120032800-120033000	Enhancers	Brain Cingulate Gyrus	brain
46	chr3:120032800-120033200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr3:120032800-120033200	Enhancers	Brain Anterior Caudate	brain
48	chr3:120032800-120034200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr3:120032800-120042400	Weak transcription	Rectal Smooth Muscle	rectum
50	chr3:120033000-120042200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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