Variant report

Variant	esv3390469
Chromosome Location	chr3:160029658-160031831
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	E2F4	chr3:160031291-160031310	MCF10A-Er-Src	breast:	n/a	n/a
2	GATA2	chr3:160030047-160030308	SH-SY5Y	brain:	n/a	n/a
3	GATA3	chr3:160030137-160030350	T-47D	breast:	n/a	n/a
4	GATA3	chr3:160030070-160030200	SH-SY5Y	brain:	n/a	n/a
5	POLR2A	chr3:160029920-160030062	A549	lung:	n/a	n/a
6	STAT3	chr3:160031162-160031370	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160031130..160033296-chr3:160034351..160037164,2	K562	blood:

Variant related genes	Relation type
IFT80	TF binding region

Extended variants
information (count: 72 )
Associated
traits (count: 58 )

Variant overlapped rSNPs/rCNVs (count:72 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs186558058	chr3:160029666-160029667	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs13082240	chr3:160029668-160029669	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs573198117	chr3:160029675-160029676	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs554312932	chr3:160029681-160029682	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs575745299	chr3:160029682-160029683	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs536706344	chr3:160029729-160029730	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs536553741	chr3:160029730-160029731	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs558131933	chr3:160029771-160029772	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs554864354	chr3:160029790-160029791	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs573085277	chr3:160029805-160029806	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs114591798	chr3:160029860-160029861	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs560601360	chr3:160029864-160029865	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs150860133	chr3:160029865-160029866	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs578063948	chr3:160029956-160029957	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs138209424	chr3:160029957-160029958	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs55687857	chr3:160029964-160029965	Weak transcription Strong transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
17	rs531847753	chr3:160029991-160029992	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs62272178	chr3:160030073-160030074	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs75440067	chr3:160030143-160030144	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs565322248	chr3:160030160-160030161	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs531973463	chr3:160030292-160030293	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs73154549	chr3:160030330-160030331	Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs368002928	chr3:160030360-160030361	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs530770767	chr3:160030384-160030385	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs565856133	chr3:160030389-160030390	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs374447000	chr3:160030457-160030458	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs191363310	chr3:160030462-160030463	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs376246378	chr3:160030501-160030502	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs183613798	chr3:160030547-160030548	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs370286821	chr3:160030574-160030575	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs72017904	chr3:160030621-160030622	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs187481910	chr3:160030630-160030631	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs190795034	chr3:160030665-160030666	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs368490573	chr3:160030686-160030687	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs532887718	chr3:160030693-160030694	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs370881844	chr3:160030721-160030722	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs536510224	chr3:160030729-160030730	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs547989377	chr3:160030730-160030731	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs569464776	chr3:160030732-160030733	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs536797335	chr3:160030774-160030775	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs534874512	chr3:160030775-160030776	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs35981629	chr3:160030805-160030806	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs546345968	chr3:160030840-160030841	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs558220054	chr3:160030902-160030903	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs545283923	chr3:160030931-160030932	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs183346456	chr3:160030936-160030937	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs35408236	chr3:160030995-160030996	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs540175106	chr3:160031011-160031012	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs186512662	chr3:160031016-160031017	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs552900073	chr3:160031056-160031057	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:58)

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
head and neck squamous cell carcinoma	17671120	CNVD
Hepatocellular carcinoma	16750200	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myelodysplastic syndrome	21251322	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Basal cell lymphoma	17170743	CNVD
Breast cancer	16608533	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Acute myeloid leukemia	20729466	CNVD
Non-small cell lung cancer	19010865	CNVD
abnormal development	18461090	CNVD
Prostate cancer	18632612	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Colorectal cancer	16272173	CNVD
Prostate cancer	16547154	CNVD
Breast cancer	21364760	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Effusion lymphoma	18079361	CNVD
Prostate cancer	16573809	CNVD
Breast cancer	21785460	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Bladder cancer	21909424	CNVD
Myelofibrosis	22110671	CNVD
Cancer	20164919	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159971400-160035800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:159974200-160038000	Weak transcription	Fetal Brain Male	brain
3	chr3:159975000-160034200	Weak transcription	Fetal Intestine Large	intestine
4	chr3:159975200-160036000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr3:159975600-160046600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:159976200-160039000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr3:159977800-160073000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:159981200-160038200	Weak transcription	Esophagus	oesophagus
9	chr3:159984800-160038200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr3:159988200-160030200	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr3:159992400-160035400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr3:159992800-160033400	Weak transcription	Fetal Kidney	kidney
13	chr3:159992800-160036400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr3:159992800-160036600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr3:159995400-160034200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr3:159996400-160037000	Weak transcription	Primary B cells from cord blood	blood
17	chr3:159996600-160038400	Weak transcription	Brain Hippocampus Middle	brain
18	chr3:159996800-160033600	Weak transcription	Primary B cells from peripheral blood	blood
19	chr3:159997000-160033800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:159997200-160037200	Weak transcription	Brain Angular Gyrus	brain
21	chr3:159997200-160046600	Weak transcription	Fetal Lung	lung
22	chr3:159997600-160035600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr3:159999800-160033800	Weak transcription	Aorta	Aorta
24	chr3:159999800-160034000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:159999800-160035400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr3:159999800-160047800	Weak transcription	Lung	lung
27	chr3:160010000-160033000	Weak transcription	Fetal Intestine Small	intestine
28	chr3:160010000-160034000	Weak transcription	Pancreas	Pancrea
29	chr3:160010000-160047800	Weak transcription	HepG2	liver
30	chr3:160010000-160048600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr3:160010000-160048800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:160010200-160034000	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr3:160010800-160032000	Weak transcription	Fetal Muscle Leg	muscle
34	chr3:160012200-160033000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:160014600-160039400	Weak transcription	GM12878-XiMat	blood
36	chr3:160014800-160037200	Weak transcription	Colon Smooth Muscle	Colon
37	chr3:160014800-160039600	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr3:160015000-160038200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr3:160015000-160044000	Weak transcription	Osteobl	bone
40	chr3:160015400-160048400	Weak transcription	A549	lung
41	chr3:160015800-160048800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:160016800-160030800	Weak transcription	Fetal Heart	heart
43	chr3:160017800-160031000	Weak transcription	Gastric	stomach
44	chr3:160018000-160048600	Weak transcription	HSMM	muscle
45	chr3:160020600-160037600	Weak transcription	NH-A	brain
46	chr3:160021000-160033000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr3:160021200-160043400	Weak transcription	NHDF-Ad	bronchial
48	chr3:160022400-160031600	Weak transcription	HMEC	breast
49	chr3:160022400-160038800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr3:160023000-160036800	Weak transcription	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links