Variant report

Variant	nsv1009143
Chromosome Location	chr3:178731525-178783915
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:54)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:4)

No data

(count:54 , 50 per page) page: 1 2

No.	Distal block	Cell Line	Cell type
1	chr3:178736144..178738008-chr3:178740817..178744400,3	K562	blood:
2	chr3:178733027..178734649-chr3:178978479..178979997,2	K562	blood:
3	chr3:178781078..178783902-chr3:178788373..178789943,2	MCF-7	breast:
4	chr3:178731577..178735974-chr3:179037653..179042692,7	K562	blood:
5	chr3:178734194..178736320-chr3:178865690..178868620,2	K562	blood:
6	chr3:178770676..178772962-chr3:178864857..178866816,2	K562	blood:
7	chr3:178743840..178745524-chr3:178976427..178980039,3	K562	blood:
8	chr3:178733474..178734188-chr3:179040675..179041525,2	MCF-7	breast:
9	chr3:178739768..178742264-chr3:178744553..178747173,2	K562	blood:
10	chr3:178734474..178738470-chr3:179037032..179039856,4	K562	blood:
11	chr3:178733091..178733955-chr3:179038794..179040035,7	MCF-7	breast:
12	chr3:178778004..178779935-chr3:178784372..178786776,2	MCF-7	breast:
13	chr3:178577358..178579188-chr3:178747184..178750158,2	K562	blood:
14	chr3:178751571..178753559-chr3:178782217..178784298,2	K562	blood:
15	chr3:178736144..178738008-chr3:178740817..178744400,3	K562	blood:
16	chr3:178763837..178765875-chr3:178785002..178787931,2	K562	blood:
17	chr3:178742128..178744484-chr3:178786941..178789605,2	MCF-7	breast:
18	chr3:178739768..178742264-chr3:178744553..178747173,2	K562	blood:
19	chr3:178780357..178782332-chr3:178782506..178785505,2	MCF-7	breast:
20	chr3:178733167..178734215-chr3:178815745..178816834,3	MCF-7	breast:
21	chr3:178743208..178744872-chr3:178748172..178749949,2	K562	blood:
22	chr3:178735573..178738499-chr3:179040054..179042168,2	MCF-7	breast:
23	chr3:178754772..178756470-chr3:179039560..179042041,2	MCF-7	breast:
24	chr3:178746545..178749111-chr3:178752950..178755283,2	MCF-7	breast:
25	chr3:178781504..178783011-chr3:178869309..178871100,2	K562	blood:
26	chr3:178780357..178782332-chr3:178782506..178785505,2	MCF-7	breast:
27	chr3:178749053..178750789-chr3:178751564..178754052,2	MCF-7	breast:
28	chr3:178743217..178745083-chr3:178864764..178866616,2	K562	blood:
29	chr3:178749053..178750789-chr3:178751564..178754052,2	MCF-7	breast:
30	chr3:178732575..178734006-chr3:179033177..179034478,10	K562	blood:
31	chr3:178733040..178733565-chr3:179039064..179039702,4	K562	blood:
32	chr3:178732951..178734901-chr3:178785761..178787497,2	K562	blood:
33	chr3:178733361..178735780-chr3:178739021..178740577,2	K562	blood:
34	chr3:178770602..178773150-chr3:178777217..178780693,3	K562	blood:
35	chr3:178737773..178739885-chr3:179056978..179059649,2	K562	blood:
36	chr3:178733073..178733959-chr3:178864672..178865566,2	MCF-7	breast:
37	chr3:178732002..178735693-chr3:178752423..178754842,3	K562	blood:
38	chr3:178726976..178728535-chr3:178731027..178733316,2	K562	blood:
39	chr3:178733385..178733982-chr3:179276676..179277195,2	K562	blood:
40	chr3:178770602..178773150-chr3:178777217..178780693,3	K562	blood:
41	chr3:178753336..178756153-chr3:178870610..178872335,2	K562	blood:
42	chr3:178744477..178746075-chr3:179040271..179042202,2	K562	blood:
43	chr3:178743208..178744872-chr3:178748172..178749949,2	K562	blood:
44	chr3:178780519..178783087-chr3:178791350..178793561,2	MCF-7	breast:
45	chr3:178741511..178744382-chr3:178747703..178750492,2	K562	blood:
46	chr3:178741058..178743011-chr3:178747228..178749203,2	K562	blood:
47	chr3:178746545..178749111-chr3:178752950..178755283,2	MCF-7	breast:
48	chr3:178747112..178748794-chr3:179040862..179042416,2	K562	blood:
49	chr3:178732002..178735693-chr3:178752423..178754842,3	K562	blood:
50	chr3:178741058..178743011-chr3:178747228..178749203,2	K562	blood:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KCNMB2-9	chr3:178739877-178739975	l_2535_chr3:178642424-178743704_colon
2	lnc-KCNMB2-9	chr3:178743681-178743704	l_2535_chr3:178642424-178743704_colon
3	lnc-ZMAT3-4	chr3:178735011-178737876	NONHSAT093385

No data

(count:4 , 50 per page) page: 1

No.	miRNA target gene	miRNA name	Chromosome Location
1	ZMAT3	hsa-miR-192-5p	chr3:178742596-178742616
2	ZMAT3	hsa-miR-215-5p	chr3:178742596-178742616
3	ZMAT3	hsa-miR-215-5p	chr3:178742184-178742202
4	ZMAT3	hsa-miR-192-5p	chr3:178742184-178742202

Variant related genes	Relation type
ENSG00000237978	chromatin interactions
ENSG00000121879	chromatin interactions
ENSG00000229102	chromatin interactions
ENSG00000171121	chromatin interactions
ENSG00000260743	chromatin interactions
ENSG00000121864	chromatin interactions
ENSG00000240429	chromatin interactions
ENSG00000172667	chromatin interactions

Extended variants
information (count: 1877 )
Associated
traits (count: 77 )

Variant overlapped rSNPs/rCNVs (count:1877 , 50 per page) page: 1 2 3 4 5 6 7 ... 38

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs566427437	chr3:178731562-178731563	Enhancers Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs73048041	chr3:178731618-178731619	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs182115291	chr3:178731632-178731633	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs538291606	chr3:178731679-178731680	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs568823577	chr3:178731732-178731733	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs187777154	chr3:178731751-178731752	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs143557810	chr3:178731782-178731783	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs78467104	chr3:178731811-178731812	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs533960370	chr3:178731922-178731923	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs4469018	chr3:178731966-178731967	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs536516336	chr3:178731974-178731975	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs573254005	chr3:178731981-178731982	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs545440706	chr3:178732021-178732022	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs373608845	chr3:178732030-178732031	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs545960903	chr3:178732052-178732053	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs190745129	chr3:178732073-178732074	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs552892875	chr3:178732113-178732114	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs12233569	chr3:178732222-178732223	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs534795175	chr3:178732250-178732251	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs544528474	chr3:178732287-178732288	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs572951462	chr3:178732288-178732289	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs544865515	chr3:178732308-178732309	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs563262282	chr3:178732321-178732322	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs561223369	chr3:178732382-178732383	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs558277288	chr3:178732440-178732441	Active TSS Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs147170557	chr3:178732448-178732449	Active TSS Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs560237051	chr3:178732453-178732454	Active TSS Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs142207135	chr3:178732465-178732466	Active TSS Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs369607176	chr3:178732466-178732467	Active TSS Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs201748383	chr3:178732467-178732468	Active TSS Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs181586883	chr3:178732486-178732487	Active TSS Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs140266815	chr3:178732530-178732531	Active TSS Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs552208919	chr3:178732534-178732535	Active TSS Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs183205324	chr3:178732564-178732565	Active TSS Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs574973515	chr3:178732586-178732587	Active TSS Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs142699121	chr3:178732595-178732596	Active TSS Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs543840331	chr3:178732614-178732615	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs548538578	chr3:178732617-178732618	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs188847661	chr3:178732619-178732620	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs71310373	chr3:178732661-178732662	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs77190931	chr3:178732680-178732681	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs553691366	chr3:178732708-178732709	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs570587720	chr3:178732734-178732735	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs538774384	chr3:178732844-178732845	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs559147739	chr3:178732852-178732853	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs542725613	chr3:178732902-178732903	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs192862133	chr3:178733025-178733026	Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs185025298	chr3:178733028-178733029	Weak transcription Enhancers Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
49	rs187839293	chr3:178733032-178733033	Weak transcription Enhancers Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
50	rs554880979	chr3:178733136-178733137	Weak transcription Enhancers Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:77)

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
Esophageal squamous carcinoma	18350619	CNVD
Myelodysplastic syndrome	21251322	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Breast cancer	16608533	CNVD
Acute myeloid leukemia	20729466	CNVD
Non-small cell lung cancer	19010865	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Prostate cancer	16573809	CNVD
Breast cancer	21785460	CNVD
Breast cancer	17133270	CNVD
epilepsy	18472482	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Myxofibrosarcoma	16751306	CNVD
Parkinson disease	21907011	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Breast cancer	21364760	CNVD
Anaplastic thyroid cancer	17989125	CNVD
Lung adenocarcinoma	19525976	CNVD
Lung cancer	19525976	CNVD
Ovarian cancer	18208621	CNVD
Thyroid cancer	17317825	CNVD
Thyroid cancer	17989125	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Non-small cell lung cancer	21829676	CNVD
Ovarian neoplasms	16753589	CNVD
Breast cancer	21806811	CNVD
Hirschsprung''s Disease	21712996	CNVD
Cancer	16751803	CNVD
abnormal development	18461090	CNVD
lymphocytic leukemia	21291569	CNVD
Autism	19653912	CNVD
Endometrial cancer	19261849	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Esophageal squamous carcinoma	17470683	CNVD
Breast cancer	21509527	CNVD
Myelofibrosis	22110671	CNVD
Prostate cancer	17217626	CNVD
Adenocarcinoma	19607727	CNVD
Squamous cell cancer	19607727	CNVD
Neurodevelopmental disorder	22521361	CNVD
small cell lung cancer	20016488	CNVD
Cancer	20164920	CNVD
Acute lymphoblastic leukemia	18458336	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD
Prostate cancer	18632612	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD
Medulloblastoma	21163964	CNVD

Chromatin state (count:1359 , 50 per page) page: 1 2 3 4 5 6 7 ... 28

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:178708800-178737800	Weak transcription	Colon Smooth Muscle	Colon
2	chr3:178716400-178755000	Weak transcription	Pancreas	Pancrea
3	chr3:178717400-178744400	Weak transcription	HMEC	breast
4	chr3:178719200-178737600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:178719600-178733000	Weak transcription	Primary T cells from cord blood	blood
6	chr3:178720400-178734200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:178720600-178737600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:178721400-178737800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr3:178721400-178738000	Weak transcription	Aorta	Aorta
10	chr3:178722200-178751600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:178723000-178732000	Weak transcription	HSMM	muscle
12	chr3:178723000-178733600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:178723400-178749800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:178723800-178754200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:178727800-178738000	Weak transcription	Fetal Heart	heart
16	chr3:178731200-178731800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
17	chr3:178731200-178735200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:178731400-178731600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr3:178731400-178731600	Genic enhancers	HSMMtube	muscle
20	chr3:178731400-178744400	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr3:178731600-178733200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:178731600-178733200	Weak transcription	GM12878-XiMat	blood
23	chr3:178731600-178733200	Weak transcription	HSMMtube	muscle
24	chr3:178732000-178733200	Strong transcription	HSMM	muscle
25	chr3:178732400-178732600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr3:178732600-178744200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr3:178732800-178738000	Weak transcription	Fetal Thymus	thymus
28	chr3:178733000-178733200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr3:178733000-178733800	Enhancers	Dnd41	blood
30	chr3:178733000-178734200	Enhancers	Primary T cells from cord blood	blood
31	chr3:178733000-178735400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr3:178733000-178735600	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr3:178733000-178738600	Weak transcription	NH-A	brain
34	chr3:178733200-178733400	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr3:178733200-178733400	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr3:178733200-178733800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr3:178733200-178733800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr3:178733200-178733800	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr3:178733200-178733800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr3:178733200-178733800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr3:178733200-178733800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr3:178733200-178733800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr3:178733200-178733800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr3:178733200-178733800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:178733200-178733800	Enhancers	Muscle Satellite Cultured Cells	--
46	chr3:178733200-178733800	Enhancers	Brain Hippocampus Middle	brain
47	chr3:178733200-178733800	Enhancers	Fetal Lung	lung
48	chr3:178733200-178733800	Enhancers	HSMMtube	muscle
49	chr3:178733200-178733800	Enhancers	K562	blood
50	chr3:178733200-178733800	Enhancers	NHDF-Ad	bronchial

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