Variant report

Variant	nsv963570
Chromosome Location	chr3:161076656-161088849
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:46)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:46 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:160999506..161001764-chr3:161085890..161088412,2	MCF-7	breast:
2	chr3:160282107..160285570-chr3:161087865..161089951,3	MCF-7	breast:
3	chr16:83986674..83988846-chr3:161086778..161089338,2	MCF-7	breast:
4	chr3:160962510..160966697-chr3:161085167..161089151,3	MCF-7	breast:
5	chr17:57181517..57184200-chr3:161086879..161089854,2	MCF-7	breast:
6	chr10:3825671..3828241-chr3:161086476..161088870,2	MCF-7	breast:
7	chr15:99190324..99192171-chr3:161086732..161088826,2	MCF-7	breast:
8	chr17:58040687..58043660-chr3:161087957..161089475,2	MCF-7	breast:
9	chr3:161041894..161044446-chr3:161076689..161079941,3	MCF-7	breast:
10	chr3:161087613..161089123-chr3:161278946..161281684,2	MCF-7	breast:
11	chr3:160934982..160947568-chr3:161079696..161093037,40	MCF-7	breast:
12	chr22:31475291..31477772-chr3:161087457..161089639,2	MCF-7	breast:
13	chr3:161086150..161088854-chr6:26156323..26158210,2	MCF-7	breast:
14	chr13:37572263..37575251-chr3:161088174..161090196,2	MCF-7	breast:
15	chr3:160956184..160959035-chr3:161087488..161089202,2	MCF-7	breast:
16	chr2:178075634..178077444-chr3:161081913..161083742,2	MCF-7	breast:
17	chr1:149858017..149860169-chr3:161088036..161090033,2	MCF-7	breast:
18	chr2:97535160..97536953-chr3:161088031..161090726,2	MCF-7	breast:
19	chr3:64035675..64038032-chr3:161075125..161077341,2	MCF-7	breast:
20	chr3:161040142..161042354-chr3:161082440..161084651,2	MCF-7	breast:
21	chr3:160817799..160820067-chr3:161084630..161087125,2	MCF-7	breast:
22	chr3:160817108..160819298-chr3:161076893..161078523,2	MCF-7	breast:
23	chr3:160813033..160824577-chr3:161083489..161092050,35	MCF-7	breast:
24	chr12:12713891..12716367-chr3:161087265..161090021,2	MCF-7	breast:
25	chr16:89786488..89788334-chr3:161087418..161089454,2	MCF-7	breast:
26	chr3:161087384..161090083-chr9:131900097..131902606,2	MCF-7	breast:
27	chr20:31169325..31171437-chr3:161088010..161089511,2	MCF-7	breast:
28	chr3:161088166..161091113-chr7:44082932..44085823,2	MCF-7	breast:
29	chr3:160819385..160821536-chr3:161081853..161083436,2	MCF-7	breast:
30	chr3:160787784..160789478-chr3:161085891..161088171,2	MCF-7	breast:
31	chr3:160790555..160793419-chr3:161085897..161087405,2	MCF-7	breast:
32	chr3:161038392..161046344-chr3:161085640..161093564,25	MCF-7	breast:
33	chr2:199451456..199452956-chr3:161085880..161088129,3	MCF-7	breast:
34	chr20:45948103..45949754-chr3:161086879..161089062,2	MCF-7	breast:
35	chr3:160936365..160960187-chr3:161078472..161094658,51	MCF-7	breast:
36	chr3:63914213..63915723-chr3:161085984..161088284,2	MCF-7	breast:
37	chr3:136470318..136472005-chr3:161088059..161090755,2	MCF-7	breast:
38	chr11:46622262..46624365-chr3:161085688..161088044,2	MCF-7	breast:
39	chr3:160970393..160971997-chr3:161083737..161085470,2	MCF-7	breast:
40	chr20:49346270..49349571-chr3:161087854..161090885,3	MCF-7	breast:
41	chr3:161088340..161091318-chr9:131938931..131941651,2	MCF-7	breast:
42	chr3:161024873..161027806-chr3:161085286..161087243,2	MCF-7	breast:
43	chr3:161087820..161090854-chr7:26238154..26241381,3	MCF-7	breast:
44	chr3:160502508..160504789-chr3:161086438..161088676,2	MCF-7	breast:
45	chr14:19019125..19019628-chr3:161087703..161088203,2	MCF-7	breast:
46	chr3:161088194..161090248-chr9:137216086..137218582,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-B3GALNT1-3	chr3:161077087-161077682	NONHSAT093015

No data

Variant related genes	Relation type
ENSG00000184270	chromatin interactions
ENSG00000229320	chromatin interactions
ENSG00000224738	chromatin interactions
ENSG00000229337	chromatin interactions
ENSG00000271052	chromatin interactions
ENSG00000170144	chromatin interactions
ENSG00000186350	chromatin interactions
ENSG00000228156	chromatin interactions
ENSG00000183963	chromatin interactions
ENSG00000267302	chromatin interactions
ENSG00000118007	chromatin interactions
ENSG00000178096	chromatin interactions
ENSG00000122565	chromatin interactions
ENSG00000186432	chromatin interactions
ENSG00000240138	chromatin interactions
ENSG00000120697	chromatin interactions
ENSG00000261758	chromatin interactions
ENSG00000136279	chromatin interactions
ENSG00000168298	chromatin interactions
ENSG00000075399	chromatin interactions
ENSG00000204055	chromatin interactions
ENSG00000119383	chromatin interactions
ENSG00000108395	chromatin interactions
ENSG00000189050	chromatin interactions
ENSG00000067082	chromatin interactions
ENSG00000184260	chromatin interactions
ENSG00000259424	chromatin interactions
ENSG00000169251	chromatin interactions
ENSG00000158805	chromatin interactions
ENSG00000124171	chromatin interactions
ENSG00000120699	chromatin interactions
ENSG00000184678	chromatin interactions
ENSG00000169255	chromatin interactions
ENSG00000122566	chromatin interactions
ENSG00000111266	chromatin interactions
ENSG00000168758	chromatin interactions
ENSG00000140961	chromatin interactions
ENSG00000188483	chromatin interactions

Extended variants
information (count: 433 )
Associated
traits (count: 58 )

Variant overlapped rSNPs/rCNVs (count:433 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs562339698	chr3:161076668-161076669	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs529719146	chr3:161076788-161076789	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs549494151	chr3:161076811-161076812	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs377329271	chr3:161076841-161076842	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs538349689	chr3:161076842-161076843	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs146479579	chr3:161076864-161076865	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs548657785	chr3:161076870-161076871	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs9811652	chr3:161076890-161076891	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs200004973	chr3:161076897-161076898	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs73878307	chr3:161076899-161076900	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs566645881	chr3:161076901-161076902	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs574631115	chr3:161076946-161076947	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs537494423	chr3:161077029-161077030	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs557075845	chr3:161077055-161077056	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs534821868	chr3:161077089-161077090	Weak transcription Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
16	rs182823380	chr3:161077090-161077091	Weak transcription Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
17	rs188196359	chr3:161077111-161077112	Weak transcription Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
18	rs375012655	chr3:161077132-161077133	Weak transcription Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
19	rs75446164	chr3:161077133-161077134	Weak transcription Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
20	rs336592	chr3:161077186-161077187	Weak transcription Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs73019416	chr3:161077200-161077201	Weak transcription Strong transcription Enhancers	Chromatin interactive region lncRNA	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs1450523	chr3:161077270-161077271	Weak transcription Strong transcription Enhancers	Chromatin interactive region lncRNA	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
23	rs531100220	chr3:161077303-161077304	Weak transcription Strong transcription Enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
24	rs549793391	chr3:161077306-161077307	Weak transcription Strong transcription Enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
25	rs16832129	chr3:161077361-161077362	Weak transcription Strong transcription Enhancers	Chromatin interactive region lncRNA	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs540113991	chr3:161077362-161077363	Weak transcription Strong transcription Enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
27	rs532615874	chr3:161077383-161077384	Weak transcription Strong transcription Enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
28	rs75052295	chr3:161077385-161077386	Weak transcription Strong transcription Enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
29	rs192759421	chr3:161077396-161077397	Weak transcription Strong transcription Enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
30	rs368423954	chr3:161077400-161077401	Weak transcription Active TSS Strong transcription Enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
31	rs565417874	chr3:161077407-161077408	Weak transcription Active TSS Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
32	rs534543440	chr3:161077414-161077415	Weak transcription Active TSS Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
33	rs62279924	chr3:161077439-161077440	Weak transcription Active TSS Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs568391719	chr3:161077455-161077456	Weak transcription Active TSS Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
35	rs28548802	chr3:161077484-161077485	Weak transcription Active TSS Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs557180461	chr3:161077493-161077494	Weak transcription Active TSS Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
37	rs570772245	chr3:161077520-161077521	Weak transcription Active TSS Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
38	rs28425747	chr3:161077521-161077522	Weak transcription Active TSS Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs564982103	chr3:161077577-161077578	Weak transcription Active TSS Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
40	rs553530644	chr3:161077586-161077587	Weak transcription Active TSS Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
41	rs1450522	chr3:161077630-161077631	Weak transcription Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
42	rs542481047	chr3:161077653-161077654	Weak transcription Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
43	rs61743491	chr3:161077670-161077671	Weak transcription Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
44	rs111883766	chr3:161077685-161077686	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs189231095	chr3:161077724-161077725	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
46	rs192384759	chr3:161077740-161077741	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
47	rs544584558	chr3:161077745-161077746	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
48	rs540057498	chr3:161077751-161077752	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
49	rs151158563	chr3:161077787-161077788	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
50	rs9874588	chr3:161077849-161077850	Weak transcription	Chromatin interactive region	2 gene(s)	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
Esophageal squamous carcinoma	18350619	CNVD
Myelodysplastic syndrome	21251322	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Breast cancer	16608533	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
Prostate cancer	16573809	CNVD
Breast cancer	21785460	CNVD
Bladder cancer	21909424	CNVD
Myelofibrosis	22110671	CNVD
Intellectual disability	21811512	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD
Sudden cardiac death	19188705	CNVD
Mantle cell lymphoma	19029149	CNVD
Malformation	19546859	CNVD
Schizophrenia	19546859	CNVD
Breast cancer	17133270	CNVD

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:161059800-161089200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:161064400-161083000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:161068200-161083200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:161068400-161083200	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr3:161068800-161079000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:161071600-161077000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr3:161076000-161077400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:161076200-161077200	Weak transcription	Esophagus	oesophagus
9	chr3:161076200-161083200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:161077000-161077800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:161077200-161077400	Enhancers	Esophagus	oesophagus
12	chr3:161077400-161077600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:161077800-161079800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr3:161079000-161081800	Enhancers	Pancreatic Islets	Pancreatic Islet
15	chr3:161081000-161081200	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr3:161081200-161082200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr3:161081600-161082400	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr3:161081800-161087200	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr3:161082200-161083800	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr3:161082400-161082800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr3:161082800-161084400	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr3:161083000-161083200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr3:161083000-161083800	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr3:161083000-161084000	Enhancers	H1 Cell Line	embryonic stem cell
25	chr3:161083000-161084000	Enhancers	H9 Cell Line	embryonic stem cell
26	chr3:161083000-161084400	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr3:161083000-161084800	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr3:161083200-161084400	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr3:161083200-161084600	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr3:161083200-161084800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr3:161083600-161084400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
32	chr3:161083800-161084000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
33	chr3:161083800-161084200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
34	chr3:161084000-161084200	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr3:161084000-161085200	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr3:161084000-161085400	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr3:161084200-161084400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr3:161084200-161084600	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr3:161084400-161085600	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr3:161084400-161087400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr3:161084400-161088400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr3:161084400-161088800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr3:161084600-161085000	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr3:161084600-161088200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr3:161084800-161085200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr3:161084800-161085400	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr3:161085000-161085200	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr3:161085200-161085400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr3:161085200-161085600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr3:161085200-161085800	Enhancers	H9 Cell Line	embryonic stem cell

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