Variant report

Variant	nsv1007459
Chromosome Location	chr3:112099647-112113334
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	chr3:112090607..112092226-chr3:112097134..112099677,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BTLA-1	chr3:112100753-112100776	NONHSAT091168
2	lnc-BTLA-1	chr3:112100753-112100776	NONHSAT091176
3	lnc-BTLA-1	chr3:112099250-112099670	NONHSAT091173
4	lnc-BTLA-1	chr3:112100753-112100780	NONHSAT091174

Extended variants
information (count: 480 )
Associated
traits (count: 56 )

Variant overlapped rSNPs/rCNVs (count:480 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs9822923	chr3:112099647-112099648	Enhancers Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs376409480	chr3:112099648-112099649	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
3	rs556418104	chr3:112099680-112099681	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs112514184	chr3:112099702-112099703	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs140716227	chr3:112099837-112099838	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs558482482	chr3:112099896-112099897	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs547878110	chr3:112099908-112099909	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs375128175	chr3:112099950-112099951	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs561569338	chr3:112099956-112099957	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs571995292	chr3:112100030-112100031	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs540516079	chr3:112100089-112100090	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs150101419	chr3:112100155-112100156	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs572375172	chr3:112100170-112100171	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs542778323	chr3:112100172-112100173	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs562946419	chr3:112100191-112100192	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs112143210	chr3:112100198-112100199	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs545216907	chr3:112100217-112100218	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs2971203	chr3:112100239-112100240	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
19	rs183892179	chr3:112100336-112100337	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs547695148	chr3:112100346-112100347	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs567541692	chr3:112100398-112100399	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs544113064	chr3:112100417-112100418	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs138622786	chr3:112100437-112100438	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs11709692	chr3:112100473-112100474	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs538724899	chr3:112100484-112100485	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs377263047	chr3:112100530-112100531	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs145829467	chr3:112100538-112100539	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs541188279	chr3:112100567-112100568	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs534290324	chr3:112100589-112100590	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs138435708	chr3:112100639-112100640	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs11709796	chr3:112100640-112100641	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs78984137	chr3:112100739-112100740	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs551337612	chr3:112100773-112100774	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
34	rs113426363	chr3:112100801-112100802	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs542915268	chr3:112100812-112100813	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs559858635	chr3:112100847-112100848	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs189452430	chr3:112100853-112100854	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs576598952	chr3:112100855-112100856	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs545467276	chr3:112100864-112100865	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs565265533	chr3:112100898-112100899	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs11710577	chr3:112100911-112100912	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs80067209	chr3:112100919-112100920	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs56153231	chr3:112100943-112100944	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs55723685	chr3:112100973-112100974	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs192658774	chr3:112101039-112101040	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs149631744	chr3:112101063-112101064	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs113507691	chr3:112101106-112101107	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs148705089	chr3:112101142-112101143	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs185568263	chr3:112101143-112101144	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs386664683	chr3:112101223-112101224	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:56)

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
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
Acute lymphoblastic leukemia	21339820	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Breast cancer	16608533	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Developmental delay	22180640	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21858162	CNVD
Multiple myeloma	17550852	CNVD
small cell lung cancer	20016488	CNVD
Myelofibrosis	22110671	CNVD
Basal cell lymphoma	21115979	CNVD
Attention deficit hyperactivity disorder	22180640	CNVD

Chromatin state (count:409 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112077600-112107200	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr3:112085800-112101400	Weak transcription	Aorta	Aorta
3	chr3:112094400-112100200	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr3:112094400-112104400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr3:112095000-112104200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr3:112095400-112103600	Weak transcription	Fetal Thymus	thymus
7	chr3:112097000-112103000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:112097000-112103800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr3:112097000-112105600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:112097200-112101400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr3:112097200-112101600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:112097600-112110400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:112098000-112103800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr3:112098000-112108800	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr3:112098400-112101800	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr3:112098400-112103800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr3:112098400-112108800	Weak transcription	NH-A	brain
18	chr3:112098800-112099800	Weak transcription	Primary B cells from cord blood	blood
19	chr3:112098800-112103600	Weak transcription	Osteobl	bone
20	chr3:112098800-112108400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:112098800-112108400	Weak transcription	HMEC	breast
22	chr3:112099400-112099800	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr3:112099400-112100200	Enhancers	Primary B cells from peripheral blood	blood
24	chr3:112099400-112100600	Weak transcription	Primary hematopoietic stem cells	blood
25	chr3:112099400-112107400	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr3:112099600-112100600	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr3:112099800-112100000	Enhancers	Primary B cells from cord blood	blood
28	chr3:112100200-112101400	Weak transcription	Primary B cells from peripheral blood	blood
29	chr3:112100200-112101400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr3:112100600-112102000	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr3:112100600-112102200	Enhancers	Primary hematopoietic stem cells	blood
32	chr3:112101400-112101800	Enhancers	Aorta	Aorta
33	chr3:112101400-112101800	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr3:112101400-112102000	Enhancers	Primary B cells from peripheral blood	blood
35	chr3:112101400-112102600	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr3:112101600-112101800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr3:112101800-112107000	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr3:112101800-112110000	Weak transcription	Aorta	Aorta
39	chr3:112102000-112104600	Weak transcription	Primary B cells from peripheral blood	blood
40	chr3:112102200-112103600	Weak transcription	Primary hematopoietic stem cells	blood
41	chr3:112102600-112103600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr3:112103000-112104200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr3:112103400-112104000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:112103600-112104200	Enhancers	iPS-20b Cell Line	embryonic stem cell
45	chr3:112103600-112104200	Enhancers	Primary hematopoietic stem cells	blood
46	chr3:112103600-112104200	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr3:112103600-112104200	Enhancers	Fetal Thymus	thymus
48	chr3:112103600-112104800	Enhancers	HUVEC	blood vessel
49	chr3:112103800-112104200	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr3:112103800-112104400	Enhancers	iPS-18 Cell Line	embryonic stem cell

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