Variant report

Variant	nsv945298
Chromosome Location	chr1:220439798-220441114
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	chr1:220440528..220443413-chr1:220443546..220445862,4	MCF-7	breast:
2	chr1:220438275..220439851-chr1:220451270..220453670,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BPNT1-2	chr1:220439327-220441093	NONHSAT009593
2	lnc-BPNT1-2	chr1:220440048-220441259	NONHSAT009595
3	lnc-BPNT1-2	chr1:220439521-220441057	NONHSAT009594

Variant related genes	Relation type
ENSG00000118873	chromatin interactions

Extended variants
information (count: 47 )
Associated
traits (count: 97 )

Variant overlapped rSNPs/rCNVs (count:47 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs111744215	chr1:220439803-220439804	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
2	rs185315084	chr1:220439821-220439822	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
3	rs191009432	chr1:220439841-220439842	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
4	rs181426640	chr1:220439891-220439892	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
5	rs186633128	chr1:220439916-220439917	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
6	rs146370576	chr1:220439964-220439965	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
7	rs191743749	chr1:220439992-220439993	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
8	rs111976509	chr1:220440002-220440003	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
9	rs187728196	chr1:220440040-220440041	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
10	rs565065884	chr1:220440063-220440064	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
11	rs546730657	chr1:220440078-220440079	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
12	rs566548264	chr1:220440200-220440201	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
13	rs538869103	chr1:220440349-220440350	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
14	rs558216017	chr1:220440350-220440351	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
15	rs527448002	chr1:220440363-220440364	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
16	rs568642577	chr1:220440366-220440367	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
17	rs367895298	chr1:220440367-220440368	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
18	rs537422118	chr1:220440374-220440375	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
19	rs41304119	chr1:220440414-220440415	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
20	rs574235001	chr1:220440453-220440454	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
21	rs542955377	chr1:220440518-220440519	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
22	rs553675876	chr1:220440524-220440525	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
23	rs139745899	chr1:220440528-220440529	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
24	rs150070001	chr1:220440557-220440558	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
25	rs374849440	chr1:220440561-220440562	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
26	rs531046539	chr1:220440640-220440641	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
27	rs144435739	chr1:220440696-220440697	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
28	rs2808017	chr1:220440718-220440719	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs529950879	chr1:220440725-220440726	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
30	rs546571262	chr1:220440731-220440732	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
31	rs148415227	chr1:220440745-220440746	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
32	rs532188433	chr1:220440843-220440844	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
33	rs567153400	chr1:220440844-220440845	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
34	rs75939080	chr1:220440851-220440852	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
35	rs537558470	chr1:220440882-220440883	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
36	rs34147613	chr1:220440885-220440886	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
37	rs397814336	chr1:220440890-220440891	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
38	rs547738054	chr1:220440914-220440915	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
39	rs567959611	chr1:220440948-220440949	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
40	rs113970850	chr1:220440950-220440951	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
41	rs367570459	chr1:220440981-220440982	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
42	rs45626633	chr1:220440986-220440987	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs573507737	chr1:220441048-220441049	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
44	rs147577815	chr1:220441053-220441054	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
45	rs559208538	chr1:220441070-220441071	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
46	rs117698410	chr1:220441092-220441093	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
47	rs529762651	chr1:220441097-220441098	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:97)

Disease	PMID	Source
Breast cancer	17603634	CNVD
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Autism	22495311	CNVD
Melanoma	18172304	CNVD
Rett syndrome	21593744	CNVD
Medulloblastoma	21979893	CNVD
Cancer	20164919	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	17133270	CNVD
Non-small cell lung cancer	21044232	CNVD
Cervical cancer	21063398	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	20632083	CNVD
Endometrial cancer	22040021	CNVD
Ewing''s sarcoma	21437220	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	21080181	CNVD
Hepatocellular carcinoma	22174799	CNVD
Medulloblastoma	21292688	CNVD
Phyllodes tumor	17334353	CNVD
Breast cancer	21264507	CNVD
Liposarcoma	21253554	CNVD
Multiple myeloma	21628407	CNVD
Cancer	16751803	CNVD
Prostate cancer	16705090	CNVD
Neuroblastoma	19435921	CNVD
Breast cancer	17850661	CNVD
Breast cancer	16461572	CNVD
Intracranial tumor	16823260	CNVD
Medulloblastoma	18056178	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Colorectal cancer	16272173	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Neuroblastoma	21899760	CNVD
Breast cancer	21858162	CNVD
Non-small cell lung cancer	21385341	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Breast cancer	16608533	CNVD
Ewing''s sarcoma	22429812	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17001317	CNVD
Acute myeloid leukemia	21251322	CNVD
Multiple myeloma	17550852	CNVD
Prostate cancer	18632612	CNVD
Acute myeloid leukemia	20729466	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Testicular germ cell tumor	18059402	CNVD
Ependymoma	18628472	CNVD
Leukemia	18628472	CNVD
Neuroblastoma	18923191	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Breast cancer	21509527	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Urothelial carcinoma	21177765	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Chordoma	18071362	CNVD
Multiple myeloma	16461302	CNVD
van der Woude syndrome	22470819	CNVD
van der Woude syndrome	20818247	CNVD
T-cell lymphomas	19863542	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Hepatocellular carcinoma	18803288	CNVD
Urothelial tumor	18831757	CNVD
Lung cancer	18438408	CNVD
small cell lung cancer	20016488	CNVD
Ovarian clear cell carcinoma	19293255	CNVD
Medulloblastoma	16783165	CNVD
Basal cell lymphoma	17170743	CNVD
Hirschsprung''s Disease	21712996	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Holoprosencephaly	19184110	CNVD
Breast cancer	21069454	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Mental retardation	19951919	CNVD
Non-syndromic sensorineural hearing loss	17873649	CNVD
Acute myeloid leukemia	17268525	CNVD
Lung cancer	16740712	CNVD
Renal cell carcinoma	18765545	CNVD
Basal cell lymphoma	17053054	CNVD
Developmental delay	21147756	CNVD
Pleomorphic liposarcoma	18784837	CNVD
Autism	14699429	CNVD
Breast cancer	21364760	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Tetralogy of Fallot	22912587	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Glioma	20126413	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD

Chromatin state (count:172 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220393000-220441000	Weak transcription	NHDF-Ad	bronchial
2	chr1:220416000-220442600	Weak transcription	Fetal Heart	heart
3	chr1:220423000-220443400	Weak transcription	Psoas Muscle	Psoas
4	chr1:220423400-220443400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr1:220423400-220443400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr1:220423600-220440400	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr1:220423800-220442600	Weak transcription	Hela-S3	cervix
8	chr1:220425200-220443400	Weak transcription	HUVEC	blood vessel
9	chr1:220426200-220440200	Weak transcription	Gastric	stomach
10	chr1:220426200-220441800	Weak transcription	Small Intestine	intestine
11	chr1:220426600-220439800	Weak transcription	NHEK	skin
12	chr1:220426600-220440000	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr1:220426600-220440200	Weak transcription	NHLF	lung
14	chr1:220426600-220440600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:220426600-220443400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr1:220426600-220443400	Weak transcription	Right Ventricle	heart
17	chr1:220426600-220444400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:220426800-220439800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr1:220426800-220440000	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr1:220426800-220440000	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr1:220426800-220440000	Weak transcription	Placenta	Placenta
22	chr1:220426800-220441800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr1:220426800-220441800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr1:220426800-220442800	Weak transcription	Esophagus	oesophagus
25	chr1:220426800-220443400	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr1:220426800-220443400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr1:220426800-220443400	Weak transcription	Ovary	ovary
28	chr1:220426800-220444000	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr1:220426800-220444200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr1:220426800-220444400	Weak transcription	Colonic Mucosa	Colon
31	chr1:220426800-220445000	Weak transcription	Aorta	Aorta
32	chr1:220426800-220445000	Weak transcription	Pancreas	Pancrea
33	chr1:220427000-220439800	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr1:220427000-220441400	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr1:220427000-220442800	Weak transcription	Lung	lung
36	chr1:220427000-220443200	Weak transcription	Thymus	Thymus
37	chr1:220427000-220444200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr1:220427000-220445000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr1:220427200-220440200	Weak transcription	Liver	Liver
40	chr1:220427600-220443400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr1:220430400-220440600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr1:220431600-220440800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr1:220431800-220440400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr1:220432200-220442400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr1:220433400-220440000	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr1:220434400-220441200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
47	chr1:220434600-220441400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr1:220434800-220440000	Weak transcription	Duodenum Mucosa	Duodenum
49	chr1:220434800-220444800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr1:220435000-220442200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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