Variant report

Variant	nsv556891
Chromosome Location	chr12:673515-690473
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:50)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:678017..679838-chr12:873854..876600,2	K562	blood:
2	chr12:681158..682660-chr12:683582..685964,2	MCF-7	breast:
3	chr12:633000..634015-chr12:680744..681736,4	MCF-7	breast:
4	chr12:679615..680590-chr12:861311..862253,3	Hela-S3	cervix:
5	chr12:678953..681132-chr12:682529..685502,2	MCF-7	breast:
6	chr12:685078..685936-chr12:860267..860986,3	MCF-7	breast:
7	chr12:688710..691360-chr12:698312..700613,2	K562	blood:
8	chr12:684961..685544-chr12:860128..860643,2	K562	blood:
9	chr12:562235..562796-chr12:678736..679457,3	MCF-7	breast:
10	chr12:671679..673633-chr12:677300..679171,2	K562	blood:
11	chr12:679685..680289-chr5:131563728..131564378,2	Hela-S3	cervix:
12	chr11:68227589..68228344-chr12:680620..681261,2	Hela-S3	cervix:
13	chr12:683230..686247-chr12:859749..863263,5	MCF-7	breast:
14	chr12:562216..562824-chr12:680454..681003,2	MCF-7	breast:
15	chr12:678886..682974-chr12:750258..753718,5	MCF-7	breast:
16	chr12:678065..682232-chr12:860322..863479,7	MCF-7	breast:
17	chr12:684659..687790-chr12:698938..701948,4	K562	blood:
18	chr12:686739..689998-chr12:691265..694339,4	K562	blood:
19	chr12:681158..682660-chr12:683582..685964,2	MCF-7	breast:
20	chr12:675655..677643-chr12:678300..680842,2	MCF-7	breast:
21	chr12:686859..689615-chr12:851283..853925,2	MCF-7	breast:
22	chr12:678491..679456-chr12:976825..977341,2	K562	blood:
23	chr12:680435..681253-chr22:39715404..39715910,2	Hela-S3	cervix:
24	chr12:679375..682562-chr12:682805..686123,3	MCF-7	breast:
25	chr12:633000..634118-chr12:680824..681736,4	MCF-7	breast:
26	chr12:683860..689942-chr12:860112..864025,8	K562	blood:
27	chr12:677202..681860-chr12:682976..687582,7	K562	blood:
28	chr12:679062..679815-chr12:923017..923659,4	K562	blood:
29	chr12:685032..685901-chr12:859937..861024,3	MCF-7	breast:
30	chr12:679375..682562-chr12:682805..686123,3	MCF-7	breast:
31	chr11:99252722..99253222-chr12:681045..681595,2	Hela-S3	cervix:
32	chr12:669669..671571-chr12:673749..675392,2	K562	blood:
33	chr12:680238..683195-chr12:984624..987352,2	K562	blood:
34	chr12:684847..686385-chr12:1701895..1703693,2	MCF-7	breast:
35	chr12:671679..673633-chr12:677300..679171,2	K562	blood:
36	chr12:679647..681193-chr12:1713500..1715289,2	K562	blood:
37	chr12:677285..679316-chr12:862449..864895,2	K562	blood:
38	chr12:684994..685885-chr12:923018..923598,3	K562	blood:
39	chr12:676546..679499-chr12:924463..926278,2	K562	blood:
40	chr12:678673..679595-chr12:860437..861048,2	K562	blood:
41	chr12:680029..685123-chr12:750606..754600,5	K562	blood:
42	chr12:689801..692487-chr12:897629..900163,2	K562	blood:
43	chr12:678953..681132-chr12:682529..685502,2	MCF-7	breast:
44	chr12:679332..680098-chrX:150565595..150566118,2	Hela-S3	cervix:
45	chr12:684050..686927-chr12:859603..861672,3	K562	blood:
46	chr12:678986..679579-chr12:860176..860988,2	MCF-7	breast:
47	chr12:675655..677643-chr12:678300..680842,2	MCF-7	breast:
48	chr12:682344..685123-chr12:752375..754600,2	K562	blood:
49	chr12:677202..681860-chr12:682976..687582,7	K562	blood:
50	chr12:682408..684558-chr12:921412..923532,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KDM5A-5	chr12:674999-675146	NONHSAT025347
2	lnc-B4GALNT3-4	chr12:682376-682425	l_576_chr12:669260-707688_adipose
3	lnc-B4GALNT3-4	chr12:690328-690539	l_576_chr12:669260-707688_adipose

No data

Variant related genes	Relation type
ENSG00000255825	chromatin interactions
ENSG00000171823	chromatin interactions
ENSG00000160131	chromatin interactions
ENSG00000238370	chromatin interactions
ENSG00000100316	chromatin interactions
ENSG00000177406	chromatin interactions
ENSG00000171840	chromatin interactions
ENSG00000110075	chromatin interactions
ENSG00000072682	chromatin interactions
ENSG00000060237	chromatin interactions

Extended variants
information (count: 748 )
Associated
traits (count: 79 )

Variant overlapped rSNPs/rCNVs (count:748 , 50 per page) page: 1 2 3 4 5 6 7 ... 15

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs2245918	chr12:673515-673516	Weak transcription Enhancers Flanking Active TSS Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs558046251	chr12:673534-673535	Weak transcription Enhancers Flanking Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs573128746	chr12:673570-673571	Weak transcription Enhancers Flanking Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs563477199	chr12:673572-673573	Weak transcription Enhancers Flanking Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs112602111	chr12:673573-673574	Weak transcription Enhancers Flanking Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs542686731	chr12:673627-673628	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs555539488	chr12:673633-673634	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs191395069	chr12:673639-673640	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs11549257	chr12:673652-673653	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs544766373	chr12:673653-673654	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs2245910	chr12:673704-673705	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs549535579	chr12:673722-673723	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs533198427	chr12:673784-673785	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs2245906	chr12:673788-673789	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs369435093	chr12:673806-673807	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs1468624	chr12:673854-673855	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
17	rs571446180	chr12:673873-673874	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs183700467	chr12:673882-673883	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs73594222	chr12:673925-673926	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs188020916	chr12:673928-673929	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs550578520	chr12:673944-673945	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs549493489	chr12:673960-673961	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs192499853	chr12:673968-673969	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs142734463	chr12:673969-673970	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs551740586	chr12:674085-674086	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs73034189	chr12:674099-674100	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs2535410	chr12:674177-674178	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs61916658	chr12:674347-674348	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs370514526	chr12:674363-674364	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs375557548	chr12:674373-674374	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs139343732	chr12:674412-674413	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs369495018	chr12:674421-674422	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs11549256	chr12:674425-674426	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs555731031	chr12:674426-674427	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs200576931	chr12:674450-674451	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs376972064	chr12:674458-674459	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs199867849	chr12:674463-674464	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs267603574	chr12:674467-674468	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs150170585	chr12:674475-674476	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs554657826	chr12:674484-674485	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs144276869	chr12:674486-674487	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs138622141	chr12:674487-674488	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs201387339	chr12:674509-674510	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs148753958	chr12:674511-674512	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs560145066	chr12:674512-674513	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs142270523	chr12:674531-674532	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs147864700	chr12:674540-674541	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs200840943	chr12:674544-674545	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs141556007	chr12:674547-674548	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs145279793	chr12:674553-674554	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:79)

Disease	PMID	Source
Cancer	20164920	CNVD
Myelofibrosis	22110671	CNVD
Non-syndromic sensorineural hearing loss	19587683	CNVD
Glaucoma	21310917	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Malignant peripheral nerve sheath tumor	19844265	CNVD
Squamous cell cancer	19607727	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Hepatocellular carcinoma	16750200	CNVD
Breast cancer	17133270	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Mental retardation	17847001	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
abnormal development	18461090	CNVD
Ovarian cancer	20844748	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Medulloblastoma	16968546	CNVD
Ovine squamous-cell carcinoma	17599052	CNVD
T-cell acute lymphoblastic leukemia	20065082	CNVD
Breast cancer	22032731	CNVD
Cancer	21183584	CNVD
Myxofibrosarcoma	16751306	CNVD
Non-small cell lung cancer	21829676	CNVD
Ovarian neoplasms	16753589	CNVD
Prostate cancer	21965145	CNVD
Acute myeloid leukemia	16864856	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Disorders of sex development	21048976	CNVD
Glioblastoma multiforme	21080181	CNVD
Liposarcoma	21253554	CNVD
Prostate cancer	19156837	CNVD
Emphysema	19352772	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Malignant germ cell tumour	17285132	CNVD
Melanoma	18172304	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Wilms tumour	21544195	CNVD
Squamous cell cancer	21044232	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	19960244	CNVD
Endometrial cancer	22040021	CNVD
Colorectal cancer	20709793	CNVD
Breast cancer	21264507	CNVD
Cancer	16751803	CNVD
Testicular cancer	18059402	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Seminomas	18059402	CNVD
Esophageal cancer	21851588	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Testicular germ cell tumor	18059402	CNVD
Malaria	21533027	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
small cell lung cancer	20016488	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
Breast cancer	21364760	CNVD
Developmental delay	21147756	CNVD
Acute lymphoblastic leukemia	21248843	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Ewing''s sarcoma	17952124	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Acute myeloid leukemia	20729466	CNVD
Breast cancer	21858162	CNVD
Breast cancer	21509527	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21785460	CNVD
Ovarian cancer	21720365	CNVD
Myelodysplastic syndrome	21251322	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Pleomorphic liposarcoma	18784837	CNVD

Chromatin state (count:1102 , 50 per page) page: 1 2 3 4 5 6 7 ... 23

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:649200-678800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr12:652200-675600	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr12:652400-678600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr12:652400-679000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr12:656200-678600	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr12:656400-678400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr12:656600-678400	Weak transcription	Brain Anterior Caudate	brain
8	chr12:656800-678800	Weak transcription	Fetal Brain Female	brain
9	chr12:657000-678200	Weak transcription	Brain Angular Gyrus	brain
10	chr12:657000-678600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr12:661800-678600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr12:662200-677000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr12:662800-678800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr12:663000-678800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr12:663400-677400	Weak transcription	Fetal Intestine Small	intestine
16	chr12:663600-676800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr12:666800-675200	Weak transcription	Fetal Heart	heart
18	chr12:667800-678800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr12:668000-678800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr12:669400-678600	Weak transcription	Stomach Mucosa	stomach
21	chr12:670000-679200	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr12:670200-673600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr12:670400-675200	Strong transcription	Brain Inferior Temporal Lobe	brain
24	chr12:670800-673600	Enhancers	GM12878-XiMat	blood
25	chr12:670800-674000	Enhancers	Primary B cells from peripheral blood	blood
26	chr12:671000-674600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr12:671000-675400	Strong transcription	Brain Hippocampus Middle	brain
28	chr12:671200-674600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
29	chr12:671200-674800	Strong transcription	Right Ventricle	heart
30	chr12:671200-678800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr12:671400-674000	Strong transcription	Left Ventricle	heart
32	chr12:671400-674400	Weak transcription	Lung	lung
33	chr12:671400-679200	Weak transcription	Aorta	Aorta
34	chr12:671600-678600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr12:671600-679000	Weak transcription	Right Atrium	heart
36	chr12:671800-674200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
37	chr12:671800-674600	Weak transcription	Colonic Mucosa	Colon
38	chr12:671800-677400	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr12:672000-673600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr12:672000-673800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
41	chr12:672000-674000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr12:672000-674000	Flanking Active TSS	Dnd41	blood
43	chr12:672000-674400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr12:672000-674400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
45	chr12:672200-673600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
46	chr12:672200-673600	Flanking Active TSS	Thymus	Thymus
47	chr12:672200-673800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
48	chr12:672200-674000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
49	chr12:672200-674000	Flanking Active TSS	Fetal Thymus	thymus
50	chr12:672200-675200	Enhancers	Esophagus	oesophagus

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