Variant report

Variant	nsv5312
Chromosome Location	chr6:55784991-55830051
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BRCA1	chr6:55818204-55818625	Hela-S3	cervix:	n/a	n/a
2	CEBPB	chr6:55802046-55802376	A549	lung:	n/a	chr6:55802178-55802189
3	CEBPB	chr6:55829280-55829512	HepG2	liver:	n/a	chr6:55829425-55829434 chr6:55829425-55829436 chr6:55829423-55829436 chr6:55829423-55829434
4	CEBPB	chr6:55802009-55802401	IMR90	lung:	n/a	chr6:55802178-55802189
5	CEBPB	chr6:55790088-55790526	IMR90	lung:	n/a	n/a
6	CEBPB	chr6:55802020-55802403	HepG2	liver:	n/a	chr6:55802178-55802189
7	CEBPB	chr6:55817974-55818575	Hela-S3	cervix:	n/a	chr6:55818273-55818286 chr6:55818270-55818287
8	CEBPB	chr6:55811961-55812252	HepG2	liver:	n/a	chr6:55812075-55812086
9	CEBPB	chr6:55812007-55812099	A549	lung:	n/a	chr6:55812075-55812086
10	CEBPB	chr6:55796212-55796270	K562	blood:	n/a	chr6:55796220-55796233
11	CEBPB	chr6:55828210-55828471	H1-hESC	embryonic stem cell:	n/a	n/a
12	CEBPB	chr6:55828224-55828463	Hela-S3	cervix:	n/a	n/a
13	CTCF	chr6:55818327-55818530	Pancreas_OC	pancreas:	n/a	chr6:55818421-55818429 chr6:55818416-55818434 chr6:55818411-55818432
14	CTCF	chr6:55828268-55828380	GM20000	blood:	n/a	n/a
15	CTCF	chr6:55828237-55828378	HepG2	liver:	n/a	n/a
16	CTCF	chr6:55806620-55806770	AG09309	skin:	n/a	n/a
17	CTCF	chr6:55828220-55828370	HUVEC	blood vessel:	n/a	n/a
18	CTCF	chr6:55828200-55828350	MCF-7	breast:	n/a	n/a
19	CTCF	chr6:55818340-55818490	AG09319	gingival:	n/a	chr6:55818421-55818429 chr6:55818416-55818434 chr6:55818411-55818432
20	CTCF	chr6:55818320-55818470	HCPEpiC	choroid plexus:	n/a	chr6:55818421-55818429 chr6:55818416-55818434 chr6:55818411-55818432
21	CTCF	chr6:55818320-55818470	HMEC	breast:	n/a	chr6:55818421-55818429 chr6:55818416-55818434 chr6:55818411-55818432
22	CTCF	chr6:55806538-55806867	GM12878	blood:	n/a	n/a
23	CTCF	chr6:55818360-55818510	AG04449	skin:	n/a	chr6:55818421-55818429 chr6:55818416-55818434 chr6:55818411-55818432
24	CTCF	chr6:55806640-55806790	HBMEC	blood vessel:	n/a	n/a
25	CTCF	chr6:55806620-55806770	NHDF-neo	bronchial:	n/a	n/a
26	CTCF	chr6:55818340-55818490	RPTEC	kidney:	n/a	chr6:55818421-55818429 chr6:55818416-55818434 chr6:55818411-55818432
27	CTCF	chr6:55828220-55828370	A549	lung:	n/a	n/a
28	CTCF	chr6:55806620-55806770	BJ	skin:	n/a	n/a
29	CTCF	chr6:55828300-55828450	GM06990	blood:	n/a	n/a
30	CTCF	chr6:55828180-55828473	HepG2	liver:	n/a	n/a
31	CTCF	chr6:55818260-55818410	HAc	cerebellar:	n/a	n/a
32	CTCF	chr6:55828220-55828370	HCPEpiC	choroid plexus:	n/a	n/a
33	CTCF	chr6:55828260-55828410	HMEC	breast:	n/a	n/a
34	CTCF	chr6:55806620-55806770	HCM	heart:	n/a	n/a
35	CTCF	chr6:55806600-55806750	NHDF-neo	bronchial:	n/a	n/a
36	CTCF	chr6:55828280-55828430	RPTEC	kidney:	n/a	n/a
37	CTCF	chr6:55828200-55828350	HEK293	kidney:	n/a	n/a
38	CTCF	chr6:55828200-55828350	SK-N-SH_RA	brain:	n/a	n/a
39	CTCF	chr6:55806500-55806650	GM12865	blood:	n/a	n/a
40	CTCF	chr6:55828190-55828414	Gliobla	brain:	n/a	n/a
41	CTCF	chr6:55806640-55806790	HCPEpiC	choroid plexus:	n/a	n/a
42	CTCF	chr6:55828181-55828419	Hela-S3	cervix:	n/a	n/a
43	CTCF	chr6:55806580-55806730	HBMEC	blood vessel:	n/a	n/a
44	CTCF	chr6:55828240-55828390	Hela-S3	cervix:	n/a	n/a
45	CTCF	chr6:55828240-55828390	GM12869	blood:	n/a	n/a
46	CTCF	chr6:55818400-55818550	GM12866	blood:	n/a	chr6:55818421-55818429 chr6:55818416-55818434 chr6:55818411-55818432
47	CTCF	chr6:55806640-55806790	HRPEpiC	eye:	n/a	n/a
48	CTCF	chr6:55828280-55828430	BJ	skin:	n/a	n/a
49	CTCF	chr6:55806720-55806870	MCF-7	breast:	n/a	n/a
50	CTCF	chr6:55828140-55828290	AG04450	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:55310627..55311224-chr6:55806307..55806968,2	MCF-7	breast:
2	chr6:55313718..55314729-chr6:55817986..55818869,4	MCF-7	breast:
3	chr6:55789954..55791634-chr6:55792206..55794273,2	MCF-7	breast:
4	chr6:55751118..55751828-chr6:55818205..55818779,2	MCF-7	breast:
5	chr6:55824417..55826728-chr6:55848243..55849781,2	K562	blood:
6	chr6:55377472..55378318-chr6:55806611..55807235,2	MCF-7	breast:
7	chr6:55309906..55311058-chr6:55817976..55819297,5	MCF-7	breast:
8	chr6:55310143..55310712-chr6:55818032..55818931,2	MCF-7	breast:
9	chr6:55141267..55142162-chr6:55817824..55818554,3	MCF-7	breast:
10	chr6:55789954..55791634-chr6:55792206..55794273,2	MCF-7	breast:
11	chr6:55313181..55315342-chr6:55800874..55802800,2	MCF-7	breast:
12	chr6:55313873..55314721-chr6:55806208..55806737,2	MCF-7	breast:

Variant related genes	Relation type
NPM1P36	TF binding region

Extended variants
information (count: 1015 )
Associated
traits (count: 82 )

Variant overlapped rSNPs/rCNVs (count:1015 , 50 per page) page: 1 2 3 4 5 6 7 ... 21

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs62404994	chr6:55785026-55785027	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs895643	chr6:55785059-55785060	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs560698823	chr6:55785065-55785066	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs79568292	chr6:55785123-55785124	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs552344973	chr6:55785139-55785140	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs569344521	chr6:55785146-55785147	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs537818329	chr6:55785177-55785178	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs111418613	chr6:55785183-55785184	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs548200797	chr6:55785186-55785187	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs5876476	chr6:55785234-55785235	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs9475474	chr6:55785242-55785243	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs78207998	chr6:55785243-55785244	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs35987021	chr6:55785244-55785245	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs545288042	chr6:55785247-55785248	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs186097657	chr6:55785256-55785257	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs537336784	chr6:55785263-55785264	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs200225414	chr6:55785321-55785322	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs539622998	chr6:55785346-55785347	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs555943601	chr6:55785352-55785353	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs576101070	chr6:55785360-55785361	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs541430231	chr6:55785368-55785369	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs16887395	chr6:55785369-55785370	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs565096745	chr6:55785382-55785383	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs575168160	chr6:55785418-55785419	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs540977620	chr6:55785431-55785432	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs560772621	chr6:55785445-55785446	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs115914370	chr6:55785460-55785461	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs190519887	chr6:55785481-55785482	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs546395759	chr6:55785571-55785572	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs562814486	chr6:55785594-55785595	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs531862815	chr6:55785658-55785659	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs548162114	chr6:55785697-55785698	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs183414489	chr6:55785706-55785707	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs527578147	chr6:55785747-55785748	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs547241248	chr6:55785768-55785769	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs895642	chr6:55785780-55785781	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs539222629	chr6:55785785-55785786	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs61391371	chr6:55785805-55785806	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs187606182	chr6:55785807-55785808	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs895641	chr6:55785861-55785862	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs147219729	chr6:55785880-55785881	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs139600737	chr6:55785975-55785976	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs554473400	chr6:55786046-55786047	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs62404996	chr6:55786047-55786048	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs546060140	chr6:55786051-55786052	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs149729593	chr6:55786180-55786181	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs531704011	chr6:55786193-55786194	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs541967395	chr6:55786195-55786196	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs375531104	chr6:55786199-55786200	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs368539241	chr6:55786201-55786202	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:82)

Disease	PMID	Source
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Leukemia	21518781	CNVD
Cancer	21637783	CNVD
Facial dysmorphism	22105932	CNVD
Medulloblastoma	21979893	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	21080181	CNVD
Hepatocellular carcinoma	22174799	CNVD
Endometrial cancer	22040021	CNVD
Acute myeloid leukemia	16864856	CNVD
Breast cancer	21264507	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Cancer	16751803	CNVD
Bladder cancer	19088036	CNVD
Wilms tumour	21544195	CNVD
Uveal melanoma	21693616	CNVD
Biliary cancer	19435499	CNVD
Malaria	21533027	CNVD
Retinoblastoma	19183342	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Breast cancer	21858162	CNVD
Ewing''s sarcoma	17952124	CNVD
Autism	21448237	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Autism	22495311	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Urothelial carcinoma	18382360	CNVD
Cancer	21183584	CNVD
small cell lung cancer	20016488	CNVD
Gastric cancer	17908304	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Neuroblastoma	16790693	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Osteosarcoma	16790693	CNVD
Biliary cancer	20360734	CNVD
Breast cancer	20360734	CNVD
Coronary artery disease	20360734	CNVD
Crohn''s disease	20360734	CNVD
Hypertension	20360734	CNVD
Rheumatoid arthritis	20360734	CNVD
Type 1 diabetes	20360734	CNVD
Type 2 diabetes	20360734	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Lung cancer	18438408	CNVD
Neuroblastoma	18923191	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	17603634	CNVD
Neurocytoma	17123091	CNVD
Systemic lupus erythematosus	17503323	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Breast cancer	16608533	CNVD
Melanoma	18172304	CNVD
Esophageal adenocarcinoma	18820669	CNVD
Neuroblastoma	19686582	CNVD
Neuroblastoma	17289879	CNVD
Breast cancer	17899364	CNVD
Breast cancer	17133270	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Myelofibrosis	22110671	CNVD
Glioblastoma multiforme	22286061	CNVD
Colorectal cancer	16912164	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	21364760	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Acute lymphoblastic leukemia	18458336	CNVD
Breast cancer	21509527	CNVD
lymphocytic leukemia	21291569	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:55780800-55785000	Enhancers	Muscle Satellite Cultured Cells	--
2	chr6:55783400-55789800	Weak transcription	NHEK	skin
3	chr6:55783600-55785000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:55784200-55785000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr6:55784200-55785000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:55784200-55789600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:55784600-55789800	Weak transcription	Hela-S3	cervix
8	chr6:55784800-55789800	Weak transcription	HMEC	breast
9	chr6:55785000-55785400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr6:55785000-55789000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:55785400-55786200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr6:55789600-55790600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:55789800-55790200	Enhancers	Hela-S3	cervix
14	chr6:55789800-55790200	Enhancers	HMEC	breast
15	chr6:55789800-55790400	Enhancers	Osteobl	bone
16	chr6:55789800-55790600	Enhancers	Muscle Satellite Cultured Cells	--
17	chr6:55789800-55790600	Enhancers	NHEK	skin
18	chr6:55793400-55794000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:55796000-55796400	Enhancers	Fetal Lung	lung
20	chr6:55801800-55802600	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr6:55801800-55802600	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr6:55802200-55802400	Weak transcription	Fetal Lung	lung
23	chr6:55802400-55803600	Enhancers	Fetal Lung	lung
24	chr6:55802800-55803600	Enhancers	Colon Smooth Muscle	Colon
25	chr6:55807000-55809600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr6:55807800-55809000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr6:55807800-55809000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr6:55807800-55809000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr6:55808000-55808800	Enhancers	NHLF	lung
30	chr6:55808000-55808800	Enhancers	Osteobl	bone
31	chr6:55813600-55815000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr6:55814000-55814600	Enhancers	Placenta	Placenta
33	chr6:55814200-55815600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
34	chr6:55814600-55814800	Weak transcription	Placenta	Placenta
35	chr6:55814600-55815600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr6:55814800-55815600	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr6:55814800-55815600	ZNF genes & repeats	Placenta	Placenta
38	chr6:55815000-55815200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr6:55815000-55815200	ZNF genes & repeats	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr6:55815000-55815600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr6:55815200-55815800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr6:55816600-55820600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr6:55817800-55818000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr6:55817800-55818000	Enhancers	Adipose Nuclei	Adipose
45	chr6:55817800-55818000	Enhancers	Colon Smooth Muscle	Colon
46	chr6:55817800-55818000	Enhancers	Fetal Lung	lung
47	chr6:55817800-55818000	Enhancers	Hela-S3	cervix
48	chr6:55817800-55818400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr6:55817800-55818400	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr6:55817800-55818600	Enhancers	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links