Variant report

Variant	nsv546418
Chromosome Location	chr1:62646182-62656809
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:55)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:55 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BCL11A	chr1:62647325-62647481	H1-hESC	embryonic stem cell:	n/a	n/a
2	CEBPB	chr1:62646350-62646662	MCF-7	breast:	n/a	n/a
3	CEBPB	chr1:62648992-62649221	H1-hESC	embryonic stem cell:	n/a	n/a
4	EP300	chr1:62647206-62647628	H1-hESC	embryonic stem cell:	n/a	n/a
5	EP300	chr1:62646420-62646656	T-47D	breast:	n/a	n/a
6	FOS	chr1:62650894-62651146	MCF10A-Er-Src	breast:	n/a	n/a
7	FOS	chr1:62650850-62651137	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr1:62650847-62651145	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr1:62650846-62651149	MCF10A-Er-Src	breast:	n/a	n/a
10	FOSL2	chr1:62650869-62651164	HepG2	liver:	n/a	n/a
11	GATA3	chr1:62645689-62646206	SH-SY5Y	brain:	n/a	n/a
12	GTF2F1	chr1:62647239-62647393	H1-hESC	embryonic stem cell:	n/a	n/a
13	HDAC2	chr1:62647215-62647461	H1-hESC	embryonic stem cell:	n/a	n/a
14	HDAC2	chr1:62647238-62647537	H1-hESC	embryonic stem cell:	n/a	n/a
15	JUND	chr1:62650660-62651331	SK-N-SH	brain:	n/a	chr1:62650988-62650999
16	JUND	chr1:62650918-62651143	HepG2	liver:	n/a	chr1:62650988-62650999
17	JUND	chr1:62650951-62651032	H1-hESC	embryonic stem cell:	n/a	chr1:62650988-62650999
18	JUND	chr1:62647323-62647482	H1-hESC	embryonic stem cell:	n/a	n/a
19	MAFK	chr1:62649750-62649775	HepG2	liver:	n/a	n/a
20	MAFK	chr1:62649738-62649804	HepG2	liver:	n/a	n/a
21	MAX	chr1:62656643-62656653	HepG2	liver:	n/a	n/a
22	MXI1	chr1:62648899-62649120	H1-hESC	embryonic stem cell:	n/a	n/a
23	NANOG	chr1:62647278-62647552	H1-hESC	embryonic stem cell:	n/a	n/a
24	NFIC	chr1:62646226-62646664	ECC-1	luminal epithelium:	n/a	n/a
25	NFIC	chr1:62646350-62646695	ECC-1	luminal epithelium:	n/a	n/a
26	POLR2A	chr1:62647213-62647463	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr1:62648806-62649410	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr1:62646778-62647476	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr1:62647746-62647770	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr1:62647183-62647495	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr1:62647158-62647465	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr1:62647132-62647470	H1-hESC	embryonic stem cell:	n/a	n/a
33	POU5F1	chr1:62647219-62647548	H1-hESC	embryonic stem cell:	n/a	n/a
34	RAD21	chr1:62647183-62647544	H1-hESC	embryonic stem cell:	n/a	n/a
35	SIN3A	chr1:62648907-62649107	H1-hESC	embryonic stem cell:	n/a	n/a
36	SP1	chr1:62646348-62646711	H1-hESC	embryonic stem cell:	n/a	n/a
37	SP1	chr1:62648909-62649405	H1-hESC	embryonic stem cell:	n/a	n/a
38	SP1	chr1:62646356-62646665	H1-hESC	embryonic stem cell:	n/a	n/a
39	SP1	chr1:62647154-62647587	H1-hESC	embryonic stem cell:	n/a	chr1:62647387-62647398
40	SP1	chr1:62647105-62647697	H1-hESC	embryonic stem cell:	n/a	chr1:62647387-62647398
41	TAF1	chr1:62647131-62647506	H1-hESC	embryonic stem cell:	n/a	n/a
42	TAF1	chr1:62647179-62647448	H1-hESC	embryonic stem cell:	n/a	n/a
43	TAF7	chr1:62647114-62647467	H1-hESC	embryonic stem cell:	n/a	n/a
44	TCF12	chr1:62647170-62647554	H1-hESC	embryonic stem cell:	n/a	n/a
45	TEAD4	chr1:62647193-62647597	H1-hESC	embryonic stem cell:	n/a	n/a
46	TEAD4	chr1:62648845-62649322	H1-hESC	embryonic stem cell:	n/a	n/a
47	TEAD4	chr1:62647217-62647631	H1-hESC	embryonic stem cell:	n/a	n/a
48	TEAD4	chr1:62648891-62649318	H1-hESC	embryonic stem cell:	n/a	n/a
49	YY1	chr1:62647200-62647596	H1-hESC	embryonic stem cell:	n/a	n/a
50	YY1	chr1:62647209-62647573	H1-hESC	embryonic stem cell:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:62644591..62647445-chr1:62694346..62697285,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-L1TD1-1	chr1:62656194-62656598	NONHSAT003628
2	lnc-L1TD1-2	chr1:62654803-62655175	NONHSAT003627
3	lnc-L1TD1-2	chr1:62655541-62655625	NONHSAT003627

No data

Variant related genes	Relation type
RPS15AP7	TF binding region
L1TD1	TF binding region
PIGPP2	TF binding region

Extended variants
information (count: 489 )
Associated
traits (count: 92 )

Variant overlapped rSNPs/rCNVs (count:489 , 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	rs12759978	chr1:62646182-62646183	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs184467001	chr1:62646184-62646185	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
3	rs35879706	chr1:62646210-62646211	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs140474619	chr1:62646272-62646273	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
5	rs188377276	chr1:62646279-62646280	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
6	rs114249015	chr1:62646288-62646289	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
7	rs76284408	chr1:62646309-62646310	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
8	rs567164689	chr1:62646333-62646334	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
9	rs146544836	chr1:62646336-62646337	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
10	rs556584101	chr1:62646358-62646359	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
11	rs141254022	chr1:62646362-62646363	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
12	rs181373164	chr1:62646432-62646433	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
13	rs553836881	chr1:62646449-62646450	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
14	rs572238136	chr1:62646479-62646480	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
15	rs542735863	chr1:62646535-62646536	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
16	rs556899470	chr1:62646556-62646557	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
17	rs568834085	chr1:62646562-62646563	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
18	rs7513842	chr1:62646586-62646587	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs117160978	chr1:62646602-62646603	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
20	rs376649556	chr1:62646653-62646654	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
21	rs2457834	chr1:62646676-62646677	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs185835583	chr1:62646706-62646707	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
23	rs545251367	chr1:62646740-62646741	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
24	rs191086856	chr1:62646750-62646751	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
25	rs2481699	chr1:62646758-62646759	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	mRNA abundance
26	rs569981829	chr1:62646760-62646761	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
27	rs567208804	chr1:62646780-62646781	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
28	rs555318882	chr1:62646810-62646811	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
29	rs181010614	chr1:62646887-62646888	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
30	rs186367448	chr1:62646948-62646949	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
31	rs12086409	chr1:62646980-62646981	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
32	rs573864863	chr1:62646983-62646984	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
33	rs138745155	chr1:62647053-62647054	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs35300500	chr1:62647064-62647065	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs565950872	chr1:62647080-62647081	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs57178450	chr1:62647162-62647163	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs182888357	chr1:62647253-62647254	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
38	rs576373575	chr1:62647264-62647265	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
39	rs187527044	chr1:62647283-62647284	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
40	rs556400800	chr1:62647289-62647290	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
41	rs577978631	chr1:62647315-62647316	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
42	rs147626133	chr1:62647333-62647334	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
43	rs544145054	chr1:62647394-62647395	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
44	rs560347806	chr1:62647395-62647396	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
45	rs114013478	chr1:62647418-62647419	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
46	rs562464438	chr1:62647436-62647437	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
47	rs75239481	chr1:62647472-62647473	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
48	rs530766670	chr1:62647484-62647485	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
49	rs560860302	chr1:62647496-62647497	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
50	rs537807670	chr1:62647524-62647525	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:92)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Colorectal cancer	16272173	CNVD
Wilms tumour	21544195	CNVD
Coronary Disease	20032323	CNVD
Prostate cancer	21965145	CNVD
Glioblastoma multiforme	21080181	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Stargardt''s disease	17277736	CNVD
Neuroblastoma	17897457	CNVD
Uveal melanoma	21693616	CNVD
Cancer	21637783	CNVD
Colorectal cancer	20709793	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-syndromic sensorineural hearing loss	22290220	CNVD
Liposarcoma	21253554	CNVD
Breast cancer	21264507	CNVD
Acute myeloid leukemia	16864856	CNVD
Astrocytoma	17387387	CNVD
Cancer	21499728	CNVD
Glioblastoma multiforme	17387387	CNVD
Oligodendroglial tumors	17285580	CNVD
Papillary thyroid carcinoma	21436994	CNVD
Neuroblastoma	17535989	CNVD
Pheochromocytoma	17535989	CNVD
Prostate cancer	16705090	CNVD
Astrocytoma	17934521	CNVD
Colorectal cancer	19359472	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Gastrointestinal stromal cancer	19259404	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Gastrointestinal stromal cancer	17535989	CNVD
Neuroblastoma	17533364	CNVD
Paraganglioma	17535989	CNVD
Pulmonary chondroma	17535989	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Breast cancer	17603634	CNVD
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Non-syndromic sensorineural hearing loss	21030649	CNVD
Thoracic aortic aneurysm	21092924	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Autism	22495311	CNVD
Non-small cell lung cancer	21385341	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Chordoma	21602918	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Melanoma	18172304	CNVD
Multiple myeloma	16461302	CNVD
Melanoma	17363583	CNVD
Cancer	21129771	CNVD
Autosomal dominant nocturnal frontal lobe epilepsy	18472482	CNVD
Hirschsprung''s Disease	21712996	CNVD
Non-small cell lung cancer	20864512	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Thrombocytopenia-absent radius syndrome	21933853	CNVD
Psychiatric disorder	22848183	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Hepatocellular carcinoma	16750200	CNVD
Burkitt''s lymphoma	18698080	CNVD
Breast cancer	20409316	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Lung cancer	18438408	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Breast cancer	17393978	CNVD
Cervical cancer	21062161	CNVD
Cancer	21183584	CNVD
Breast cancer	21785460	CNVD
Breast cancer	21364760	CNVD
Rett syndrome	21593744	CNVD
Breast cancer	16620391	CNVD
Prostate cancer	16573809	CNVD
Breast cancer	16608533	CNVD
Ovarian cancer	21720365	CNVD
small cell lung cancer	20016488	CNVD
Developmental delay	21147756	CNVD
Breast cancer	17133270	CNVD
Myelofibrosis	22110671	CNVD
CNS Malformation Syndrome	17530927	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Type 2 diabetes	21956041	CNVD
Uveal melanoma	20484589	CNVD
Colorectal cancer	20459617	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Medullary thyroid carcinoma	18765511	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:129 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62636200-62649000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:62638200-62649000	Weak transcription	Fetal Intestine Small	intestine
3	chr1:62640600-62651200	Enhancers	H1 Cell Line	embryonic stem cell
4	chr1:62643400-62647400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:62645000-62647000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:62645000-62649000	Weak transcription	Colonic Mucosa	Colon
7	chr1:62645200-62647000	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr1:62645400-62646400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:62645400-62646800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:62645400-62647000	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr1:62645400-62647200	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr1:62645400-62647200	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr1:62645600-62646200	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr1:62645600-62646600	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr1:62645600-62646600	Enhancers	HMEC	breast
16	chr1:62645600-62646800	Enhancers	NHEK	skin
17	chr1:62645600-62647000	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr1:62645600-62647200	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr1:62645600-62647200	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr1:62645600-62649400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr1:62645800-62646200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr1:62645800-62646400	Enhancers	Fetal Kidney	kidney
23	chr1:62645800-62646400	Enhancers	Fetal Lung	lung
24	chr1:62645800-62646400	Enhancers	Stomach Mucosa	stomach
25	chr1:62645800-62646600	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr1:62645800-62647600	Enhancers	Placenta	Placenta
27	chr1:62645800-62648200	Enhancers	H9 Cell Line	embryonic stem cell
28	chr1:62646000-62646200	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:62646000-62646200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
30	chr1:62646000-62646400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:62646000-62646400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr1:62646000-62646400	Enhancers	Duodenum Mucosa	Duodenum
33	chr1:62646000-62647400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
34	chr1:62646000-62648200	Enhancers	Fetal Muscle Leg	muscle
35	chr1:62646000-62649400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr1:62646200-62646400	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr1:62646200-62647600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr1:62646200-62649000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr1:62646400-62646600	Enhancers	Right Atrium	heart
40	chr1:62646400-62647400	Enhancers	Fetal Muscle Trunk	muscle
41	chr1:62646400-62648800	Weak transcription	Fetal Lung	lung
42	chr1:62646400-62649000	Weak transcription	Fetal Kidney	kidney
43	chr1:62646600-62647000	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr1:62646600-62660400	Weak transcription	Right Atrium	heart
45	chr1:62646800-62649600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr1:62647000-62647400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:62647000-62647400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr1:62647000-62647600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr1:62647000-62647800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
50	chr1:62647000-62648200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links