Variant report

Variant	nsv528673
Chromosome Location	chr1:57048961-57059571
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	ARID3A	chr1:57050515-57050928	K562	blood:	n/a	n/a
2	ARID3A	chr1:57052300-57052438	HepG2	liver:	n/a	n/a
3	ARID3A	chr1:57050609-57051019	HepG2	liver:	n/a	n/a
4	BACH1	chr1:57057271-57057306	H1-hESC	embryonic stem cell:	n/a	n/a
5	CEBPB	chr1:57056184-57056592	ECC-1	luminal epithelium:	n/a	n/a
6	CEBPB	chr1:57056167-57056579	ECC-1	luminal epithelium:	n/a	n/a
7	CEBPB	chr1:57056162-57056563	MCF-7	breast:	n/a	n/a
8	CEBPB	chr1:57056255-57056567	HepG2	liver:	n/a	n/a
9	CEBPB	chr1:57056248-57056377	HepG2	liver:	n/a	n/a
10	CHD1	chr1:57050217-57051145	IMR90	lung:	n/a	n/a
11	CHD2	chr1:57050623-57050988	GM12878	blood:	n/a	n/a
12	CHD2	chr1:57050679-57050905	K562	blood:	n/a	n/a
13	CHD2	chr1:57050637-57050989	H1-hESC	embryonic stem cell:	n/a	n/a
14	CHD2	chr1:57050617-57050973	Hela-S3	cervix:	n/a	n/a
15	CTCF	chr1:57050720-57050870	GM12866	blood:	n/a	chr1:57050764-57050785 chr1:57050769-57050787
16	CTCF	chr1:57050690-57050907	GM10266	blood:	n/a	chr1:57050764-57050785 chr1:57050769-57050787
17	CTCF	chr1:57050744-57050840	GM19239	blood:	n/a	chr1:57050764-57050785 chr1:57050769-57050787
18	CTCF	chr1:57050700-57050850	GM12865	blood:	n/a	chr1:57050764-57050785 chr1:57050769-57050787
19	CTCF	chr1:57050740-57050890	A549	lung:	n/a	chr1:57050764-57050785 chr1:57050769-57050787
20	CTCF	chr1:57050724-57050879	GM20000	blood:	n/a	chr1:57050764-57050785 chr1:57050769-57050787
21	CTCF	chr1:57050663-57050928	Pancreas_OC	pancreas:	n/a	chr1:57050764-57050785 chr1:57050769-57050787
22	CTCF	chr1:57050740-57050890	GM12873	blood:	n/a	chr1:57050764-57050785 chr1:57050769-57050787
23	CTCF	chr1:57050662-57050833	SK-N-SH_RA	brain:	n/a	chr1:57050764-57050785 chr1:57050769-57050787
24	CTCF	chr1:57050660-57050810	GM12866	blood:	n/a	chr1:57050764-57050785 chr1:57050769-57050787
25	CTCF	chr1:57050315-57051296	SK-N-SH	brain:	n/a	chr1:57050764-57050785 chr1:57050769-57050787
26	CTCF	chr1:57050720-57050870	AG09319	gingival:	n/a	chr1:57050764-57050785 chr1:57050769-57050787
27	CTCF	chr1:57050700-57050850	WERI-Rb-1	eye:	n/a	chr1:57050764-57050785 chr1:57050769-57050787
28	CTCF	chr1:57050680-57050830	MCF-7	breast:	n/a	chr1:57050764-57050785 chr1:57050769-57050787
29	CTCF	chr1:57050680-57050830	HVMF	connective:	n/a	chr1:57050764-57050785 chr1:57050769-57050787
30	CTCF	chr1:57050720-57050870	HCT-116	colon:	n/a	chr1:57050764-57050785 chr1:57050769-57050787
31	CTCF	chr1:57050680-57050830	GM12872	blood:	n/a	chr1:57050764-57050785 chr1:57050769-57050787
32	CTCF	chr1:57050298-57051145	A549	lung:	n/a	chr1:57050764-57050785 chr1:57050769-57050787
33	CTCF	chr1:57050660-57050810	Caco-2	colon:	n/a	chr1:57050764-57050785 chr1:57050769-57050787
34	CTCF	chr1:57050542-57050987	K562	blood:	n/a	chr1:57050764-57050785 chr1:57050769-57050787
35	CTCF	chr1:57050720-57050870	GM06990	blood:	n/a	chr1:57050764-57050785 chr1:57050769-57050787
36	CTCF	chr1:57050740-57050890	GM06990	blood:	n/a	chr1:57050764-57050785 chr1:57050769-57050787
37	CTCF	chr1:57050860-57051010	HEK293	kidney:	n/a	n/a
38	CTCF	chr1:57050620-57050770	HVMF	connective:	n/a	n/a
39	CTCF	chr1:57050720-57050870	Hela-S3	cervix:	n/a	chr1:57050764-57050785 chr1:57050769-57050787
40	CTCF	chr1:57050700-57050850	NB4	blood:	n/a	chr1:57050764-57050785 chr1:57050769-57050787
41	CTCF	chr1:57050720-57050870	AG04449	skin:	n/a	chr1:57050764-57050785 chr1:57050769-57050787
42	CTCF	chr1:57050700-57050850	K562	blood:	n/a	chr1:57050764-57050785 chr1:57050769-57050787
43	CTCF	chr1:57050720-57050870	HBMEC	blood vessel:	n/a	chr1:57050764-57050785 chr1:57050769-57050787
44	CTCF	chr1:57050780-57050930	GM12870	blood:	n/a	n/a
45	CTCF	chr1:57050740-57050890	AG04450	lung:	n/a	chr1:57050764-57050785 chr1:57050769-57050787
46	CTCF	chr1:57049214-57049370	GM12878	blood:	n/a	n/a
47	CTCF	chr1:57050700-57050850	HCPEpiC	choroid plexus:	n/a	chr1:57050764-57050785 chr1:57050769-57050787
48	CTCF	chr1:57050720-57050870	HAc	cerebellar:	n/a	chr1:57050764-57050785 chr1:57050769-57050787
49	CTCF	chr1:57050676-57050863	A549	lung:	n/a	chr1:57050764-57050785 chr1:57050769-57050787
50	CTCF	chr1:57050638-57050936	A549	lung:	n/a	chr1:57050764-57050785 chr1:57050769-57050787

No.	Distal block	Cell Line	Cell type
1	chr1:55750289..55751004-chr1:57050246..57051040,3	MCF-7	breast:
2	chr1:56874449..56875324-chr1:57050573..57051262,2	K562	blood:
3	chr1:55750125..55751076-chr1:57049065..57050023,2	MCF-7	breast:
4	chr1:55751139..55751909-chr1:57050295..57051207,2	MCF-7	breast:
5	chr1:57050265..57050916-chr1:57286447..57287375,2	MCF-7	breast:
6	chr1:57043720..57045227-chr1:57047518..57050298,2	K562	blood:
7	chr1:57044467..57046769-chr1:57047569..57049948,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C1orf168-4	chr1:57051285-57051474	NONHSAT003453
2	lnc-C1orf168-4	chr1:57051673-57051915	NONHSAT003453

Variant related genes	Relation type
ENSG00000224980	TF binding region
PPAP2B	TF binding region
ENSG00000162407	chromatin interactions

Extended variants
information (count: 302 )
Associated
traits (count: 93 )

Variant overlapped rSNPs/rCNVs (count:302 , 50 per page) page: 1 2 3 4 5 6 7

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs2404983	chr1:57048961-57048962	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs529205335	chr1:57049075-57049076	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs563949239	chr1:57049163-57049164	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs12035839	chr1:57049186-57049187	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs568382618	chr1:57049248-57049249	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs113830066	chr1:57049256-57049257	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs545781055	chr1:57049291-57049292	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs527635648	chr1:57049318-57049319	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs370332034	chr1:57049348-57049349	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs571000170	chr1:57049358-57049359	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs539936946	chr1:57049361-57049362	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs12021802	chr1:57049394-57049395	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs111789399	chr1:57049399-57049400	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs556824399	chr1:57049410-57049411	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs553166061	chr1:57049445-57049446	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs150944097	chr1:57049493-57049494	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs142056789	chr1:57049508-57049509	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs370953783	chr1:57049606-57049607	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs571950673	chr1:57049621-57049622	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs184838097	chr1:57049639-57049640	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs72664395	chr1:57049640-57049641	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs577344535	chr1:57049641-57049642	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs145884528	chr1:57049643-57049644	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs563158186	chr1:57049676-57049677	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs188617727	chr1:57049709-57049710	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs542559042	chr1:57049710-57049711	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs559557275	chr1:57049722-57049723	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs191974532	chr1:57049731-57049732	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs552867136	chr1:57049880-57049881	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs4475779	chr1:57049977-57049978	Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs184347366	chr1:57049978-57049979	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs533502089	chr1:57049987-57049988	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
33	rs550267158	chr1:57050025-57050026	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs570179220	chr1:57050111-57050112	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
35	rs536000477	chr1:57050179-57050180	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs138441471	chr1:57050218-57050219	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs566408152	chr1:57050286-57050287	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs534983153	chr1:57050313-57050314	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs144016625	chr1:57050315-57050316	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs577183680	chr1:57050316-57050317	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs536771572	chr1:57050422-57050423	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs556591393	chr1:57050488-57050489	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs189174116	chr1:57050523-57050524	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs150262517	chr1:57050559-57050560	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs559281150	chr1:57050574-57050575	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs112776358	chr1:57050575-57050576	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs12749908	chr1:57050578-57050579	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs573119818	chr1:57050612-57050613	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs199637501	chr1:57050663-57050664	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs113278704	chr1:57050664-57050665	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:93)

Disease	PMID	Source
Papillary thyroid carcinoma	21436994	CNVD
Adenoid cystic carcinoma	18698036	CNVD
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
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
Meckel-Gruber syndrome	21572526	CNVD
Breast cancer	16620391	CNVD
Multiple myeloma	16616336	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Prostate cancer	16573809	CNVD
Breast cancer	16608533	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	21509527	CNVD
Myelofibrosis	22110671	CNVD
Developmental delay	19490664	CNVD
Glioblastoma multiforme	22286061	CNVD
Ovarian cancer	21720365	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57045400-57050800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:57045400-57051800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:57046000-57049000	Weak transcription	Fetal Muscle Leg	muscle
4	chr1:57046000-57050200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr1:57046000-57050200	Weak transcription	Brain Angular Gyrus	brain
6	chr1:57046000-57050200	Weak transcription	Brain Hippocampus Middle	brain
7	chr1:57046000-57050400	Weak transcription	HSMM	muscle
8	chr1:57046000-57050800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:57046200-57050200	Weak transcription	Brain Substantia Nigra	brain
10	chr1:57046200-57050400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr1:57046200-57050400	Weak transcription	A549	lung
12	chr1:57046200-57051400	Weak transcription	Osteobl	bone
13	chr1:57046400-57050200	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr1:57047200-57050200	Weak transcription	NHLF	lung
15	chr1:57047400-57050200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:57047600-57050200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:57047600-57050200	Weak transcription	Fetal Lung	lung
18	chr1:57047600-57050200	Weak transcription	HepG2	liver
19	chr1:57047600-57050200	Weak transcription	NHDF-Ad	bronchial
20	chr1:57047600-57050400	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr1:57048000-57050200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:57048000-57050800	Weak transcription	Liver	Liver
23	chr1:57048000-57056000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:57048800-57049200	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr1:57049000-57049200	Enhancers	Fetal Muscle Leg	muscle
26	chr1:57049200-57050200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr1:57050000-57050400	Enhancers	GM12878-XiMat	blood
28	chr1:57050200-57050400	Enhancers	HepG2	liver
29	chr1:57050200-57050600	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr1:57050200-57050600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr1:57050200-57050600	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr1:57050200-57050600	Enhancers	Brain Hippocampus Middle	brain
33	chr1:57050200-57050600	Enhancers	NHLF	lung
34	chr1:57050200-57050800	Enhancers	Fetal Lung	lung
35	chr1:57050200-57052000	Enhancers	NHDF-Ad	bronchial
36	chr1:57050200-57052400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:57050400-57050600	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr1:57050400-57050600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr1:57050400-57050600	Enhancers	A549	lung
40	chr1:57050400-57050800	Weak transcription	HepG2	liver
41	chr1:57050400-57051000	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr1:57050400-57051000	Enhancers	Brain Cingulate Gyrus	brain
43	chr1:57050400-57051000	Enhancers	HSMM	muscle
44	chr1:57050400-57052000	Enhancers	Muscle Satellite Cultured Cells	--
45	chr1:57050600-57051000	Weak transcription	A549	lung
46	chr1:57050600-57051600	Weak transcription	NHLF	lung
47	chr1:57050800-57051800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:57050800-57052000	Enhancers	Liver	Liver
49	chr1:57050800-57052200	Enhancers	HepG2	liver
50	chr1:57051000-57052000	Enhancers	A549	lung

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