Variant report

Variant	nsv977870
Chromosome Location	chr15:54129750-54137194
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	chr15:54136050-54137124	HepG2	liver:	n/a	n/a
2	CEBPB	chr15:54136388-54136773	HepG2	liver:	n/a	n/a
3	CTCF	chr15:54129660-54129810	HRE	kidney:	n/a	n/a
4	CTCF	chr15:54129820-54129970	SK-N-SH_RA	brain:	n/a	n/a
5	CTCF	chr15:54129740-54129890	MCF-7	breast:	n/a	n/a
6	CTCF	chr15:54129780-54129930	Caco-2	colon:	n/a	n/a
7	EP300	chr15:54136451-54136826	HepG2	liver:	n/a	n/a
8	EP300	chr15:54136211-54136934	HepG2	liver:	n/a	chr15:54136243-54136257
9	EP300	chr15:54136228-54136999	HepG2	liver:	n/a	chr15:54136243-54136257
10	FOXA1	chr15:54136440-54136818	HepG2	liver:	n/a	n/a
11	FOXA1	chr15:54136284-54136982	HepG2	liver:	n/a	n/a
12	FOXA1	chr15:54136192-54136884	HepG2	liver:	n/a	n/a
13	FOXA1	chr15:54136314-54136973	HepG2	liver:	n/a	n/a
14	FOXA2	chr15:54136464-54136829	A549	lung:	n/a	n/a
15	FOXA2	chr15:54136370-54136868	HepG2	liver:	n/a	n/a
16	GATA3	chr15:54129258-54129964	MCF-7	breast:	n/a	n/a
17	GATA3	chr15:54129168-54130015	MCF-7	breast:	n/a	n/a
18	GATA3	chr15:54129185-54129866	MCF-7	breast:	n/a	n/a
19	GATA3	chr15:54129393-54129754	MCF-7	breast:	n/a	n/a
20	GATA3	chr15:54129395-54129803	T-47D	breast:	n/a	n/a
21	HDAC2	chr15:54129421-54129870	MCF-7	breast:	n/a	n/a
22	HDAC2	chr15:54129476-54129838	MCF-7	breast:	n/a	n/a
23	HDAC2	chr15:54136250-54136886	HepG2	liver:	n/a	chr15:54136350-54136364 chr15:54136349-54136363 chr15:54136474-54136483 chr15:54136277-54136291
24	HEY1	chr15:54136334-54136951	HepG2	liver:	n/a	n/a
25	HNF4A	chr15:54136353-54136750	HepG2	liver:	n/a	chr15:54136502-54136517
26	HNF4G	chr15:54136327-54136760	HepG2	liver:	n/a	chr15:54136508-54136523
27	JUN	chr15:54136290-54137178	HepG2	liver:	n/a	chr15:54137016-54137029
28	JUND	chr15:54136308-54137188	HepG2	liver:	n/a	n/a
29	MAFF	chr15:54136412-54136844	HepG2	liver:	n/a	n/a
30	MAFK	chr15:54136525-54136830	HepG2	liver:	n/a	n/a
31	MXI1	chr15:54136427-54136825	HepG2	liver:	n/a	n/a
32	MYBL2	chr15:54136176-54136974	HepG2	liver:	n/a	n/a
33	MYBL2	chr15:54136345-54136866	HepG2	liver:	n/a	n/a
34	NFIC	chr15:54136398-54136831	HepG2	liver:	n/a	n/a
35	NFIC	chr15:54136080-54136990	HepG2	liver:	n/a	n/a
36	NR2F2	chr15:54129343-54129904	MCF-7	breast:	n/a	n/a
37	POLR2A	chr15:54136679-54137100	HepG2	liver:	n/a	n/a
38	POLR2A	chr15:54134952-54135019	MCF10A-Er-Src	breast:	n/a	n/a
39	POLR2A	chr15:54136183-54136978	HepG2	liver:	n/a	n/a
40	POLR2A	chr15:54136626-54136842	HepG2	liver:	n/a	n/a
41	POLR2A	chr15:54135803-54136015	MCF10A-Er-Src	breast:	n/a	n/a
42	POLR2A	chr15:54136210-54136368	HepG2	liver:	n/a	n/a
43	POLR2A	chr15:54136634-54136877	HepG2	liver:	n/a	n/a
44	REST	chr15:54129455-54129791	PFSK-1	brain:	n/a	n/a
45	REST	chr15:54129358-54129929	A549	lung:	n/a	n/a
46	REST	chr15:54129436-54129960	MCF-7	breast:	n/a	n/a
47	REST	chr15:54129350-54129922	MCF-7	breast:	n/a	n/a
48	RXRA	chr15:54136394-54136824	HepG2	liver:	n/a	n/a
49	SIN3AK20	chr15:54129135-54130064	MCF-7	breast:	n/a	n/a
50	SIN3AK20	chr15:54129195-54129970	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:54131232..54133067-chr15:54139996..54141988,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-WDR72-3	chr15:54129468-54129757	NONHSAT043971

Variant related genes	Relation type
ENSG00000259301	TF binding region

Extended variants
information (count: 295 )
Associated
traits (count: 57 )

Variant overlapped rSNPs/rCNVs (count:295 , 50 per page) page: 1 2 3 4 5 6

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs549845320	chr15:54129777-54129778	Enhancers Weak transcription Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs569966086	chr15:54129789-54129790	Enhancers Weak transcription Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs538939526	chr15:54129808-54129809	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs552048355	chr15:54129817-54129818	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs111756449	chr15:54129837-54129838	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs146256943	chr15:54129865-54129866	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs369674804	chr15:54129871-54129872	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs7172643	chr15:54129900-54129901	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs79435203	chr15:54129923-54129924	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs537044440	chr15:54129924-54129925	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs559319438	chr15:54129928-54129929	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs369062121	chr15:54129975-54129976	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs139258801	chr15:54129979-54129980	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs79544747	chr15:54130034-54130035	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs546102534	chr15:54130080-54130081	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs553260704	chr15:54130095-54130096	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs142387297	chr15:54130104-54130105	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs193002647	chr15:54130116-54130117	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs561031169	chr15:54130135-54130136	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs529865350	chr15:54130138-54130139	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs76917169	chr15:54130158-54130159	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs185733999	chr15:54130186-54130187	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs532415760	chr15:54130230-54130231	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs555651854	chr15:54130257-54130258	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs112608291	chr15:54130268-54130269	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs567899732	chr15:54130277-54130278	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs565863939	chr15:54130309-54130310	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs538074805	chr15:54130317-54130318	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs190558423	chr15:54130344-54130345	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs181875622	chr15:54130361-54130362	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs568169015	chr15:54130403-54130404	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs118082128	chr15:54130425-54130426	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs76881330	chr15:54130515-54130516	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs77478456	chr15:54130516-54130517	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs185289642	chr15:54130522-54130523	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs17793577	chr15:54130539-54130540	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs539474635	chr15:54130546-54130547	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs188487985	chr15:54130557-54130558	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs375480268	chr15:54130573-54130574	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs573495880	chr15:54130580-54130581	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs76195124	chr15:54130594-54130595	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs555688403	chr15:54130630-54130631	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs144048874	chr15:54130646-54130647	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs1904112	chr15:54130679-54130680	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs181252826	chr15:54130684-54130685	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs532124693	chr15:54130709-54130710	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs545516256	chr15:54130720-54130721	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs559594982	chr15:54130738-54130739	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs79981533	chr15:54130764-54130765	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs1478212	chr15:54130795-54130796	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:57)

Disease	PMID	Source
Ewing''s sarcoma	21437220	CNVD
Schizophrenia	19415332	CNVD
Breast cancer	22522925	CNVD
Autism	22495311	CNVD
Wilms tumour	21544195	CNVD
Testicular germ cell tumor	18059402	CNVD
cataract	16735990	CNVD
Cancer	21637783	CNVD
Colorectal cancer	20709793	CNVD
Medulloblastoma	21979893	CNVD
spastic paraplegia with thinning of corpus callosum	19105190	CNVD
Schizophrenia	21324950	CNVD
Astrocytoma	17387387	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Disease	21824424	CNVD
Melanoma	18172304	CNVD
Colorectal cancer	16774939	CNVD
Gastric cancer	17167181	CNVD
Neuroblastoma	19435921	CNVD
Colorectal cancer	19359472	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Colorectal cancer	16272173	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Multiple myeloma	17550852	CNVD
Intellectual disability	22102821	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute myeloid leukemia	20729466	CNVD
Prostate cancer	16573809	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Multiple myeloma	20724749	CNVD
Lung cancer	18438408	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Prostate cancer	18632612	CNVD
small cell lung cancer	20016488	CNVD
Basal cell lymphoma	17053054	CNVD
Breast cancer	22032731	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Hirschsprung''s Disease	21712996	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Cancer	21129771	CNVD
Breast cancer	16272173	CNVD
Hepatocellular carcinoma	16750200	CNVD
Abnormal phenotypes	18644119	CNVD
Cancer	16751803	CNVD
Esophageal adenocarcinoma	18820669	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Myelofibrosis	22110671	CNVD
Acute monocytic leukemia	16498392	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Breast cancer	17133270	CNVD
Breast cancer	21509527	CNVD

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:54122400-54129800	Enhancers	Fetal Intestine Small	intestine
2	chr15:54123400-54130000	Enhancers	Fetal Intestine Large	intestine
3	chr15:54125600-54130200	Enhancers	HepG2	liver
4	chr15:54126000-54136200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr15:54127800-54135800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr15:54128200-54135400	Weak transcription	Gastric	stomach
7	chr15:54128400-54129800	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr15:54128400-54129800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr15:54128400-54130000	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr15:54128800-54129800	Enhancers	NH-A	brain
11	chr15:54128800-54130000	Enhancers	Fetal Kidney	kidney
12	chr15:54129000-54129800	Enhancers	Duodenum Mucosa	Duodenum
13	chr15:54129000-54130000	Enhancers	Stomach Mucosa	stomach
14	chr15:54129200-54129800	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr15:54129400-54129800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr15:54129400-54129800	Enhancers	Fetal Stomach	stomach
17	chr15:54129400-54130000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr15:54129600-54129800	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr15:54129600-54129800	Enhancers	Fetal Brain Male	brain
20	chr15:54129600-54130000	Flanking Active TSS	A549	lung
21	chr15:54129600-54134200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr15:54129600-54136600	Weak transcription	Fetal Lung	lung
23	chr15:54129800-54134000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr15:54130000-54130200	Enhancers	A549	lung
25	chr15:54130000-54134400	Weak transcription	Stomach Mucosa	stomach
26	chr15:54130000-54135400	Weak transcription	Fetal Intestine Large	intestine
27	chr15:54130200-54133000	Weak transcription	HepG2	liver
28	chr15:54133000-54133200	Enhancers	HepG2	liver
29	chr15:54133200-54133600	Weak transcription	HepG2	liver
30	chr15:54133600-54136200	Enhancers	HepG2	liver
31	chr15:54134000-54134400	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr15:54134200-54135000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr15:54134400-54137200	Enhancers	Stomach Mucosa	stomach
34	chr15:54135400-54135600	Enhancers	Fetal Intestine Large	intestine
35	chr15:54135400-54135600	Enhancers	Gastric	stomach
36	chr15:54135600-54136000	Weak transcription	Fetal Intestine Large	intestine
37	chr15:54135600-54136200	Weak transcription	Gastric	stomach
38	chr15:54135800-54136800	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr15:54135800-54137400	Enhancers	Fetal Intestine Small	intestine
40	chr15:54136000-54136200	Enhancers	Fetal Intestine Large	intestine
41	chr15:54136000-54136800	Enhancers	A549	lung
42	chr15:54136200-54136800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr15:54136200-54137000	Flanking Active TSS	HepG2	liver
44	chr15:54136200-54137200	Enhancers	Gastric	stomach
45	chr15:54136200-54137200	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr15:54136200-54143800	Weak transcription	Fetal Intestine Large	intestine
47	chr15:54136400-54136800	Enhancers	Duodenum Mucosa	Duodenum
48	chr15:54136600-54137200	Enhancers	Fetal Lung	lung
49	chr15:54136800-54140400	Weak transcription	A549	lung
50	chr15:54137000-54140200	Enhancers	HepG2	liver

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