Variant report

Variant	nsv1013013
Chromosome Location	chr4:28323465-28419673
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:353)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:6)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:353 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BACH1	chr4:28326757-28326842	H1-hESC	embryonic stem cell:	n/a	n/a
2	BATF	chr4:28388451-28388626	GM12878	blood:	n/a	n/a
3	CBX3	chr4:28343642-28344004	HCT-116	colon:	n/a	n/a
4	CEBPB	chr4:28375043-28375520	Hela-S3	cervix:	n/a	chr4:28375352-28375363
5	CEBPB	chr4:28405639-28405926	HepG2	liver:	n/a	n/a
6	CEBPB	chr4:28375258-28375474	H1-hESC	embryonic stem cell:	n/a	chr4:28375352-28375363
7	CEBPB	chr4:28405644-28405975	H1-hESC	embryonic stem cell:	n/a	n/a
8	CEBPB	chr4:28371126-28371438	HepG2	liver:	n/a	chr4:28371255-28371266
9	CEBPB	chr4:28352159-28352506	IMR90	lung:	n/a	chr4:28352486-28352499
10	CEBPB	chr4:28375169-28375539	HepG2	liver:	n/a	chr4:28375352-28375363
11	CEBPB	chr4:28371159-28371430	A549	lung:	n/a	chr4:28371255-28371266
12	CEBPB	chr4:28371101-28371445	Hela-S3	cervix:	n/a	chr4:28371255-28371266
13	CEBPB	chr4:28375189-28375517	A549	lung:	n/a	chr4:28375352-28375363
14	CEBPB	chr4:28375209-28375515	K562	blood:	n/a	chr4:28375352-28375363
15	CEBPB	chr4:28343607-28343927	H1-hESC	embryonic stem cell:	n/a	n/a
16	CEBPB	chr4:28416991-28417301	A549	lung:	n/a	chr4:28417145-28417156
17	CEBPB	chr4:28416996-28417324	HepG2	liver:	n/a	chr4:28417145-28417156
18	CEBPB	chr4:28405651-28405923	A549	lung:	n/a	n/a
19	CEBPB	chr4:28371070-28371522	IMR90	lung:	n/a	chr4:28371255-28371266
20	CEBPB	chr4:28375151-28375617	IMR90	lung:	n/a	chr4:28375352-28375363
21	CEBPB	chr4:28416982-28417305	IMR90	lung:	n/a	chr4:28417145-28417156
22	CEBPB	chr4:28405660-28405956	IMR90	lung:	n/a	n/a
23	CEBPB	chr4:28389924-28390443	IMR90	lung:	n/a	n/a
24	CTCF	chr4:28359689-28359926	MCF-7	breast:	n/a	n/a
25	CTCF	chr4:28380180-28380330	GM12869	blood:	n/a	n/a
26	CTCF	chr4:28359660-28359810	HCM	heart:	n/a	n/a
27	CTCF	chr4:28359720-28359870	HVMF	connective:	n/a	n/a
28	CTCF	chr4:28359632-28359997	GM12878	blood:	n/a	n/a
29	CTCF	chr4:28352080-28352230	HMEC	breast:	n/a	n/a
30	CTCF	chr4:28359720-28359870	AG09309	skin:	n/a	n/a
31	CTCF	chr4:28380200-28380350	HMEC	breast:	n/a	n/a
32	CTCF	chr4:28380200-28380350	HCT-116	colon:	n/a	n/a
33	CTCF	chr4:28359753-28359877	A549	lung:	n/a	n/a
34	CTCF	chr4:28359720-28359870	BJ	skin:	n/a	n/a
35	CTCF	chr4:28359700-28359850	SAEC	small airway:	n/a	n/a
36	CTCF	chr4:28352260-28352410	BJ	skin:	n/a	chr4:28352269-28352278 chr4:28352265-28352278
37	CTCF	chr4:28359681-28359947	MCF-7	breast:	n/a	n/a
38	CTCF	chr4:28352140-28352290	AG09309	skin:	n/a	chr4:28352269-28352278 chr4:28352265-28352278
39	CTCF	chr4:28359712-28359928	MCF-7	breast:	n/a	n/a
40	CTCF	chr4:28380200-28380350	HPF	lung:	n/a	n/a
41	CTCF	chr4:28380240-28380390	HVMF	connective:	n/a	n/a
42	CTCF	chr4:28359737-28359922	H1-hESC	embryonic stem cell:	n/a	n/a
43	CTCF	chr4:28359700-28359850	AG09309	skin:	n/a	n/a
44	CTCF	chr4:28380180-28380330	AG04449	skin:	n/a	n/a
45	CTCF	chr4:28380280-28380430	NHEK	skin:	n/a	n/a
46	CTCF	chr4:28380080-28380230	HFF-Myc	foreskin:	n/a	n/a
47	CTCF	chr4:28359733-28359880	Hela-S3	cervix:	n/a	n/a
48	CTCF	chr4:28380180-28380330	HMF	breast:	n/a	n/a
49	CTCF	chr4:28360080-28360230	HMEC	breast:	n/a	n/a
50	CTCF	chr4:28359700-28359850	BE2_C	brain:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:28372854..28374483-chr4:28376190..28379147,2	K562	blood:
2	chr4:28375818..28378318-chr4:28378628..28381458,2	MCF-7	breast:
3	chr4:28398298..28400403-chr4:28402842..28404450,2	MCF-7	breast:
4	chr4:28342479..28345187-chr4:28356107..28357849,2	MCF-7	breast:
5	chr4:28375818..28378318-chr4:28378628..28381458,2	MCF-7	breast:
6	chr17:21448876..21451207-chr4:28392146..28394451,2	MCF-7	breast:
7	chr4:28372854..28374483-chr4:28376190..28379147,2	K562	blood:
8	chr4:28342479..28345187-chr4:28356107..28357849,2	MCF-7	breast:
9	chr4:28418048..28418924-chr6:12148728..12149328,2	MCF-7	breast:

(count:6 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCKAR-5	chr4:28364016-28364214	XLOC_003917
2	lnc-CCKAR-5	chr4:28389343-28389444	XLOC_003917
3	lnc-CCKAR-5	chr4:28372322-28372431	XLOC_003917
4	lnc-CCKAR-5	chr4:28363940-28364214	XLOC_003917
5	lnc-CCKAR-5	chr4:28372322-28372431	XLOC_003917
6	lnc-CCKAR-5	chr4:28394826-28394837	XLOC_003917

No data

Variant related genes	Relation type
ENSG00000250038	TF binding region
ENSG00000250038	chromatin interactions
SLC37A3	miRNA target sites
MPL	miRNA target sites
MPHOSPH9	miRNA target sites
SLC37A2	miRNA target sites

Extended variants
information (count: 2276 )
Associated
traits (count: 56 )

Variant overlapped rSNPs/rCNVs (count:2276 , 50 per page) page: 1 2 3 4 5 6 7 ... 46

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs186764058	chr4:28340701-28340702	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs573036023	chr4:28340706-28340707	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs149249494	chr4:28340723-28340724	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs544981859	chr4:28340742-28340743	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs564909116	chr4:28340746-28340747	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs530952190	chr4:28340831-28340832	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs544541320	chr4:28340859-28340860	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs368986556	chr4:28340940-28340941	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs11730308	chr4:28340959-28340960	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs529173678	chr4:28341063-28341064	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs530225836	chr4:28341071-28341072	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs541095465	chr4:28341092-28341093	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs200730816	chr4:28341096-28341097	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs184857671	chr4:28341107-28341108	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs377501291	chr4:28341125-28341126	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs554520777	chr4:28341408-28341409	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs554051032	chr4:28341416-28341417	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs574044838	chr4:28341522-28341523	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs568384394	chr4:28341543-28341544	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs34524998	chr4:28341548-28341549	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs559920939	chr4:28341579-28341580	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs189139865	chr4:28341623-28341624	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs533732943	chr4:28341678-28341679	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs553580897	chr4:28341722-28341723	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs576650779	chr4:28341740-28341741	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs559695806	chr4:28341761-28341762	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs566580971	chr4:28341780-28341781	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs147324075	chr4:28341805-28341806	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs545067399	chr4:28341830-28341831	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs115061541	chr4:28341871-28341872	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs181747901	chr4:28341926-28341927	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs558241002	chr4:28341947-28341948	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs185144409	chr4:28341961-28341962	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs7686530	chr4:28342046-28342047	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs114766093	chr4:28342150-28342151	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs12507595	chr4:28342172-28342173	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs560639949	chr4:28342179-28342180	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs532768839	chr4:28342187-28342188	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs189667051	chr4:28342202-28342203	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs562606714	chr4:28342237-28342238	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs531198866	chr4:28342268-28342269	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs548202542	chr4:28342294-28342295	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs561026681	chr4:28342322-28342323	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs563132915	chr4:28342341-28342342	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs568244510	chr4:28342370-28342371	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs200752695	chr4:28342384-28342385	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs201614739	chr4:28342428-28342429	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs12511255	chr4:28342430-28342431	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs534067116	chr4:28342432-28342433	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs200691823	chr4:28342434-28342435	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:56)

Disease	PMID	Source
Chronic lymphocytic leukemia	21546498	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Colorectal cancer	19359472	CNVD
Neuroblastoma	17533364	CNVD
Oral squamous cell carcinoma	17134496	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Cancer	21637783	CNVD
Melanoma	21693616	CNVD
Squamous cell cancer	21044232	CNVD
Colorectal cancer	20709793	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Non-small cell lung cancer	21044232	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	17387387	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Cervical cancer	21062161	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Glioblastoma multiforme	21080181	CNVD
Chordoma	21602918	CNVD
HIV/AIDS	22032296	CNVD
Neuroblastoma	18923191	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Breast cancer	21785460	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Lung cancer	18438408	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	21858162	CNVD
small cell lung cancer	20016488	CNVD
Cancer	21183584	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Gastric cancer	21586687	CNVD
lymphocytic leukemia	21291569	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	16608533	CNVD
Non-small cell lung cancer	21829676	CNVD
Melanoma	22183965	CNVD
Multiple myeloma	17550852	CNVD
Prostate cancer	18632612	CNVD
Olfactory neuroblastoma	18408657	CNVD
Burkitt''s lymphoma	20823134	CNVD
Cancer	22183965	CNVD
Melanoma	18172304	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Prostate cancer	16573809	CNVD
Myelofibrosis	22110671	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:154 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:28340600-28341000	Enhancers	iPS-18 Cell Line	embryonic stem cell
2	chr4:28340600-28341200	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr4:28341400-28343000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:28342800-28356600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr4:28343000-28344800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:28344800-28352400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:28351600-28352600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr4:28351800-28353200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr4:28352000-28352800	Enhancers	Muscle Satellite Cultured Cells	--
10	chr4:28352200-28353200	Enhancers	Brain Hippocampus Middle	brain
11	chr4:28352200-28353200	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr4:28352400-28352800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr4:28352600-28354000	Enhancers	HMEC	breast
14	chr4:28352600-28356200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr4:28352800-28353200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr4:28352800-28353200	Enhancers	Brain Cingulate Gyrus	brain
17	chr4:28352800-28353200	Enhancers	Brain Substantia Nigra	brain
18	chr4:28352800-28353600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr4:28352800-28356400	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr4:28353200-28356000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr4:28353200-28356600	Weak transcription	Brain Substantia Nigra	brain
22	chr4:28353600-28353800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr4:28353600-28353800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr4:28353600-28353800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr4:28353600-28353800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr4:28353800-28354000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr4:28353800-28354000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr4:28353800-28354000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr4:28354000-28362200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr4:28354600-28355000	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr4:28355000-28356000	Enhancers	HUVEC	blood vessel
32	chr4:28356000-28357000	Flanking Active TSS	HUVEC	blood vessel
33	chr4:28356000-28357400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr4:28356000-28357600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr4:28356200-28357200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr4:28356400-28356800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr4:28356400-28357000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr4:28356400-28357200	Enhancers	Muscle Satellite Cultured Cells	--
39	chr4:28356600-28356800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr4:28356600-28356800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr4:28356600-28357000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr4:28356600-28357200	Enhancers	Brain Substantia Nigra	brain
43	chr4:28356600-28357400	Enhancers	Brain Hippocampus Middle	brain
44	chr4:28357000-28358000	Enhancers	HUVEC	blood vessel
45	chr4:28357200-28359600	Weak transcription	Brain Substantia Nigra	brain
46	chr4:28357200-28362600	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr4:28357400-28358800	Weak transcription	Brain Hippocampus Middle	brain
48	chr4:28358800-28359000	Enhancers	Brain Hippocampus Middle	brain
49	chr4:28359000-28359400	Weak transcription	Brain Hippocampus Middle	brain
50	chr4:28359400-28359800	Enhancers	Brain Hippocampus Middle	brain

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