Variant report

Variant	esv3384845
Chromosome Location	chr3:58274062-58278060
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:89)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:89 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:58273920-58274070	AG04450	lung:	n/a	n/a
2	CTCF	chr3:58273980-58274130	GM12875	blood:	n/a	n/a
3	CTCF	chr3:58273980-58274130	GM12864	blood:	n/a	n/a
4	CTCF	chr3:58274000-58274150	SK-N-SH_RA	brain:	n/a	n/a
5	CTCF	chr3:58274000-58274150	NHDF-neo	bronchial:	n/a	n/a
6	CTCF	chr3:58273940-58274090	HEEpiC	esophagus:	n/a	n/a
7	CTCF	chr3:58273940-58274090	Hela-S3	cervix:	n/a	n/a
8	CTCF	chr3:58273980-58274130	HBMEC	blood vessel:	n/a	n/a
9	CTCF	chr3:58274060-58274210	HFF-Myc	foreskin:	n/a	n/a
10	CTCF	chr3:58274000-58274150	HCT-116	colon:	n/a	n/a
11	CTCF	chr3:58273904-58274104	HepG2	liver:	n/a	n/a
12	CTCF	chr3:58273920-58274070	Caco-2	colon:	n/a	n/a
13	CTCF	chr3:58273873-58274178	K562	blood:	n/a	n/a
14	CTCF	chr3:58273872-58274213	K562	blood:	n/a	n/a
15	CTCF	chr3:58273920-58274070	HBMEC	blood vessel:	n/a	n/a
16	CTCF	chr3:58273940-58274090	HRPEpiC	eye:	n/a	n/a
17	CTCF	chr3:58273960-58274110	GM12865	blood:	n/a	n/a
18	CTCF	chr3:58273950-58274132	K562	blood:	n/a	n/a
19	CTCF	chr3:58273980-58274130	NB4	blood:	n/a	n/a
20	CTCF	chr3:58273960-58274110	HPAF	blood vessel:	n/a	n/a
21	CTCF	chr3:58273980-58274130	MCF-7	breast:	n/a	n/a
22	CTCF	chr3:58273940-58274090	HA-sp	spinal cord:	n/a	n/a
23	CTCF	chr3:58273920-58274070	HMF	breast:	n/a	n/a
24	CTCF	chr3:58273960-58274110	RPTEC	kidney:	n/a	n/a
25	CTCF	chr3:58273952-58274095	MCF-7	breast:	n/a	n/a
26	CTCF	chr3:58273884-58274139	K562	blood:	n/a	n/a
27	CTCF	chr3:58273980-58274130	AG09319	gingival:	n/a	n/a
28	CTCF	chr3:58273940-58274090	HepG2	liver:	n/a	n/a
29	CTCF	chr3:58273972-58274126	HepG2	liver:	n/a	n/a
30	CTCF	chr3:58273980-58274130	NHEK	skin:	n/a	n/a
31	CTCF	chr3:58273980-58274130	GM12868	blood:	n/a	n/a
32	CTCF	chr3:58273980-58274130	HPF	lung:	n/a	n/a
33	CTCF	chr3:58273975-58274113	MCF-7	breast:	n/a	n/a
34	CTCF	chr3:58273980-58274130	HCFaa	heart:	n/a	n/a
35	CTCF	chr3:58273920-58274070	GM12869	blood:	n/a	n/a
36	CTCF	chr3:58273920-58274070	GM12872	blood:	n/a	n/a
37	CTCF	chr3:58273960-58274110	A549	lung:	n/a	n/a
38	CTCF	chr3:58273999-58274065	Hela-S3	cervix:	n/a	n/a
39	CTCF	chr3:58273980-58274130	BJ	skin:	n/a	n/a
40	CTCF	chr3:58273920-58274070	AoAF	blood vessel:	n/a	n/a
41	CTCF	chr3:58273969-58274079	GM12878	blood:	n/a	n/a
42	CTCF	chr3:58273920-58274070	HVMF	connective:	n/a	n/a
43	CTCF	chr3:58273920-58274070	GM12873	blood:	n/a	n/a
44	CTCF	chr3:58273886-58274143	K562	blood:	n/a	n/a
45	CTCF	chr3:58273940-58274090	HCPEpiC	choroid plexus:	n/a	n/a
46	CTCF	chr3:58273960-58274110	HVMF	connective:	n/a	n/a
47	CTCF	chr3:58273940-58274090	GM12878	blood:	n/a	n/a
48	CTCF	chr3:58273980-58274130	HEK293	kidney:	n/a	n/a
49	CTCF	chr3:58273940-58274090	GM12868	blood:	n/a	n/a
50	CTCF	chr3:58273983-58274066	MCF-7	breast:	n/a	n/a

No data

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DNASE1L3-2	chr3:58277993-58279527	ENSG00000248224

No data

Variant related genes	Relation type
ABHD6	TF binding region
RPS6KA5	miRNA target sites

Extended variants
information (count: 200 )
Associated
traits (count: 81 )

Variant overlapped rSNPs/rCNVs (count:200 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs537518960	chr3:58274143-58274144	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs74955367	chr3:58274168-58274169	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs570779040	chr3:58274180-58274181	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs574248582	chr3:58274238-58274239	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs539462139	chr3:58274248-58274249	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs10630887	chr3:58274340-58274341	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs33963256	chr3:58274341-58274342	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs10667352	chr3:58274343-58274344	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs79881147	chr3:58274344-58274345	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs552842448	chr3:58274381-58274382	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs572850832	chr3:58274392-58274393	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs149004730	chr3:58274479-58274480	Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs184304651	chr3:58274505-58274506	Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs551735766	chr3:58274539-58274540	Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs560344020	chr3:58274612-58274613	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs143783412	chr3:58274674-58274675	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs200243952	chr3:58274724-58274725	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs544265359	chr3:58274726-58274727	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs564029826	chr3:58274728-58274729	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs77288778	chr3:58274776-58274777	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs189255008	chr3:58274873-58274874	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs560084393	chr3:58274888-58274889	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs542775359	chr3:58274905-58274906	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs548915317	chr3:58274922-58274923	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs569916540	chr3:58274934-58274935	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs568642327	chr3:58274942-58274943	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs371775380	chr3:58274943-58274944	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs79405799	chr3:58274954-58274955	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs199570026	chr3:58274955-58274956	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs397746484	chr3:58274963-58274964	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs6767273	chr3:58274964-58274965	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs6769780	chr3:58274965-58274966	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs181006500	chr3:58274971-58274972	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs6767276	chr3:58274972-58274973	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs6769785	chr3:58274973-58274974	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs12330500	chr3:58275049-58275050	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	mRNA abundance
37	rs373924293	chr3:58275060-58275061	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs570899059	chr3:58275101-58275102	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
39	rs376021656	chr3:58275106-58275107	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
40	rs539819505	chr3:58275116-58275117	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
41	rs34465704	chr3:58275185-58275186	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	mRNA abundance
42	rs7619120	chr3:58275215-58275216	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	mRNA abundance
43	rs377520520	chr3:58275275-58275276	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
44	rs552979975	chr3:58275308-58275309	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
45	rs377765862	chr3:58275318-58275319	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
46	rs566412634	chr3:58275330-58275331	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
47	rs535328715	chr3:58275359-58275360	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
48	rs369888386	chr3:58275360-58275361	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
49	rs534877747	chr3:58275395-58275396	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
50	rs555261651	chr3:58275400-58275401	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:81)

Disease	PMID	Source
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	CNVD
Acute myeloid leukemia	20729466	CNVD
Glioblastoma multiforme	21080181	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Insulin resistance	16721378	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Oral cancer	19627613	CNVD
Renal cell carcinoma	19461508	CNVD
Epithelial cancer	22065749	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Acute myeloid leukemia	16864856	CNVD
Liposarcoma	21253554	CNVD
Basal cell lymphoma	21115979	CNVD
Endometrial cancer	22040021	CNVD
Pancreatic endocrine tumor	20981439	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Oral cancer	21386901	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Lung cancer	18438408	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Esophageal cancer	20955586	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Breast cancer	17133270	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Acute myeloid leukemia	21251322	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21183584	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Non-muscle invasive bladder neoplasm	19445696	CNVD
Breast cancer	21785460	CNVD
Neuroblastoma	17327916	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Squamous cell cancer	20885788	CNVD
Breast cancer	16608533	CNVD
Prostate cancer	21965145	CNVD
Cancer	21129771	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Renal cell carcinoma	18765545	CNVD
small cell lung cancer	20016488	CNVD
Prostate cancer	18632612	CNVD
Myelofibrosis	22110671	CNVD
Urothelial cell carcinoma	18451213	CNVD
Breast cancer	19490591	CNVD
Autism	18414403	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Non-small cell lung cancer	20864512	CNVD
Metastatic melanoma	17975146	CNVD
Cancer	18162546	CNVD
Acute lymphoblastic leukemia	18458336	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:161 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:58237400-58275600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr3:58238000-58276000	Weak transcription	Stomach Mucosa	stomach
3	chr3:58238600-58277400	Weak transcription	GM12878-XiMat	blood
4	chr3:58240600-58281600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr3:58243400-58275200	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr3:58245000-58275600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr3:58246600-58274400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:58246800-58274200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:58251800-58276200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr3:58254800-58276200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:58255200-58276400	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr3:58258000-58275800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr3:58258800-58281600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr3:58258800-58282000	Weak transcription	NHEK	skin
15	chr3:58259000-58274400	Weak transcription	NHLF	lung
16	chr3:58259600-58275000	Weak transcription	K562	blood
17	chr3:58260600-58282400	Weak transcription	NHDF-Ad	bronchial
18	chr3:58260800-58285400	Weak transcription	Fetal Brain Male	brain
19	chr3:58261000-58281000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:58261000-58284000	Weak transcription	Pancreas	Pancrea
21	chr3:58261400-58282200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:58264800-58278000	Weak transcription	Fetal Thymus	thymus
23	chr3:58265600-58274800	Strong transcription	Fetal Intestine Large	intestine
24	chr3:58265800-58274800	Strong transcription	Adipose Nuclei	Adipose
25	chr3:58266000-58274600	Strong transcription	Duodenum Mucosa	Duodenum
26	chr3:58266200-58274200	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr3:58266200-58274400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr3:58266200-58274600	Strong transcription	Primary B cells from peripheral blood	blood
29	chr3:58266400-58274600	Strong transcription	Liver	Liver
30	chr3:58266400-58275000	Strong transcription	Fetal Intestine Small	intestine
31	chr3:58266600-58274400	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr3:58267000-58274600	Strong transcription	Fetal Brain Female	brain
33	chr3:58267200-58274600	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr3:58267200-58274600	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr3:58267200-58276000	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr3:58268000-58280600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr3:58269200-58282000	Weak transcription	Colonic Mucosa	Colon
38	chr3:58270600-58274400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr3:58270600-58274600	Strong transcription	Fetal Stomach	stomach
40	chr3:58270600-58275000	Strong transcription	Brain Germinal Matrix	brain
41	chr3:58270800-58274600	Genic enhancers	Brain Hippocampus Middle	brain
42	chr3:58270800-58275400	Weak transcription	Small Intestine	intestine
43	chr3:58271000-58274600	Strong transcription	Primary T cells from cord blood	blood
44	chr3:58271400-58276600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:58271400-58280000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr3:58271400-58280400	Weak transcription	Primary hematopoietic stem cells	blood
47	chr3:58271400-58281000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr3:58271400-58282000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr3:58272200-58274400	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr3:58272200-58274600	Strong transcription	Duodenum Smooth Muscle	Duodenum

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