Variant report

Variant	nsv1064973
Chromosome Location	chr18:39623604-39711798
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	chr18:39627775-39627961	HepG2	liver:	n/a	n/a
2	ARID3A	chr18:39693941-39694141	K562	blood:	n/a	n/a
3	ARID3A	chr18:39693801-39694659	HepG2	liver:	n/a	n/a
4	ARID3A	chr18:39692657-39693205	HepG2	liver:	n/a	n/a
5	ATF1	chr18:39681004-39681204	K562	blood:	n/a	n/a
6	BATF	chr18:39694341-39694593	GM12878	blood:	n/a	n/a
7	BCL11A	chr18:39693887-39694158	GM12878	blood:	n/a	n/a
8	BHLHE40	chr18:39694015-39694627	GM12878	blood:	n/a	n/a
9	BHLHE40	chr18:39692743-39693176	HepG2	liver:	n/a	n/a
10	BHLHE40	chr18:39680937-39681019	K562	blood:	n/a	n/a
11	BHLHE40	chr18:39633170-39633508	GM12878	blood:	n/a	n/a
12	CCNT2	chr18:39639300-39639506	K562	blood:	n/a	n/a
13	CEBPB	chr18:39635278-39635296	K562	blood:	n/a	chr18:39635281-39635294 chr18:39635281-39635294
14	CEBPB	chr18:39669715-39669927	HepG2	liver:	n/a	chr18:39669902-39669913
15	CEBPB	chr18:39628103-39628489	HepG2	liver:	n/a	chr18:39628290-39628301
16	CEBPB	chr18:39652095-39652530	Hela-S3	cervix:	n/a	chr18:39652130-39652143 chr18:39652130-39652143 chr18:39652472-39652485
17	CEBPB	chr18:39652042-39652166	K562	blood:	n/a	chr18:39652130-39652143 chr18:39652130-39652143
18	CEBPB	chr18:39647958-39648448	HepG2	liver:	n/a	chr18:39647970-39647981 chr18:39647965-39647982 chr18:39648314-39648325 chr18:39647968-39647981
19	CEBPB	chr18:39694046-39694188	H1-hESC	embryonic stem cell:	n/a	n/a
20	CEBPB	chr18:39628173-39628430	HepG2	liver:	n/a	chr18:39628290-39628301
21	CEBPB	chr18:39692670-39693072	HepG2	liver:	n/a	n/a
22	CEBPB	chr18:39669660-39669930	IMR90	lung:	n/a	chr18:39669902-39669913
23	CEBPB	chr18:39628182-39628413	ECC-1	luminal epithelium:	n/a	chr18:39628290-39628301
24	CEBPB	chr18:39628107-39628479	A549	lung:	n/a	chr18:39628290-39628301
25	CEBPB	chr18:39629868-39630086	H1-hESC	embryonic stem cell:	n/a	chr18:39629962-39629971 chr18:39629962-39629971 chr18:39629962-39629971
26	CEBPB	chr18:39667263-39667436	K562	blood:	n/a	chr18:39667298-39667309
27	CEBPB	chr18:39629885-39630036	K562	blood:	n/a	chr18:39629962-39629971 chr18:39629962-39629971 chr18:39629962-39629971
28	CEBPB	chr18:39648205-39648478	A549	lung:	n/a	chr18:39648314-39648325
29	CEBPB	chr18:39629854-39630110	A549	lung:	n/a	chr18:39629962-39629971 chr18:39629962-39629971 chr18:39629962-39629971
30	CEBPB	chr18:39697899-39698038	Hela-S3	cervix:	n/a	chr18:39697953-39697964
31	CEBPB	chr18:39693765-39694280	HCT-116	colon:	n/a	chr18:39694042-39694053
32	CEBPB	chr18:39693858-39694232	HepG2	liver:	n/a	chr18:39694042-39694053
33	CEBPB	chr18:39693864-39694214	HepG2	liver:	n/a	chr18:39694042-39694053
34	CEBPB	chr18:39693873-39694205	K562	blood:	n/a	chr18:39694042-39694053
35	CEBPB	chr18:39628040-39628537	Hela-S3	cervix:	n/a	chr18:39628290-39628301
36	CEBPB	chr18:39693866-39694191	K562	blood:	n/a	chr18:39694042-39694053
37	CEBPB	chr18:39629819-39630086	HepG2	liver:	n/a	chr18:39629962-39629971 chr18:39629962-39629971 chr18:39629962-39629971
38	CEBPB	chr18:39628115-39628508	MCF-7	breast:	n/a	chr18:39628290-39628301
39	CEBPB	chr18:39628127-39628433	H1-hESC	embryonic stem cell:	n/a	chr18:39628290-39628301
40	CEBPB	chr18:39627997-39628587	MCF-7	breast:	n/a	chr18:39628290-39628301
41	CEBPB	chr18:39693929-39694143	HepG2	liver:	n/a	chr18:39694042-39694053
42	CEBPB	chr18:39697809-39698139	HepG2	liver:	n/a	chr18:39697953-39697964
43	CEBPB	chr18:39651980-39652598	IMR90	lung:	n/a	chr18:39652130-39652143 chr18:39652130-39652143 chr18:39652472-39652485
44	CEBPB	chr18:39628182-39628448	HepG2	liver:	n/a	chr18:39628290-39628301
45	CEBPB	chr18:39693875-39694578	Hela-S3	cervix:	n/a	chr18:39694042-39694053
46	CEBPB	chr18:39624351-39624566	H1-hESC	embryonic stem cell:	n/a	chr18:39624432-39624443
47	CEBPB	chr18:39667259-39667419	HepG2	liver:	n/a	chr18:39667298-39667309
48	CEBPB	chr18:39697904-39698025	H1-hESC	embryonic stem cell:	n/a	chr18:39697953-39697964
49	CEBPB	chr18:39693879-39694190	HepG2	liver:	n/a	chr18:39694042-39694053
50	CEBPB	chr18:39624311-39624566	HepG2	liver:	n/a	chr18:39624432-39624443

No.	Distal block	Cell Line	Cell type
1	chr18:39634544..39636615-chr18:39639116..39640932,2	K562	blood:
2	chr18:39653176..39655902-chr18:39657058..39659990,2	MCF-7	breast:
3	chr18:39694318..39694934-chr18:40851655..40852415,2	MCF-7	breast:
4	chr18:39653176..39655902-chr18:39657058..39659990,2	MCF-7	breast:
5	chr18:39631810..39632517-chr18:39878504..39879351,2	MCF-7	breast:
6	chr18:39634544..39636615-chr18:39639116..39640932,2	K562	blood:
7	chr18:39631949..39632783-chr18:41143572..41144215,2	MCF-7	breast:
8	chr18:39633144..39633820-chr18:39854093..39855052,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PIK3C3-3	chr18:39669276-39669716	NONHSAT059060
2	lnc-SETBP1-8	chr18:39661838-39663348	NONHSAT059059

No.	miRNA target gene	miRNA name	Chromosome Location	mirBase accession
1	PIK3C3	hsa-miR-98-5p	chr18:39630215-39630240
2	PIK3C3	hsa-miR-98-5p	chr18:39630469-39630491

Variant related genes	Relation type
ENSG00000267088	TF binding region
PIK3C3	TF binding region
ENSG00000132872	chromatin interactions

Extended variants
information (count: 2706 )
Associated
traits (count: 67 )

Variant overlapped rSNPs/rCNVs (count:2706 , 50 per page) page: 1 2 3 4 5 6 7 ... 55

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs79723155	chr18:39623607-39623608	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs193275333	chr18:39623611-39623612	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs376815298	chr18:39623649-39623650	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs562461717	chr18:39623664-39623665	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs532994170	chr18:39623675-39623676	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs201615084	chr18:39623696-39623697	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs141681761	chr18:39623769-39623770	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs188415744	chr18:39623816-39623817	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs144413269	chr18:39623817-39623818	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs191339501	chr18:39623818-39623819	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs538136325	chr18:39623890-39623891	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs534507	chr18:39623942-39623943	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs146617972	chr18:39623969-39623970	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs184333089	chr18:39624028-39624029	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs553895550	chr18:39624030-39624031	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs141347467	chr18:39624041-39624042	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs189804092	chr18:39624053-39624054	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs150277824	chr18:39624068-39624069	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs573925874	chr18:39624257-39624258	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs544517882	chr18:39624309-39624310	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs562801099	chr18:39624312-39624313	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs199797920	chr18:39624316-39624317	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs34725564	chr18:39624335-39624336	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs537532784	chr18:39624336-39624337	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs397722376	chr18:39624345-39624346	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs372010751	chr18:39624375-39624376	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs373188898	chr18:39624397-39624398	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs181120881	chr18:39624411-39624412	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs368500695	chr18:39624415-39624416	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
30	rs112941935	chr18:39624416-39624417	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs115510562	chr18:39624467-39624468	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs542063893	chr18:39624498-39624499	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
33	rs371444195	chr18:39624501-39624502	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs548706183	chr18:39624502-39624503	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
35	rs185290324	chr18:39624599-39624600	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs577171559	chr18:39624703-39624704	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs189865393	chr18:39624726-39624727	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs560316208	chr18:39624741-39624742	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs181910747	chr18:39624746-39624747	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs571874309	chr18:39624785-39624786	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs536017832	chr18:39624804-39624805	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs547724269	chr18:39624811-39624812	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs373210284	chr18:39624812-39624813	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs148932654	chr18:39624817-39624818	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs186180545	chr18:39624863-39624864	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs368612974	chr18:39624955-39624956	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs377286791	chr18:39624964-39624965	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs564210590	chr18:39624986-39624987	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs143640435	chr18:39625023-39625024	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs573861502	chr18:39625040-39625041	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:67)

Disease	PMID	Source
Follicular lymphoma	20505157	CNVD
Chordoma	21602918	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	18923191	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	21080181	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Cancer	21637783	CNVD
Medulloblastoma	21979893	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Trisomy 18 syndrome	17576883	CNVD
lymphocytic leukemia	21291569	CNVD
Barrett''s syndrome	19417022	CNVD
Ewing''s sarcoma	17952124	CNVD
Multiple myeloma	17550852	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Melanoma	18172304	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
18q deletion syndrome	19533772	CNVD
Acute myeloid leukemia	16864856	CNVD
Colorectal cancer	21102417	CNVD
Colorectal cancer	20709793	CNVD
Pancreatic cancer	21811562	CNVD
Basal cell lymphoma	21115979	CNVD
Mucosa-associated lymphoid tissue lymphomas	21459788	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Oligodendroglial tumors	17285580	CNVD
colon cancer	17210682	CNVD
Breast cancer	21785460	CNVD
Hepatocellular carcinoma	16750200	CNVD
Prostate cancer	16573809	CNVD
Autism	16446308	CNVD
Colorectal cancer	19359472	CNVD
Colorectal cancer	16272173	CNVD
Human rectal carcinomas	16397240	CNVD
Medulloblastoma	18056178	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Cancer	16751803	CNVD
Metanephric adenoma	20802469	CNVD
small cell lung cancer	20016488	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Colorectal cancer	16774939	CNVD
Colorectal cancer	21297112	CNVD
Cancer	21183584	CNVD
Breast cancer	17603634	CNVD
Thyroid cancer	19087340	CNVD
Urothelial carcinoma	21177765	CNVD
Oral cancer	21386901	CNVD
Colorectal cancer	19150955	CNVD
Acute myeloid leukemia	21251322	CNVD
Colorectal cancer	16912164	CNVD
Lung cancer	18438408	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Myelofibrosis	22110671	CNVD
Schizophrenia	22241247	CNVD
Seminomas	18059402	CNVD
Breast cancer	16272173	CNVD
Pancreatic cancer	21811587	CNVD
Congenital anomalies of the kidney and urinary tract	20467480	CNVD
Breast cancer	17133270	CNVD
prenatal diagnosis	22389664	CNVD
Prostate cancer	22341455	CNVD

Chromatin state (count:1346 , 50 per page) page: 1 2 3 4 5 6 7 ... 27

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:39536800-39633600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr18:39548400-39670000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr18:39572000-39654400	Weak transcription	Colonic Mucosa	Colon
4	chr18:39578400-39663200	Weak transcription	Fetal Heart	heart
5	chr18:39581000-39647400	Weak transcription	Spleen	Spleen
6	chr18:39581000-39666200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr18:39585000-39646000	Weak transcription	Pancreas	Pancrea
8	chr18:39585000-39658600	Weak transcription	Small Intestine	intestine
9	chr18:39585400-39627600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr18:39586600-39647400	Weak transcription	Thymus	Thymus
11	chr18:39590600-39668000	Weak transcription	Esophagus	oesophagus
12	chr18:39592200-39629400	Weak transcription	Fetal Brain Female	brain
13	chr18:39594600-39638800	Weak transcription	K562	blood
14	chr18:39599000-39646000	Weak transcription	Psoas Muscle	Psoas
15	chr18:39601600-39668200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr18:39606200-39628200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr18:39607400-39626000	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr18:39607600-39634600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr18:39608600-39627400	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr18:39608800-39631400	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr18:39609000-39625600	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr18:39609000-39628600	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr18:39609200-39624000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr18:39609200-39624200	Strong transcription	Duodenum Smooth Muscle	Duodenum
25	chr18:39609200-39625800	Strong transcription	Primary T cells from cord blood	blood
26	chr18:39609200-39626000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr18:39609200-39626600	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr18:39609200-39631400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr18:39609200-39631600	Strong transcription	Primary B cells from peripheral blood	blood
30	chr18:39609400-39626200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr18:39609800-39630400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr18:39610200-39626200	Strong transcription	Liver	Liver
33	chr18:39610600-39628000	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr18:39611600-39627600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr18:39612200-39647400	Weak transcription	Aorta	Aorta
36	chr18:39612200-39666400	Weak transcription	Gastric	stomach
37	chr18:39612200-39669800	Weak transcription	Fetal Stomach	stomach
38	chr18:39612200-39670000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr18:39612400-39624000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr18:39613400-39626200	Strong transcription	Duodenum Mucosa	Duodenum
41	chr18:39613800-39631200	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr18:39613800-39631400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr18:39614200-39624000	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr18:39614400-39631400	Strong transcription	Primary B cells from cord blood	blood
45	chr18:39615000-39649600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr18:39615400-39663400	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr18:39617000-39623800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr18:39617400-39624600	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr18:39617400-39626400	Strong transcription	Adipose Nuclei	Adipose
50	chr18:39618000-39647400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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