Variant report

Variant	nsv525562
Chromosome Location	chr18:39749562-39800893
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	chr18:39772671-39773280	HepG2	liver:	n/a	n/a
2	ARID3A	chr18:39751178-39751423	HepG2	liver:	n/a	n/a
3	ATF2	chr18:39767923-39768305	GM12878	blood:	n/a	n/a
4	BACH1	chr18:39763737-39764096	H1-hESC	embryonic stem cell:	n/a	chr18:39763920-39763934
5	BATF	chr18:39756655-39756883	GM12878	blood:	n/a	n/a
6	BATF	chr18:39767884-39768290	GM12878	blood:	n/a	n/a
7	BATF	chr18:39772309-39772479	GM12878	blood:	n/a	n/a
8	BCL11A	chr18:39767875-39768269	GM12878	blood:	n/a	n/a
9	BCL11A	chr18:39781152-39781461	GM12878	blood:	n/a	n/a
10	BCL11A	chr18:39770644-39770908	GM12878	blood:	n/a	n/a
11	BCL11A	chr18:39767938-39768307	GM12878	blood:	n/a	n/a
12	BCL11A	chr18:39770691-39770876	GM12878	blood:	n/a	n/a
13	BHLHE40	chr18:39781246-39781446	GM12878	blood:	n/a	n/a
14	BHLHE40	chr18:39767925-39768326	GM12878	blood:	n/a	n/a
15	BHLHE40	chr18:39770695-39770944	GM12878	blood:	n/a	n/a
16	BHLHE40	chr18:39756693-39756906	GM12878	blood:	n/a	n/a
17	CEBPB	chr18:39750942-39751500	HepG2	liver:	n/a	chr18:39751342-39751353
18	CEBPB	chr18:39772684-39773133	HepG2	liver:	n/a	chr18:39772945-39772956
19	CEBPB	chr18:39772841-39773103	IMR90	lung:	n/a	chr18:39772945-39772956
20	CEBPB	chr18:39775810-39776051	HepG2	liver:	n/a	chr18:39775912-39775923
21	CEBPB	chr18:39765236-39765310	K562	blood:	n/a	chr18:39765263-39765272 chr18:39765261-39765274 chr18:39765263-39765274 chr18:39765263-39765272 chr18:39765261-39765272 chr18:39765263-39765272 chr18:39765263-39765272
22	CEBPB	chr18:39765115-39765395	IMR90	lung:	n/a	chr18:39765263-39765272 chr18:39765261-39765274 chr18:39765263-39765274 chr18:39765263-39765272 chr18:39765261-39765272 chr18:39765263-39765272 chr18:39765263-39765272
23	CEBPB	chr18:39772756-39773149	A549	lung:	n/a	chr18:39772945-39772956
24	CEBPB	chr18:39765202-39765309	H1-hESC	embryonic stem cell:	n/a	chr18:39765263-39765272 chr18:39765261-39765274 chr18:39765263-39765274 chr18:39765263-39765272 chr18:39765261-39765272 chr18:39765263-39765272 chr18:39765263-39765272
25	CEBPB	chr18:39772729-39773151	Hela-S3	cervix:	n/a	chr18:39772945-39772956
26	CEBPB	chr18:39772777-39773099	A549	lung:	n/a	chr18:39772945-39772956
27	CEBPB	chr18:39765105-39765439	HepG2	liver:	n/a	chr18:39765263-39765272 chr18:39765261-39765274 chr18:39765263-39765274 chr18:39765263-39765272 chr18:39765261-39765272 chr18:39765263-39765272 chr18:39765263-39765272
28	CEBPB	chr18:39753625-39753888	HepG2	liver:	n/a	chr18:39753687-39753698
29	CEBPB	chr18:39756563-39756928	HepG2	liver:	n/a	n/a
30	CEBPB	chr18:39756673-39756835	H1-hESC	embryonic stem cell:	n/a	n/a
31	CHD1	chr18:39762616-39762819	GM12878	blood:	n/a	n/a
32	CHD1	chr18:39767591-39767769	GM12878	blood:	n/a	n/a
33	CHD1	chr18:39768100-39768768	GM12878	blood:	n/a	n/a
34	CHD2	chr18:39767653-39768363	GM12878	blood:	n/a	n/a
35	CHD2	chr18:39762819-39763035	GM12878	blood:	n/a	n/a
36	CTCF	chr18:39770060-39770210	WERI-Rb-1	eye:	n/a	n/a
37	CTCF	chr18:39766506-39766563	GM13976	blood:	n/a	n/a
38	CTCF	chr18:39795040-39795190	HFF-Myc	foreskin:	n/a	n/a
39	CTCF	chr18:39781245-39781267	Lung_OC	lung:	n/a	n/a
40	CTCF	chr18:39783180-39783330	NHEK	skin:	n/a	chr18:39783243-39783252
41	CTCF	chr18:39766540-39766690	WERI-Rb-1	eye:	n/a	n/a
42	CTCF	chr18:39776350-39776387	GM20000	blood:	n/a	n/a
43	CTCF	chr18:39795180-39795330	WERI-Rb-1	eye:	n/a	n/a
44	CTCF	chr18:39766520-39766670	WERI-Rb-1	eye:	n/a	n/a
45	CTCF	chr18:39795000-39795150	WERI-Rb-1	eye:	n/a	n/a
46	CTCF	chr18:39789238-39789275	Medullo	brain:	n/a	n/a
47	CUX1	chr18:39762314-39762431	GM12878	blood:	n/a	n/a
48	CUX1	chr18:39767848-39768426	GM12878	blood:	n/a	n/a
49	CUX1	chr18:39781095-39781492	GM12878	blood:	n/a	n/a
50	CUX1	chr18:39770672-39770868	GM12878	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PIK3C3-5	chr18:39766633-39766727	NONHSAT059068
2	lnc-PIK3C3-5	chr18:39766633-39766727	ENSG00000267586.2
3	lnc-PIK3C3-5	chr18:39766657-39766727	ENSG00000267586.2
4	lnc-PIK3C3-5	chr18:39766635-39766727	ENSG00000267586.2
5	lnc-PIK3C3-5	chr18:39766641-39766727	ENSG00000267586.2
6	lnc-PIK3C3-5	chr18:39792329-39792491	NONHSAT059068
7	lnc-PIK3C3-5	chr18:39792329-39792491	ENSG00000267586.2
8	lnc-PIK3C3-5	chr18:39792329-39792491	ENSG00000267586.2
9	lnc-PIK3C3-5	chr18:39792329-39792491	ENSG00000267586.2
10	lnc-PIK3C3-5	chr18:39792329-39792491	ENSG00000267586.2
11	lnc-PIK3C3-5	chr18:39792329-39792491	NONHSAT059065
12	lnc-PIK3C3-5	chr18:39766633-39766727	ENSG00000267586.2
13	lnc-PIK3C3-5	chr18:39766635-39766727	ENSG00000267586.2
14	lnc-PIK3C3-5	chr18:39766654-39766727	ENSG00000267586.2
15	lnc-PIK3C3-5	chr18:39792329-39792491	NONHSAT059066
16	lnc-PIK3C3-5	chr18:39792329-39792491	ENSG00000267586.2
17	lnc-PIK3C3-5	chr18:39766633-39766727	NONHSAT059065
18	lnc-PIK3C3-5	chr18:39766132-39766356	ENSG00000267586.2
19	lnc-PIK3C3-5	chr18:39792329-39792491	ENSG00000267586.2
20	lnc-PIK3C3-5	chr18:39766633-39766727	NONHSAT059064
21	lnc-RIT2-1	chr18:39766366-39766725	XLOC_012829
22	lnc-PIK3C3-5	chr18:39766668-39766727	ENSG00000267586.2
23	lnc-PIK3C3-5	chr18:39766633-39766727	NONHSAT059066
24	lnc-PIK3C3-5	chr18:39792329-39792491	NONHSAT059064
25	lnc-PIK3C3-5	chr18:39792329-39792491	ENSG00000267586.2
26	lnc-PIK3C3-5	chr18:39766635-39766727	ENSG00000267586.2
27	lnc-PIK3C3-5	chr18:39766650-39766727	ENSG00000267586.2

Variant related genes	Relation type
LINC00907	TF binding region
AKAP12	miRNA target sites

Extended variants
information (count: 952 )
Associated
traits (count: 66 )

Variant overlapped rSNPs/rCNVs (count:952 , 50 per page) page: 1 2 3 4 5 6 7 ... 20

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs16975707	chr18:39749562-39749563	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs536996447	chr18:39749571-39749572	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs558566695	chr18:39749622-39749623	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs576807594	chr18:39749743-39749744	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs540646721	chr18:39749759-39749760	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs559420136	chr18:39749790-39749791	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs143310463	chr18:39749794-39749795	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs561682147	chr18:39749902-39749903	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs542450628	chr18:39749912-39749913	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs539117652	chr18:39749922-39749923	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs563822755	chr18:39749924-39749925	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs531121240	chr18:39749987-39749988	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs75462928	chr18:39750020-39750021	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs564607051	chr18:39750040-39750041	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs150837542	chr18:39750076-39750077	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs9955098	chr18:39750079-39750080	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs1941530	chr18:39750126-39750127	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs535512648	chr18:39750138-39750139	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs116850246	chr18:39750169-39750170	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs569555484	chr18:39750172-39750173	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs536834581	chr18:39750195-39750196	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs571402	chr18:39750200-39750201	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs558841915	chr18:39750230-39750231	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs10502777	chr18:39750263-39750264	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs550304501	chr18:39750268-39750269	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs377565613	chr18:39750304-39750305	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs534626376	chr18:39750320-39750321	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs74821776	chr18:39750328-39750329	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs116253906	chr18:39750334-39750335	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs574587785	chr18:39750375-39750376	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs144270680	chr18:39750396-39750397	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs193167180	chr18:39750423-39750424	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs575942793	chr18:39750424-39750425	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs76267437	chr18:39750454-39750455	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs143330954	chr18:39750455-39750456	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs528741342	chr18:39750475-39750476	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs377361308	chr18:39750512-39750513	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs16975711	chr18:39750521-39750522	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs374719772	chr18:39750564-39750565	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs575053715	chr18:39750607-39750608	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs561796291	chr18:39750611-39750612	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs529240331	chr18:39750648-39750649	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs542474826	chr18:39750672-39750673	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs550696959	chr18:39750682-39750683	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs60666143	chr18:39750697-39750698	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs398079412	chr18:39750702-39750703	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs568988445	chr18:39750703-39750704	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs368191117	chr18:39750704-39750705	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs536867798	chr18:39750709-39750710	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs184995404	chr18:39750756-39750757	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:66)

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

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:39740000-39750000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr18:39749200-39752800	Enhancers	HepG2	liver
3	chr18:39750400-39750600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr18:39758000-39759000	Enhancers	Fetal Brain Male	brain
5	chr18:39758600-39758800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr18:39759600-39760400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr18:39760000-39762600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr18:39762000-39762200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr18:39762000-39764200	Enhancers	NH-A	brain
10	chr18:39762000-39764600	Enhancers	HMEC	breast
11	chr18:39762200-39762600	Enhancers	Fetal Heart	heart
12	chr18:39762200-39762800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr18:39762600-39763000	Weak transcription	Fetal Heart	heart
14	chr18:39762600-39764400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr18:39762600-39764400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr18:39762600-39764400	Enhancers	Placenta Amnion	Placenta Amnion
17	chr18:39762600-39764400	Enhancers	HSMM	muscle
18	chr18:39762800-39763600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr18:39762800-39764200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr18:39762800-39764400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr18:39762800-39764400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr18:39762800-39764400	Enhancers	Muscle Satellite Cultured Cells	--
23	chr18:39762800-39764400	Enhancers	NHEK	skin
24	chr18:39763000-39763600	Enhancers	Fetal Heart	heart
25	chr18:39763000-39764200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr18:39763000-39764200	Enhancers	A549	lung
27	chr18:39763000-39764200	Enhancers	Osteobl	bone
28	chr18:39763200-39763400	Enhancers	Aorta	Aorta
29	chr18:39763200-39764200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr18:39763200-39764200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr18:39763200-39764200	Enhancers	HSMMtube	muscle
32	chr18:39763200-39764200	Enhancers	NHDF-Ad	bronchial
33	chr18:39763200-39764400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr18:39763200-39764400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr18:39763400-39764000	Enhancers	Left Ventricle	heart
36	chr18:39763400-39764000	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr18:39763400-39764200	Enhancers	Esophagus	oesophagus
38	chr18:39763400-39764200	Enhancers	Hela-S3	cervix
39	chr18:39763800-39764200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr18:39764000-39764200	Enhancers	Aorta	Aorta
41	chr18:39764400-39766200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr18:39764400-39767200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr18:39764400-39767800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr18:39764600-39767200	Weak transcription	HMEC	breast
45	chr18:39765200-39767600	Weak transcription	Ovary	ovary
46	chr18:39766800-39768800	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr18:39767200-39768200	Enhancers	HMEC	breast
48	chr18:39767200-39768400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr18:39767600-39768000	Enhancers	Ovary	ovary
50	chr18:39767800-39768000	Bivalent Enhancer	HSMMtube	muscle

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