Variant report

Variant	nsv518540
Chromosome Location	chr19:39697974-39731783
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	ATF3	chr19:39712607-39712845	K562	blood:	n/a	n/a
2	BACH1	chr19:39703059-39703329	H1-hESC	embryonic stem cell:	n/a	n/a
3	BHLHE40	chr19:39703056-39703213	K562	blood:	n/a	n/a
4	BHLHE40	chr19:39728457-39728802	HepG2	liver:	n/a	chr19:39728593-39728609 chr19:39728579-39728595
5	BHLHE40	chr19:39728423-39728840	GM12878	blood:	n/a	chr19:39728593-39728609 chr19:39728579-39728595
6	BHLHE40	chr19:39728458-39728820	K562	blood:	n/a	chr19:39728593-39728609 chr19:39728579-39728595
7	CBX3	chr19:39709790-39710233	HCT-116	colon:	n/a	n/a
8	CBX3	chr19:39706993-39707340	K562	blood:	n/a	n/a
9	CBX3	chr19:39703053-39703437	K562	blood:	n/a	n/a
10	CEBPB	chr19:39731085-39731436	K562	blood:	n/a	chr19:39731251-39731262
11	CEBPB	chr19:39729120-39729238	HepG2	liver:	n/a	chr19:39729176-39729187
12	CEBPB	chr19:39703149-39703448	A549	lung:	n/a	chr19:39703385-39703398
13	CEBPB	chr19:39731146-39731288	Hela-S3	cervix:	n/a	chr19:39731251-39731262
14	CEBPB	chr19:39698122-39698372	K562	blood:	n/a	chr19:39698299-39698310
15	CEBPB	chr19:39698148-39698406	A549	lung:	n/a	chr19:39698299-39698310
16	CEBPB	chr19:39731134-39731355	A549	lung:	n/a	chr19:39731251-39731262
17	CEBPB	chr19:39712673-39712947	IMR90	lung:	n/a	chr19:39712789-39712800
18	CEBPB	chr19:39712765-39712932	H1-hESC	embryonic stem cell:	n/a	chr19:39712789-39712800
19	CEBPB	chr19:39712646-39712965	A549	lung:	n/a	chr19:39712789-39712800
20	CEBPB	chr19:39703111-39703433	K562	blood:	n/a	chr19:39703385-39703398
21	CEBPB	chr19:39712639-39712975	K562	blood:	n/a	chr19:39712789-39712800
22	CEBPB	chr19:39704062-39704196	A549	lung:	n/a	n/a
23	CEBPB	chr19:39731155-39731303	HepG2	liver:	n/a	chr19:39731251-39731262
24	CEBPB	chr19:39698140-39698393	IMR90	lung:	n/a	chr19:39698299-39698310
25	CEBPB	chr19:39703111-39703523	K562	blood:	n/a	chr19:39703385-39703398
26	CEBPB	chr19:39731139-39731423	H1-hESC	embryonic stem cell:	n/a	chr19:39731251-39731262
27	CEBPB	chr19:39698216-39698405	H1-hESC	embryonic stem cell:	n/a	chr19:39698299-39698310
28	CEBPB	chr19:39731092-39731382	K562	blood:	n/a	chr19:39731251-39731262
29	CEBPB	chr19:39703014-39703650	A549	lung:	n/a	chr19:39703385-39703398
30	CEBPB	chr19:39698116-39698407	K562	blood:	n/a	chr19:39698299-39698310
31	CEBPB	chr19:39703010-39703446	H1-hESC	embryonic stem cell:	n/a	chr19:39703385-39703398
32	CEBPB	chr19:39731115-39731428	IMR90	lung:	n/a	chr19:39731251-39731262
33	CEBPB	chr19:39712632-39712945	HepG2	liver:	n/a	chr19:39712789-39712800
34	CEBPB	chr19:39731083-39731426	HepG2	liver:	n/a	chr19:39731251-39731262
35	CEBPB	chr19:39731088-39731408	A549	lung:	n/a	chr19:39731251-39731262
36	CEBPB	chr19:39731083-39731405	A549	lung:	n/a	chr19:39731251-39731262
37	CEBPB	chr19:39698146-39698385	HepG2	liver:	n/a	chr19:39698299-39698310
38	CHD2	chr19:39703116-39703312	H1-hESC	embryonic stem cell:	n/a	n/a
39	CHD2	chr19:39728561-39728708	Hela-S3	cervix:	n/a	n/a
40	CREB1	chr19:39702967-39703279	A549	lung:	n/a	n/a
41	CTCF	chr19:39703080-39703230	HPF	lung:	n/a	n/a
42	CTCF	chr19:39702827-39703464	A549	lung:	n/a	chr19:39702921-39702930 chr19:39702918-39702936 chr19:39702918-39702931 chr19:39702921-39702934
43	CTCF	chr19:39703080-39703230	AG04449	skin:	n/a	n/a
44	CTCF	chr19:39703052-39703294	Medullo	brain:	n/a	n/a
45	CTCF	chr19:39715600-39715750	HBMEC	blood vessel:	n/a	chr19:39715724-39715745 chr19:39715725-39715738 chr19:39715722-39715740
46	CTCF	chr19:39715580-39715730	GM12866	blood:	n/a	n/a
47	CTCF	chr19:39702900-39703050	SK-N-SH_RA	brain:	n/a	chr19:39702921-39702930 chr19:39702918-39702936 chr19:39702918-39702931 chr19:39702921-39702934
48	CTCF	chr19:39703140-39703290	GM12872	blood:	n/a	n/a
49	CTCF	chr19:39715600-39715750	MCF-7	breast:	n/a	chr19:39715724-39715745 chr19:39715725-39715738 chr19:39715722-39715740
50	CTCF	chr19:39703120-39703270	GM12866	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:39699475..39701716-chr19:39889022..39890849,2	MCF-7	breast:
2	chr19:39730623..39732344-chr19:39738357..39741028,2	K562	blood:
3	chr19:39702433..39703702-chr19:39818478..39819662,6	MCF-7	breast:
4	chr19:39715052..39717382-chr19:39902085..39904188,2	MCF-7	breast:
5	chr19:39698828..39701571-chr19:39895887..39898728,2	K562	blood:
6	chr19:39699114..39701619-chr19:39703320..39705265,2	K562	blood:
7	chr19:39727142..39728696-chr19:39832975..39834941,2	K562	blood:
8	chr19:39703112..39705306-chr19:39710340..39712292,2	K562	blood:
9	chr19:39612566..39613389-chr19:39702383..39703279,2	MCF-7	breast:
10	chr19:39694662..39698816-chr19:39700094..39703085,3	K562	blood:
11	chr19:39703112..39705306-chr19:39710340..39712292,2	K562	blood:
12	chr19:39703124..39705684-chr19:39814866..39817784,2	K562	blood:
13	chr19:39727742..39730631-chr19:39743095..39745930,2	K562	blood:
14	chr19:39703124..39706234-chr19:39814866..39817784,3	K562	blood:
15	chr19:39699114..39701619-chr19:39703320..39705265,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NCCRP1-1	chr19:39722411-39722463	NONHSAT066277
2	lnc-NCCRP1-1	chr19:39722730-39722971	NONHSAT066277

Variant related genes	Relation type
IFNL3P1	TF binding region
SYCN	TF binding region
ENSG00000130755	chromatin interactions
ENSG00000213926	chromatin interactions
ENSG00000179134	chromatin interactions
ENSG00000090924	chromatin interactions
ENSG00000272395	chromatin interactions
ENSG00000179751	chromatin interactions
ENSG00000128016	chromatin interactions

Extended variants
information (count: 983 )
Associated
traits (count: 65 )

Variant overlapped rSNPs/rCNVs (count:983 , 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	rs11083515	chr19:39697974-39697975	Weak transcription Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs376658318	chr19:39697984-39697985	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs573778684	chr19:39698032-39698033	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs192646593	chr19:39698033-39698034	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs562482328	chr19:39698042-39698043	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs532857116	chr19:39698085-39698086	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs184407952	chr19:39698089-39698090	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs147255989	chr19:39698101-39698102	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs527259039	chr19:39698156-39698157	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs549432527	chr19:39698200-39698201	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs190467990	chr19:39698233-39698234	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs538090727	chr19:39698260-39698261	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs550341386	chr19:39698285-39698286	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs571816624	chr19:39698305-39698306	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs539139559	chr19:39698316-39698317	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs554270824	chr19:39698328-39698329	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs34318263	chr19:39698372-39698373	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs572490175	chr19:39698380-39698381	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs193098646	chr19:39698392-39698393	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs534625723	chr19:39698462-39698463	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs563693700	chr19:39698465-39698466	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs555406847	chr19:39698482-39698483	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs554877306	chr19:39698500-39698501	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs573868723	chr19:39698522-39698523	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs544121997	chr19:39698599-39698600	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs6508847	chr19:39698601-39698602	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs372984418	chr19:39698640-39698641	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs577376406	chr19:39698644-39698645	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs544718899	chr19:39698649-39698650	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs559786680	chr19:39698665-39698666	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs200206382	chr19:39698740-39698741	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs542593067	chr19:39698798-39698799	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs574631062	chr19:39698799-39698800	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs184315602	chr19:39698821-39698822	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs377112784	chr19:39698915-39698916	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs531471917	chr19:39698921-39698922	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs550161407	chr19:39699088-39699089	Active TSS Bivalent Enhancer Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs149337605	chr19:39699101-39699102	Active TSS Bivalent Enhancer Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs77246584	chr19:39699116-39699117	Active TSS Bivalent Enhancer Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs547935950	chr19:39699140-39699141	Active TSS Bivalent Enhancer Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs566158895	chr19:39699141-39699142	Active TSS Bivalent Enhancer Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs144737200	chr19:39699156-39699157	Active TSS Bivalent Enhancer Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs35862324	chr19:39699215-39699216	Active TSS Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs35203665	chr19:39699226-39699227	Active TSS Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs554943947	chr19:39699227-39699228	Active TSS Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs569902204	chr19:39699255-39699256	Active TSS Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs537293380	chr19:39699256-39699257	Active TSS Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs189087585	chr19:39699290-39699291	Active TSS Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs80336871	chr19:39699324-39699325	Active TSS Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs556876107	chr19:39699333-39699334	Active TSS Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:65)

Disease	PMID	Source
Myelodysplastic syndrome	17634407	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Chordoma	21602918	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Cancer	21637783	CNVD
Retinoblastoma	21504564	CNVD
Medulloblastoma	21979893	CNVD
Ovarian cancer	21720365	CNVD
Cancer	20164919	CNVD
Thoracic aortic aneurysm	21092924	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Prostate cancer	18632612	CNVD
Autism	22495311	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Ductal carcinoma	22052326	CNVD
Pleomorphic liposarcoma	18784837	CNVD
Congenital nephrotic syndrome	18421352	CNVD
Astrocytoma	17934521	CNVD
Leukemia	17361228	CNVD
Adenoid cystic carcinoma	17372589	CNVD
Breast cancer	21858162	CNVD
Breast cancer	17603634	CNVD
Glioma	21971842	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Endometrial cancer	22040021	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Oligodendroglial tumors	17285580	CNVD
renal disease	20603712	CNVD
Salivary gland adenoid cystic carcinoma	17545515	CNVD
Disorders of sex development	21048976	CNVD
Ovarian cancer	22174824	CNVD
Breast cancer	16608533	CNVD
Neuroblastoma	18923191	CNVD
Breast cancer	21364760	CNVD
Invasive pancreatic ductal carcinoma	18765526	CNVD
Rhabdomyosarcoma	16790082	CNVD
Chordoma	18071362	CNVD
Urothelial carcinoma	21177765	CNVD
small cell lung cancer	20016488	CNVD
Wilms tumour	21544195	CNVD
Mental retardation	19951919	CNVD
19q13.11 deletion syndrome	22378287	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	21045282	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Ovarian neoplasms	16753589	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Metanephric adenoma	20802469	CNVD
Acute myeloid leukemia	16864856	CNVD
Lung cancer	21569311	CNVD
Bladder cancer	21909424	CNVD
Medulloblastoma	16783165	CNVD
Breast cancer	21509527	CNVD
Gastric cancer	18160780	CNVD
Hepatocellular carcinoma	16750200	CNVD
Basal cell lymphoma	19029149	CNVD
Breast cancer	20409316	CNVD
Diffuse large b-cell lymphoma	19029149	CNVD
Multiple myeloma	16616336	CNVD
Renal cell carcinoma	18765545	CNVD
Acute myeloid leukemia	20729466	CNVD
Lung cancer	18438408	CNVD

Chromatin state (count:138 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39693600-39699200	Weak transcription	Gastric	stomach
2	chr19:39695800-39702200	Weak transcription	A549	lung
3	chr19:39697200-39700000	Enhancers	Pancreas	Pancrea
4	chr19:39698800-39700400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr19:39699000-39699200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr19:39699000-39699200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
7	chr19:39699000-39699200	Bivalent Enhancer	Stomach Smooth Muscle	stomach
8	chr19:39699000-39699400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr19:39699000-39699400	Enhancers	Spleen	Spleen
10	chr19:39699200-39699400	Enhancers	Gastric	stomach
11	chr19:39699200-39705600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr19:39702200-39703200	Enhancers	A549	lung
13	chr19:39702800-39703000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr19:39702800-39703200	Enhancers	Esophagus	oesophagus
15	chr19:39710600-39710800	Bivalent Enhancer	A549	lung
16	chr19:39711800-39713400	Enhancers	Spleen	Spleen
17	chr19:39715000-39715800	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr19:39715200-39715800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr19:39715200-39716000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr19:39715200-39716000	Enhancers	Monocytes-CD14+_RO01746	blood
21	chr19:39715400-39715800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr19:39715400-39715800	Enhancers	Spleen	Spleen
23	chr19:39715600-39716000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr19:39720600-39720800	Flanking Active TSS	HSMM	muscle
25	chr19:39721200-39721400	Active TSS	Stomach Mucosa	stomach
26	chr19:39721400-39728200	Weak transcription	Stomach Mucosa	stomach
27	chr19:39723200-39727200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr19:39724000-39727200	Weak transcription	Pancreas	Pancrea
29	chr19:39725600-39728200	Weak transcription	Primary T cells from cord blood	blood
30	chr19:39726000-39726200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr19:39726600-39726800	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr19:39726600-39726800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr19:39726600-39729400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr19:39726800-39727400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr19:39726800-39728200	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr19:39726800-39729200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr19:39727000-39728200	Enhancers	Primary T cells fromperipheralblood	blood
38	chr19:39727000-39728200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr19:39727000-39728400	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr19:39727200-39728200	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr19:39727200-39728200	Enhancers	Pancreas	Pancrea
42	chr19:39727200-39729000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr19:39727200-39729200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr19:39727200-39729800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr19:39727400-39728000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr19:39727400-39728200	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr19:39727400-39728400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr19:39727400-39728400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
49	chr19:39727800-39728000	Enhancers	GM12878-XiMat	blood
50	chr19:39728000-39728200	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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