Variant report

Variant	nsv978785
Chromosome Location	chr19:19698523-19699427
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	GABPA	chr19:19699142-19699233	HepG2	liver:	n/a	n/a
2	GABPA	chr19:19699112-19699268	Hela-S3	cervix:	n/a	n/a
3	GABPA	chr19:19699138-19699234	HepG2	liver:	n/a	n/a
4	GABPA	chr19:19699131-19699242	GM12878	blood:	n/a	n/a
5	HEY1	chr19:19699127-19699244	HepG2	liver:	n/a	n/a
6	POLR2A	chr19:19699127-19699243	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr19:19699104-19699268	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr19:19699140-19699225	A549	lung:	n/a	n/a
9	POLR2A	chr19:19699124-19699238	HepG2	liver:	n/a	n/a
10	POLR2A	chr19:19699000-19699817	GM12892	blood:	n/a	n/a
11	POLR2A	chr19:19699117-19699256	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr19:19699091-19699232	GM12878	blood:	n/a	n/a
13	POLR2A	chr19:19699189-19699216	K562	blood:	n/a	n/a
14	POLR2A	chr19:19699082-19699265	GM12878	blood:	n/a	n/a
15	POLR2A	chr19:19698892-19699484	GM12892	blood:	n/a	n/a
16	POLR2A	chr19:19699097-19699269	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr19:19699094-19699236	GM12878	blood:	n/a	n/a
18	POLR2A	chr19:19699190-19699227	ProgFib	skin:	n/a	n/a
19	POLR2A	chr19:19699066-19699300	GM12878	blood:	n/a	n/a
20	POLR2A	chr19:19699098-19699262	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr19:19699179-19699338	HUVEC	blood vessel:	n/a	n/a
22	RCOR1	chr19:19699321-19699967	IMR90	lung:	n/a	n/a
23	RFX5	chr19:19699224-19699777	IMR90	lung:	n/a	chr19:19699531-19699540 chr19:19699529-19699543
24	TAF1	chr19:19699094-19699323	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:19699149..19708161-chr19:19735507..19742255,11	MCF-7	breast:

Variant related genes	Relation type
PHF5CP	TF binding region
ENSG00000064547	chromatin interactions

Extended variants
information (count: 42 )
Associated
traits (count: 62 )

Variant overlapped rSNPs/rCNVs (count:42 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs183231323	chr19:19698524-19698525	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs117171447	chr19:19698528-19698529	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs111724333	chr19:19698529-19698530	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs553143893	chr19:19698541-19698542	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs572650766	chr19:19698548-19698549	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs541479998	chr19:19698612-19698613	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs112286031	chr19:19698629-19698630	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs575101379	chr19:19698631-19698632	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs544171091	chr19:19698632-19698633	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs564255318	chr19:19698658-19698659	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs533251626	chr19:19698670-19698671	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs147097281	chr19:19698672-19698673	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs16982921	chr19:19698678-19698679	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs186441869	chr19:19698740-19698741	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs548357244	chr19:19698871-19698872	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs138190145	chr19:19698915-19698916	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs537078991	chr19:19698940-19698941	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs191204120	chr19:19698968-19698969	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs570850364	chr19:19698996-19698997	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs539744592	chr19:19699040-19699041	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs553156117	chr19:19699049-19699050	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs182250783	chr19:19699063-19699064	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs113497924	chr19:19699082-19699083	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs555196975	chr19:19699099-19699100	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs575280720	chr19:19699114-19699115	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs113276622	chr19:19699118-19699119	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs148301125	chr19:19699143-19699144	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs576671117	chr19:19699156-19699157	Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs375124632	chr19:19699160-19699161	Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs7255953	chr19:19699174-19699175	Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs560403161	chr19:19699192-19699193	Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs529070788	chr19:19699222-19699223	Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs542787176	chr19:19699287-19699288	Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs562077219	chr19:19699302-19699303	Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs187986559	chr19:19699316-19699317	Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs550748405	chr19:19699335-19699336	Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
37	rs570468179	chr19:19699347-19699348	Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
38	rs533457348	chr19:19699348-19699349	Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
39	rs546857650	chr19:19699368-19699369	Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
40	rs566800944	chr19:19699396-19699397	Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
41	rs140229040	chr19:19699399-19699400	Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
42	rs79178529	chr19:19699418-19699419	Weak transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:62)

Disease	PMID	Source
Follicular lymphoma	20505157	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Non-syndromic sensorineural hearing loss	20179077	CNVD
Melanoma	18172304	CNVD
Glioblastoma multiforme	21080181	CNVD
Metanephric adenoma	20802469	CNVD
Prostate cancer	16573809	CNVD
Breast cancer	16608533	CNVD
Lung cancer	17297452	CNVD
Salivary gland adenoid cystic carcinoma	17545515	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Medulloblastoma	16783165	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Chordoma	18071362	CNVD
Ewing''s sarcoma	21437220	CNVD
Medulloblastoma	21979893	CNVD
Oligodendroglial tumors	17285580	CNVD
Oral cancer	21386901	CNVD
ovarian endometriomas	16273235	CNVD
Endometrial cancer	22040021	CNVD
Acute myeloid leukemia	16864856	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Cervical cancer	21063398	CNVD
Myelodysplastic syndrome	17634407	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Chordoma	21602918	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Cancer	21637783	CNVD
Retinoblastoma	21504564	CNVD
Ovarian cancer	21720365	CNVD
Urothelial carcinoma	21177765	CNVD
Cancer	20164919	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Basal cell lymphoma	21115979	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Prostate cancer	18632612	CNVD
Autism	22495311	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	21248843	CNVD
Breast cancer	21364760	CNVD
Mycobacterial infection	18421352	CNVD
Glioblastoma multiforme	22286061	CNVD
Acute monocytic leukemia	16498392	CNVD
Lung cancer	18438408	CNVD
Barrett''s adenocarcinoma	18663352	CNVD
Liver carcinoma	19366792	CNVD
Colorectal cancer	19455253	CNVD
Lujan-Fryns syndrom	21521776	CNVD
Breast cancer	20409316	CNVD
Cancer	17160897	CNVD
Cancer	17440070	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Breast cancer	21509527	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Glioma	20126413	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD
Non-syndromic sensorineural hearing loss	19587683	CNVD

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19671600-19701800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr19:19672000-19704800	Weak transcription	Brain Angular Gyrus	brain
3	chr19:19674200-19699800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr19:19676200-19701600	Weak transcription	GM12878-XiMat	blood
5	chr19:19681200-19701600	Weak transcription	NHLF	lung
6	chr19:19681400-19701600	Weak transcription	Fetal Lung	lung
7	chr19:19681600-19701600	Weak transcription	Esophagus	oesophagus
8	chr19:19681600-19703200	Weak transcription	Dnd41	blood
9	chr19:19682000-19702200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr19:19682600-19700600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr19:19686600-19700600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr19:19687000-19701600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr19:19688400-19699000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr19:19689800-19698800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr19:19689800-19700600	Weak transcription	Thymus	Thymus
16	chr19:19689800-19701800	Weak transcription	Fetal Brain Female	brain
17	chr19:19691000-19698600	Weak transcription	Brain Germinal Matrix	brain
18	chr19:19691200-19699600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr19:19691200-19700600	Weak transcription	Primary T cells from cord blood	blood
20	chr19:19691400-19699200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr19:19691400-19699400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr19:19693000-19701600	Weak transcription	Fetal Stomach	stomach
23	chr19:19693200-19701000	Weak transcription	Duodenum Mucosa	Duodenum
24	chr19:19693200-19702200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr19:19693400-19698800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr19:19693400-19698800	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr19:19693400-19699000	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr19:19693400-19700400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr19:19693400-19700600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr19:19693800-19698600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr19:19693800-19698800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr19:19693800-19699400	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr19:19696000-19700600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr19:19696400-19701600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr19:19696600-19702000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr19:19698400-19702200	Weak transcription	Brain Cingulate Gyrus	brain
37	chr19:19698600-19699000	Enhancers	Brain Germinal Matrix	brain
38	chr19:19698600-19699200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr19:19698600-19699200	Enhancers	Fetal Brain Male	brain
40	chr19:19698800-19699200	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr19:19698800-19699400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr19:19698800-19700400	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr19:19698800-19708400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr19:19699000-19699600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr19:19699000-19699600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr19:19699000-19699600	Weak transcription	Brain Germinal Matrix	brain
47	chr19:19699000-19700000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr19:19699000-19700000	Enhancers	NHDF-Ad	bronchial
49	chr19:19699000-19703200	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr19:19699200-19699400	Enhancers	HMEC	breast

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