Variant report

Variant	nsv578956
Chromosome Location	chr19:21751578-21753703
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	CHD2	chr19:21752031-21752238	H1-hESC	embryonic stem cell:	n/a	n/a
2	ELF1	chr19:21751768-21752387	MCF-7	breast:	n/a	n/a
3	ELF1	chr19:21751794-21752441	MCF-7	breast:	n/a	n/a
4	GABPA	chr19:21751655-21752522	MCF-7	breast:	n/a	n/a
5	GABPA	chr19:21751741-21752336	MCF-7	breast:	n/a	n/a
6	HEY1	chr19:21751803-21752127	HepG2	liver:	n/a	n/a
7	HEY1	chr19:21751841-21751988	HepG2	liver:	n/a	n/a
8	HEY1	chr19:21751782-21752096	K562	blood:	n/a	n/a
9	HEY1	chr19:21751817-21752053	K562	blood:	n/a	n/a
10	MAX	chr19:21752172-21752173	NB4	blood:	n/a	n/a
11	MAZ	chr19:21751797-21752330	IMR90	lung:	n/a	n/a
12	NFYA	chr19:21751948-21752166	K562	blood:	n/a	chr19:21752106-21752119 chr19:21752107-21752117 chr19:21752078-21752088 chr19:21752100-21752118 chr19:21752105-21752119
13	NFYB	chr19:21751859-21752289	K562	blood:	n/a	chr19:21752106-21752119 chr19:21752107-21752117 chr19:21752078-21752088 chr19:21752105-21752119
14	NFYB	chr19:21751951-21752188	GM12878	blood:	n/a	chr19:21752106-21752119 chr19:21752107-21752117 chr19:21752078-21752088 chr19:21752105-21752119
15	POLR2A	chr19:21751841-21752007	GM12878	blood:	n/a	n/a
16	POLR2A	chr19:21751697-21752184	GM12891	blood:	n/a	n/a
17	POLR2A	chr19:21751706-21752653	MCF-7	breast:	n/a	n/a
18	POLR2A	chr19:21751776-21752042	GM12878	blood:	n/a	n/a
19	POLR2A	chr19:21752117-21752311	GM12891	blood:	n/a	n/a
20	POLR2A	chr19:21752009-21752030	Gliobla	brain:	n/a	n/a
21	POLR2A	chr19:21751868-21751966	A549	lung:	n/a	n/a
22	POLR2A	chr19:21751548-21752730	PBDE	blood:	n/a	n/a
23	POLR2A	chr19:21751702-21752696	PFSK-1	brain:	n/a	n/a
24	POLR2A	chr19:21751782-21752056	GM12891	blood:	n/a	n/a
25	POLR2A	chr19:21751831-21751995	A549	lung:	n/a	n/a
26	POLR2A	chr19:21751759-21752117	GM12891	blood:	n/a	n/a
27	POLR2A	chr19:21751821-21751998	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr19:21751712-21752114	ProgFib	skin:	n/a	n/a
29	POLR2A	chr19:21751785-21752030	GM12892	blood:	n/a	n/a
30	POLR2A	chr19:21751771-21752191	GM12892	blood:	n/a	n/a
31	POLR2A	chr19:21751844-21751972	A549	lung:	n/a	n/a
32	POLR2A	chr19:21751779-21752078	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr19:21751832-21751986	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr19:21752137-21752281	ProgFib	skin:	n/a	n/a
35	POLR2A	chr19:21751812-21752423	GM12891	blood:	n/a	n/a
36	POLR2A	chr19:21751712-21752254	MCF-7	breast:	n/a	n/a
37	POLR2A	chr19:21751770-21752175	GM12891	blood:	n/a	n/a
38	POLR2A	chr19:21751828-21751988	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr19:21751720-21752289	MCF-7	breast:	n/a	n/a
40	POLR2A	chr19:21751780-21752008	GM12878	blood:	n/a	n/a
41	POLR2A	chr19:21751779-21752014	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr19:21751475-21752310	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr19:21751655-21752026	GM12892	blood:	n/a	n/a
44	POLR2A	chr19:21752460-21752495	MCF-7	breast:	n/a	n/a
45	POLR2A	chr19:21751845-21751977	HepG2	liver:	n/a	n/a
46	POLR2A	chr19:21751812-21752372	Raji	blood:	n/a	n/a
47	POU2F2	chr19:21751757-21752322	GM12891	blood:	n/a	n/a
48	RXRA	chr19:21753061-21753420	HepG2	liver:	n/a	n/a
49	SIN3AK20	chr19:21751850-21751998	HepG2	liver:	n/a	n/a
50	SP1	chr19:21751929-21752321	H1-hESC	embryonic stem cell:	n/a	chr19:21752127-21752136 chr19:21752128-21752137 chr19:21752127-21752141

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF100-2	chr19:21752904-21754341	NONHSAT063726
2	lnc-ZNF100-3	chr19:21751906-21752039	ENSG00000268081.1
3	lnc-ZNF100-2	chr19:21753139-21754341	ENSG00000249473
4	lnc-ZNF100-2	chr19:21753624-21754341	ENSG00000268555.1
5	lnc-ZNF100-3	chr19:21751906-21752048	XLOC_013263

Variant related genes	Relation type
ENSG00000268081	TF binding region

Extended variants
information (count: 158 )
Associated
traits (count: 38 )

Variant overlapped rSNPs/rCNVs (count:158 , 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	rs10854051	chr19:21751578-21751579	Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs186707118	chr19:21751581-21751582	Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
3	rs370717861	chr19:21751611-21751612	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
4	rs572047466	chr19:21751660-21751661	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
5	rs539442252	chr19:21751666-21751667	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
6	rs566073059	chr19:21751668-21751669	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
7	rs576112578	chr19:21751673-21751674	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
8	rs543476951	chr19:21751707-21751708	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
9	rs562231509	chr19:21751745-21751746	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
10	rs369231922	chr19:21751754-21751755	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
11	rs371860226	chr19:21751759-21751760	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
12	rs374815838	chr19:21751770-21751771	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
13	rs370117581	chr19:21751771-21751772	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
14	rs11085464	chr19:21751778-21751779	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	mRNA abundance
15	rs11085465	chr19:21751790-21751791	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
16	rs559793766	chr19:21751791-21751792	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
17	rs11085466	chr19:21751811-21751812	Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs552187077	chr19:21751815-21751816	Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
19	rs564039738	chr19:21751818-21751819	Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
20	rs191677742	chr19:21751825-21751826	Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
21	rs377193938	chr19:21751829-21751830	Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
22	rs374291661	chr19:21751831-21751832	Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
23	rs377722840	chr19:21751832-21751833	Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
24	rs369707988	chr19:21751835-21751836	Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
25	rs11085467	chr19:21751843-21751844	Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
26	rs73025873	chr19:21751847-21751848	Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
27	rs568155294	chr19:21751848-21751849	Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
28	rs11085468	chr19:21751889-21751890	Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
29	rs76475343	chr19:21751895-21751896	Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
30	rs539382711	chr19:21751908-21751909	Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
31	rs142994406	chr19:21751936-21751937	Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
32	rs575998342	chr19:21751977-21751978	Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
33	rs4809135	chr19:21751988-21751989	Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	mRNA abundance
34	rs147229255	chr19:21751996-21751997	Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
35	rs139614387	chr19:21752004-21752005	Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
36	rs555572196	chr19:21752007-21752008	Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
37	rs4808279	chr19:21752009-21752010	Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
38	rs73025877	chr19:21752023-21752024	Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
39	rs552691700	chr19:21752024-21752025	Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	lncRNA	n/a	Overlapped CNVs	n/a
40	rs541244511	chr19:21752040-21752041	Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
41	rs553566245	chr19:21752046-21752047	Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
42	rs73025880	chr19:21752057-21752058	Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region	1 gene(s)	Overlapped CNVs	n/a
43	rs73025883	chr19:21752077-21752078	Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region	1 gene(s)	Overlapped CNVs	n/a
44	rs578228403	chr19:21752078-21752079	Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region	1 gene(s)	Overlapped CNVs	n/a
45	rs545691370	chr19:21752114-21752115	Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region	1 gene(s)	Overlapped CNVs	n/a
46	rs144533425	chr19:21752119-21752120	Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region	1 gene(s)	Overlapped CNVs	n/a
47	rs148433320	chr19:21752129-21752130	Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region	1 gene(s)	Overlapped CNVs	n/a
48	rs531293882	chr19:21752135-21752136	Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region	1 gene(s)	Overlapped CNVs	n/a
49	rs543443447	chr19:21752137-21752138	Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region	1 gene(s)	Overlapped CNVs	n/a
50	rs561622925	chr19:21752138-21752139	Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:38)

Disease	PMID	Source
Medulloblastoma	16783165	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Prostate cancer	16573809	CNVD
Chordoma	18071362	CNVD
Metanephric adenoma	20802469	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	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
Cancer	20164919	CNVD
Thoracic aortic aneurysm	21092924	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Prostate cancer	18632612	CNVD
Autism	22495311	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Acute lymphoblastic leukemia	21248843	CNVD
Lung cancer	18438408	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Myelofibrosis	22110671	CNVD
Cancer	21183584	CNVD
Colorectal cancer	20459617	CNVD
small cell lung cancer	20016488	CNVD
Ductal carcinoma	22052326	CNVD

Chromatin state (count:156 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21738600-21751600	Weak transcription	Osteobl	bone
2	chr19:21743600-21751600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr19:21746600-21751600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr19:21746600-21751600	Weak transcription	Fetal Brain Male	brain
5	chr19:21748400-21751600	Weak transcription	Stomach Mucosa	stomach
6	chr19:21749800-21752800	Active TSS	Duodenum Mucosa	Duodenum
7	chr19:21750200-21752600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr19:21750400-21752800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
9	chr19:21750400-21752800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr19:21750400-21752800	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr19:21750400-21752800	Active TSS	Rectal Smooth Muscle	rectum
12	chr19:21750400-21752800	Active TSS	Right Ventricle	heart
13	chr19:21750400-21753200	Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr19:21750600-21752800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr19:21750600-21752800	Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr19:21750800-21751600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr19:21750800-21751600	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr19:21750800-21751600	Weak transcription	Primary B cells from cord blood	blood
19	chr19:21750800-21751600	Enhancers	Primary B cells from peripheral blood	blood
20	chr19:21750800-21751600	Enhancers	Primary T cells fromperipheralblood	blood
21	chr19:21750800-21751600	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr19:21750800-21751600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr19:21750800-21751600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr19:21750800-21751600	Weak transcription	Liver	Liver
25	chr19:21750800-21751600	Weak transcription	Brain Anterior Caudate	brain
26	chr19:21750800-21751600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr19:21750800-21751600	Weak transcription	Brain Hippocampus Middle	brain
28	chr19:21750800-21751600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr19:21750800-21751600	Weak transcription	Colonic Mucosa	Colon
30	chr19:21750800-21751600	Weak transcription	Esophagus	oesophagus
31	chr19:21750800-21751600	Weak transcription	Placenta	Placenta
32	chr19:21750800-21751600	Weak transcription	Ovary	ovary
33	chr19:21750800-21751600	Weak transcription	Pancreas	Pancrea
34	chr19:21750800-21751600	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr19:21750800-21751600	Weak transcription	Psoas Muscle	Psoas
36	chr19:21750800-21751600	Weak transcription	Right Atrium	heart
37	chr19:21750800-21751600	Active TSS	Dnd41	blood
38	chr19:21750800-21751600	Weak transcription	NHDF-Ad	bronchial
39	chr19:21750800-21751800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr19:21750800-21752400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr19:21750800-21752400	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr19:21750800-21752800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr19:21750800-21752800	Active TSS	Primary T cells from cord blood	blood
44	chr19:21750800-21752800	Active TSS	Adipose Nuclei	Adipose
45	chr19:21750800-21752800	Active TSS	Fetal Lung	lung
46	chr19:21750800-21752800	Active TSS	Thymus	Thymus
47	chr19:21750800-21753200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr19:21751000-21751600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr19:21751000-21751600	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr19:21751000-21752800	Active TSS	Brain Germinal Matrix	brain

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