Variant report

Variant	rs559982420
Chromosome Location	chr19:42037763-42037764
allele	C/T
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	PML	chr19:42037417-42038526	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:42037723-42038093	ProgFib	skin:	n/a	n/a
3	POLR2A	chr19:42035639-42038770	GM12892	blood:	n/a	n/a
4	POLR2A	chr19:42037705-42038141	GM19193	blood:	n/a	n/a
5	POLR2A	chr19:42037680-42038123	GM12878	blood:	n/a	n/a
6	POLR2A	chr19:42037732-42038137	HL-60	blood:	n/a	n/a
7	POLR2A	chr19:42035603-42038761	GM12892	blood:	n/a	n/a
8	POLR2A	chr19:42037312-42038131	HUVEC	blood vessel:	n/a	n/a
9	GATA2	chr19:42036805-42038499	HUVEC	blood vessel:	n/a	chr19:42037364-42037378
10	MTA3	chr19:42037542-42038726	GM12878	blood:	n/a	n/a
11	POLR2A	chr19:42037710-42038520	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr19:42035835-42038400	GM12892	blood:	n/a	n/a
13	BCLAF1	chr19:42037618-42038574	GM12878	blood:	n/a	n/a
14	POU2F2	chr19:42037685-42038146	GM12891	blood:	n/a	n/a
15	POLR2A	chr19:42036966-42038325	HUVEC	blood vessel:	n/a	n/a
16	POU2F2	chr19:42037743-42037982	GM12878	blood:	n/a	n/a
17	POLR2A	chr19:42037347-42038286	GM12891	blood:	n/a	n/a
18	RUNX3	chr19:42037051-42038600	GM12878	blood:	n/a	n/a
19	POLR2A	chr19:42037702-42038215	GM15510	blood:	n/a	n/a
20	POLR2A	chr19:42037623-42038291	SK-N-MC	brain:	n/a	n/a
21	SP1	chr19:42037691-42038174	GM12878	blood:	n/a	chr19:42037987-42037996 chr19:42038010-42038031 chr19:42037985-42037997
22	POLR2A	chr19:42037642-42038624	GM12878	blood:	n/a	n/a
23	POLR2A	chr19:42037699-42038283	GM19099	blood:	n/a	n/a
24	PML	chr19:42037733-42038275	GM12878	blood:	n/a	n/a
25	ATF2	chr19:42037562-42038519	GM12878	blood:	n/a	n/a
26	POLR2A	chr19:42037393-42038119	GM12878	blood:	n/a	n/a
27	POLR2A	chr19:42035831-42038634	GM18505	blood:	n/a	n/a
28	POLR2A	chr19:42037719-42038040	MCF-7	breast:	n/a	n/a
29	POLR2A	chr19:42036880-42038248	GM12878	blood:	n/a	n/a
30	POLR2A	chr19:42036953-42037848	PFSK-1	brain:	n/a	n/a
31	POLR2A	chr19:42037689-42038238	GM18951	blood:	n/a	n/a
32	SETDB1	chr19:42034208-42038482	U2OS	brain:	n/a	n/a
33	CREB1	chr19:42037640-42038535	GM12878	blood:	n/a	n/a
34	FOS	chr19:42036986-42038293	HUVEC	blood vessel:	n/a	chr19:42038013-42038022
35	POLR2A	chr19:42037008-42038245	GM12892	blood:	n/a	n/a
36	POLR2A	chr19:42037759-42038064	MCF-7	breast:	n/a	n/a
37	RUNX3	chr19:42035847-42038620	GM12878	blood:	n/a	chr19:42036623-42036632 chr19:42036623-42036632
38	TAF1	chr19:42037723-42038023	GM12891	blood:	n/a	n/a
39	POLR2A	chr19:42037700-42038142	GM12878	blood:	n/a	n/a
40	CREB1	chr19:42037728-42038519	GM12878	blood:	n/a	n/a
41	POLR2A	chr19:42037001-42038122	GM12891	blood:	n/a	n/a
42	POLR2A	chr19:42035800-42038175	GM12891	blood:	n/a	n/a
43	POLR2A	chr19:42037707-42038256	MCF10A-Er-Src	breast:	n/a	n/a
44	TBP	chr19:42037756-42038080	K562	blood:	n/a	n/a
45	POLR2A	chr19:42037713-42038109	Raji	blood:	n/a	n/a
46	POLR2A	chr19:42037680-42038236	GM12892	blood:	n/a	n/a
47	MEF2A	chr19:42037712-42038529	GM12878	blood:	n/a	chr19:42038215-42038236
48	ZNF263	chr19:42037435-42038280	HEK293-T-REx	kidney:	n/a	n/a
49	TAF1	chr19:42037678-42038162	GM12878	blood:	n/a	n/a
50	POLR2A	chr19:42036915-42038505	HUVEC	blood vessel:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CEACAM21-3	chr19:42037647-42037935	ENSG00000268355.1

Variant related genes	Relation type
ENSG00000270164	TF binding region

Extended variants
information (count: 8 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv510767	chr19:41962486-42049165	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv911770	chr19:41962486-42066279	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv911771	chr19:41962486-42085873	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv1055515	chr19:41968797-42057334	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv911772	chr19:41985624-42066279	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv911773	chr19:42001210-42085873	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv579602	chr19:42015468-42047924	Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv978751	chr19:42036596-42073874	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42035000-42038400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:42036200-42038000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr19:42036200-42038200	Active TSS	HSMMtube	muscle
4	chr19:42036400-42038400	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr19:42036600-42038000	Bivalent Enhancer	Fetal Thymus	thymus
6	chr19:42036600-42038800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
7	chr19:42036600-42038800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr19:42036800-42038000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr19:42036800-42038000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr19:42036800-42038000	Enhancers	Spleen	Spleen
11	chr19:42036800-42038800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr19:42036800-42039400	Flanking Active TSS	Primary B cells from cord blood	blood
13	chr19:42037000-42037800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
14	chr19:42037000-42037800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr19:42037000-42037800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
16	chr19:42037000-42037800	Weak transcription	Lung	lung
17	chr19:42037000-42038600	Flanking Active TSS	Primary T cells from cord blood	blood
18	chr19:42037000-42038800	Enhancers	Fetal Muscle Leg	muscle
19	chr19:42037200-42037800	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr19:42037200-42038000	Flanking Active TSS	Primary hematopoietic stem cells	blood
21	chr19:42037200-42038000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
22	chr19:42037200-42038000	Enhancers	HMEC	breast
23	chr19:42037200-42038400	Weak transcription	Left Ventricle	heart
24	chr19:42037200-42038600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
25	chr19:42037200-42038800	Flanking Active TSS	Adipose Nuclei	Adipose
26	chr19:42037200-42042200	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr19:42037400-42037800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr19:42037400-42037800	Active TSS	Primary T cells fromperipheralblood	blood
29	chr19:42037400-42037800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
30	chr19:42037400-42037800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr19:42037400-42037800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
32	chr19:42037400-42037800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
33	chr19:42037400-42037800	Flanking Active TSS	Thymus	Thymus
34	chr19:42037400-42037800	Flanking Active TSS	HUVEC	blood vessel
35	chr19:42037400-42038200	Flanking Active TSS	NHDF-Ad	bronchial
36	chr19:42037400-42038400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
37	chr19:42037400-42038600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
38	chr19:42037400-42038800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
39	chr19:42037400-42038800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr19:42037600-42037800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr19:42037600-42037800	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr19:42037600-42038000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr19:42037600-42038000	Bivalent Enhancer	Stomach Smooth Muscle	stomach
44	chr19:42037600-42038200	Active TSS	Primary T helper naive cells from peripheral blood	blood
45	chr19:42037600-42038200	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr19:42037600-42038200	Flanking Active TSS	GM12878-XiMat	blood
47	chr19:42037600-42038400	Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr19:42037600-42038400	Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr19:42037600-42038400	Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr19:42037600-42038400	Flanking Bivalent TSS/Enh	A549	lung

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