Variant report

Variant	rs561430070
Chromosome Location	chr19:56988643-56988644
allele	A/C
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	NRF1	chr19:56988221-56989850	SK-N-SH	brain:	n/a	chr19:56989497-56989511 chr19:56989209-56989218 chr19:56988924-56988938 chr19:56988702-56988711 chr19:56989500-56989514 chr19:56988783-56988792 chr19:56988927-56988938 chr19:56989207-56989218 chr19:56988697-56988711 chr19:56988929-56988938 chr19:56988700-56988714 chr19:56989204-56989218 chr19:56989500-56989511 chr19:56989207-56989221 chr19:56988927-56988941 chr19:56988700-56988711
2	POLR2A	chr19:56987970-56990186	IMR90	lung:	n/a	n/a
3	SIN3AK20	chr19:56988480-56989016	PFSK-1	brain:	n/a	n/a
4	TEAD4	chr19:56988390-56988694	H1-hESC	embryonic stem cell:	n/a	n/a
5	MYC	chr19:56988538-56989762	H1-hESC	embryonic stem cell:	n/a	chr19:56988596-56988605 chr19:56988800-56988809 chr19:56988774-56988783
6	MAX	chr19:56988153-56989883	SK-N-SH	brain:	n/a	chr19:56988596-56988605 chr19:56988800-56988809 chr19:56989847-56989857 chr19:56988525-56988534 chr19:56988774-56988783
7	HDAC2	chr19:56988345-56989035	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr19:56988461-56988662	H1-hESC	embryonic stem cell:	n/a	n/a
9	MAX	chr19:56988166-56989814	H1-hESC	embryonic stem cell:	n/a	chr19:56988596-56988605 chr19:56988800-56988809 chr19:56988525-56988534 chr19:56988774-56988783
10	POLR2A	chr19:56988438-56989828	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr19:56987914-56989927	H1-neurons	neurons:	n/a	n/a
12	BACH1	chr19:56988129-56989735	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr19:56987837-56989882	H1-neurons	neurons:	n/a	n/a
14	MXI1	chr19:56987781-56990043	IMR90	lung:	n/a	n/a
15	POLR2A	chr19:56988531-56989847	PFSK-1	brain:	n/a	n/a
16	POLR2A	chr19:56988579-56989762	SK-N-SH	brain:	n/a	n/a
17	SIN3AK20	chr19:56988594-56989833	SK-N-SH	brain:	n/a	n/a
18	MAX	chr19:56988208-56989757	H1-hESC	embryonic stem cell:	n/a	chr19:56988596-56988605 chr19:56988800-56988809 chr19:56988525-56988534 chr19:56988774-56988783
19	MAX	chr19:56988074-56990138	SK-N-SH	brain:	n/a	chr19:56988596-56988605 chr19:56988800-56988809 chr19:56989847-56989857 chr19:56988525-56988534 chr19:56988774-56988783
20	MAZ	chr19:56987654-56990331	IMR90	lung:	n/a	chr19:56988596-56988605 chr19:56988800-56988809 chr19:56989847-56989857 chr19:56988525-56988534 chr19:56988774-56988783
21	POLR2A	chr19:56988250-56989844	Gliobla	brain:	n/a	n/a
22	POLR2A	chr19:56988556-56989768	H1-hESC	embryonic stem cell:	n/a	n/a
23	SIN3A	chr19:56988034-56990073	H1-hESC	embryonic stem cell:	n/a	chr19:56989351-56989364 chr19:56988699-56988708 chr19:56989198-56989209 chr19:56988812-56988823
24	REST	chr19:56987745-56989992	H1-neurons	neurons:	n/a	chr19:56989351-56989364
25	NRF1	chr19:56988545-56989697	H1-hESC	embryonic stem cell:	n/a	chr19:56989497-56989511 chr19:56989209-56989218 chr19:56988924-56988938 chr19:56988702-56988711 chr19:56989500-56989514 chr19:56988783-56988792 chr19:56988927-56988938 chr19:56989207-56989218 chr19:56988697-56988711 chr19:56988929-56988938 chr19:56988700-56988714 chr19:56989204-56989218 chr19:56989500-56989511 chr19:56989207-56989221 chr19:56988927-56988941 chr19:56988700-56988711
26	E2F6	chr19:56988203-56989479	H1-hESC	embryonic stem cell:	n/a	chr19:56988928-56988937 chr19:56988701-56988710 chr19:56988590-56988599 chr19:56989208-56989217 chr19:56988483-56988492 chr19:56988783-56988792
27	TBP	chr19:56988596-56989740	H1-hESC	embryonic stem cell:	n/a	n/a
28	MXI1	chr19:56987494-56990858	SK-N-SH	brain:	n/a	n/a
29	POLR2A	chr19:56988379-56989811	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr19:56988288-56989855	SK-N-MC	brain:	n/a	n/a
31	POLR2A	chr19:56987976-56990044	HL-60	blood:	n/a	n/a
32	ZNF143	chr19:56988586-56989748	H1-hESC	embryonic stem cell:	n/a	chr19:56989448-56989466 chr19:56989450-56989459 chr19:56989448-56989457 chr19:56988842-56988852
33	MXI1	chr19:56988365-56989933	H1-hESC	embryonic stem cell:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC004696.1-1	chr19:56988619-56990056	ENSG00000166770.6

Variant related genes	Relation type
ZNF667-AS1	TF binding region
ZNF667	TF binding region

Extended variants
information (count: 11 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949121	chr19:56754719-57591038	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1062341	chr19:56794070-57273332	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv544094	chr19:56794070-57273332	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
4	nsv1056713	chr19:56799151-57265682	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
5	nsv544095	chr19:56799151-57265682	Strong transcription ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv580385	chr19:56918598-57072433	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv1057240	chr19:56919831-57153659	Flanking Active TSS Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv544097	chr19:56919831-57153659	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv580386	chr19:56924761-57072433	Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	nsv1055357	chr19:56933632-57190007	ZNF genes & repeats Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
11	esv3358424	chr19:56987565-56990113	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56985400-56990400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr19:56985400-56991400	ZNF genes & repeats	Liver	Liver
3	chr19:56987000-56990000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr19:56987000-56990400	ZNF genes & repeats	Gastric	stomach
5	chr19:56987400-56990000	ZNF genes & repeats	Placenta	Placenta
6	chr19:56987400-56990800	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr19:56987400-56992400	ZNF genes & repeats	Lung	lung
8	chr19:56987600-56989600	ZNF genes & repeats	Pancreas	Pancrea
9	chr19:56987600-56989800	Active TSS	Primary T cells from cord blood	blood
10	chr19:56987600-56990200	ZNF genes & repeats	Spleen	Spleen
11	chr19:56987600-56990600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr19:56987600-56990600	Active TSS	Brain Anterior Caudate	brain
13	chr19:56987600-56990800	Active TSS	H1 Cell Line	embryonic stem cell
14	chr19:56987600-56990800	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr19:56987600-56991000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr19:56987600-56991200	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr19:56987800-56989800	Active TSS	Osteobl	bone
18	chr19:56987800-56990000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr19:56987800-56990200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr19:56987800-56990400	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr19:56987800-56990400	Flanking Active TSS	Adipose Nuclei	Adipose
22	chr19:56987800-56990400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
23	chr19:56987800-56990400	Active TSS	Fetal Muscle Trunk	muscle
24	chr19:56987800-56990400	Active TSS	Rectal Smooth Muscle	rectum
25	chr19:56987800-56990400	Active TSS	NHDF-Ad	bronchial
26	chr19:56987800-56990600	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
27	chr19:56987800-56990600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr19:56987800-56990600	ZNF genes & repeats	Colonic Mucosa	Colon
29	chr19:56987800-56990600	Active TSS	Rectal Mucosa Donor 29	rectum
30	chr19:56988000-56989800	Active TSS	Fetal Thymus	thymus
31	chr19:56988000-56990000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr19:56988000-56990000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
33	chr19:56988000-56990000	Active TSS	Colon Smooth Muscle	Colon
34	chr19:56988000-56990200	Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr19:56988000-56990200	Active TSS	Rectal Mucosa Donor 31	rectum
36	chr19:56988000-56990200	Active TSS	HUVEC	blood vessel
37	chr19:56988000-56990400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr19:56988000-56990400	Active TSS	Fetal Intestine Large	intestine
39	chr19:56988000-56990600	Active TSS	Brain Cingulate Gyrus	brain
40	chr19:56988000-56990600	Active TSS	Fetal Brain Female	brain
41	chr19:56988000-56990600	Active TSS	Psoas Muscle	Psoas
42	chr19:56988000-56990600	Active TSS	HSMM	muscle
43	chr19:56988000-56990600	Active TSS	HSMMtube	muscle
44	chr19:56988000-56990600	Active TSS	NH-A	brain
45	chr19:56988000-56991000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr19:56988000-56991000	Active TSS	Muscle Satellite Cultured Cells	--
47	chr19:56988200-56989000	Active TSS	Primary T helper cells fromperipheralblood	blood
48	chr19:56988200-56989200	Flanking Active TSS	Primary B cells from cord blood	blood
49	chr19:56988200-56989200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr19:56988200-56989400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood

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