Variant report

Variant	rs546780474
Chromosome Location	chr19:53103992-53103993
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	FOSL2	chr19:53103887-53104722	HepG2	liver:	n/a	chr19:53104343-53104350
2	ZNF263	chr19:53103937-53104383	HEK293-T-REx	kidney:	n/a	chr19:53104085-53104094
3	POLR2A	chr19:53103966-53103992	HepG2	liver:	n/a	n/a
4	MAZ	chr19:53103779-53105120	GM12878	blood:	n/a	chr19:53104498-53104508 chr19:53104431-53104441
5	POLR2A	chr19:53103911-53104203	H1-hESC	embryonic stem cell:	n/a	n/a
6	MXI1	chr19:53103720-53105408	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr19:53103762-53105129	K562	blood:	n/a	n/a
8	POLR2A	chr19:53103946-53104735	HepG2	liver:	n/a	n/a
9	POLR2A	chr19:53103911-53104782	HepG2	liver:	n/a	n/a
10	POU2F2	chr19:53103917-53104833	GM12878	blood:	n/a	chr19:53104500-53104512 chr19:53104284-53104297
11	POLR2A	chr19:53103938-53104180	GM12878	blood:	n/a	n/a
12	ZNF143	chr19:53103990-53104605	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr19:53103825-53105098	GM12878	blood:	n/a	n/a
14	RUNX3	chr19:53103916-53104185	GM12878	blood:	n/a	n/a
15	E2F6	chr19:53103963-53104178	K562	blood:	n/a	n/a
16	RAD21	chr19:53103898-53104606	SK-N-SH_RA	brain:	n/a	chr19:53104432-53104444
17	ELF1	chr19:53103888-53104114	K562	blood:	n/a	n/a
18	POLR2A	chr19:53103912-53104086	H1-hESC	embryonic stem cell:	n/a	n/a
19	MAX	chr19:53103961-53104210	K562	blood:	n/a	n/a
20	CTCF	chr19:53103960-53104110	HepG2	liver:	n/a	n/a
21	POLR2A	chr19:53103904-53105174	MCF-7	breast:	n/a	n/a
22	POLR2A	chr19:53103932-53104778	HepG2	liver:	n/a	n/a
23	POLR2A	chr19:53103962-53104829	ECC-1	luminal epithelium:	n/a	n/a
24	POLR2A	chr19:53103950-53104196	HepG2	liver:	n/a	n/a
25	CTCF	chr19:53103911-53104654	IMR90	lung:	n/a	chr19:53104432-53104450 chr19:53104434-53104447
26	RAD21	chr19:53103849-53104423	HepG2	liver:	n/a	n/a
27	MAZ	chr19:53103821-53106145	IMR90	lung:	n/a	chr19:53104498-53104508 chr19:53104431-53104441
28	CTCF	chr19:53103940-53104090	SK-N-SH_RA	brain:	n/a	n/a
29	POLR2A	chr19:53103932-53104383	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr19:53103876-53105236	K562	blood:	n/a	n/a
31	HEY1	chr19:53103832-53104762	HepG2	liver:	n/a	n/a
32	ELF1	chr19:53103866-53104806	GM12878	blood:	n/a	chr19:53104425-53104437 chr19:53104481-53104490 chr19:53104432-53104444 chr19:53104480-53104493
33	CTCF	chr19:53103956-53104100	Pancreas_OC	pancreas:	n/a	n/a
34	HEY1	chr19:53103967-53104706	HepG2	liver:	n/a	n/a
35	MXI1	chr19:53103865-53105115	IMR90	lung:	n/a	n/a
36	HNF4G	chr19:53103915-53104155	HepG2	liver:	n/a	n/a
37	POLR2A	chr19:53103912-53105297	K562	blood:	n/a	n/a
38	POLR2A	chr19:53103803-53104902	GM12892	blood:	n/a	n/a
39	ZNF384	chr19:53103971-53104070	K562	blood:	n/a	n/a
40	POLR2A	chr19:53103883-53105351	H1-hESC	embryonic stem cell:	n/a	n/a
41	CTCF	chr19:53103980-53104130	HCPEpiC	choroid plexus:	n/a	n/a
42	HMGN3	chr19:53103986-53105157	K562	blood:	n/a	n/a
43	YY1	chr19:53103909-53104201	HepG2	liver:	n/a	n/a
44	POLR2A	chr19:53103986-53104154	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:53098815..53100632-chr19:53103081..53105260,2	K562	blood:
2	chr19:53098492..53100632-chr19:53102754..53104581,2	K562	blood:
3	chr19:53030382..53031999-chr19:53102744..53106373,4	K562	blood:
4	chr19:53103475..53106137-chr19:53106571..53108256,2	K562	blood:
5	chr10:79800834..79801581-chr19:53103963..53104926,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000268970	TF binding region
ENSG00000123870	Chromatin interaction
ENSG00000198482	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057296	chr19:52950339-53396986	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv1065584	chr19:53043126-53127459	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv833874	chr19:53058014-53257875	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv458743	chr19:53065661-53114267	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv580027	chr19:53065661-53114267	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv912304	chr19:53071155-53114267	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv963070	chr19:53091108-53105222	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv912305	chr19:53092465-53349850	Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv912306	chr19:53092465-53400760	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
10	nsv912307	chr19:53092465-53433054	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
11	nsv912308	chr19:53092465-53436337	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
12	nsv912309	chr19:53092465-53440653	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
13	nsv912310	chr19:53092465-53451291	Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
14	nsv828616	chr19:53095216-53137823	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
15	nsv912311	chr19:53103875-53212361	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
16	nsv912312	chr19:53103875-53296371	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
17	nsv912313	chr19:53103875-53436337	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised 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	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53091000-53104200	Weak transcription	Spleen	Spleen
2	chr19:53096000-53104000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:53099600-53104000	Weak transcription	Ovary	ovary
4	chr19:53100000-53104200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:53101000-53104200	Weak transcription	Small Intestine	intestine
6	chr19:53101800-53104000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr19:53103000-53104000	Enhancers	Fetal Lung	lung
8	chr19:53103400-53104000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr19:53103400-53104000	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr19:53103400-53104000	Enhancers	Placenta Amnion	Placenta Amnion
11	chr19:53103400-53104000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
12	chr19:53103400-53104200	Flanking Active TSS	Dnd41	blood
13	chr19:53103400-53105200	Active TSS	HSMMtube	muscle
14	chr19:53103400-53105600	Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr19:53103600-53104000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
16	chr19:53103600-53104000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr19:53103600-53104000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr19:53103600-53104000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr19:53103600-53104000	Flanking Active TSS	Primary T cells from cord blood	blood
20	chr19:53103600-53104000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr19:53103600-53104000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr19:53103600-53104000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr19:53103600-53104000	Enhancers	Brain Angular Gyrus	brain
24	chr19:53103600-53104000	Flanking Active TSS	Brain Germinal Matrix	brain
25	chr19:53103600-53104000	Flanking Active TSS	Fetal Intestine Small	intestine
26	chr19:53103600-53104000	Enhancers	Gastric	stomach
27	chr19:53103600-53104000	Enhancers	Left Ventricle	heart
28	chr19:53103600-53104000	Enhancers	Lung	lung
29	chr19:53103600-53104000	Enhancers	Pancreas	Pancrea
30	chr19:53103600-53104000	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr19:53103600-53104000	Enhancers	Stomach Mucosa	stomach
32	chr19:53103600-53104200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr19:53103600-53104200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr19:53103600-53104200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr19:53103600-53104200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr19:53103600-53104200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr19:53103600-53104200	Flanking Active TSS	Adipose Nuclei	Adipose
38	chr19:53103600-53104200	Flanking Active TSS	Brain Hippocampus Middle	brain
39	chr19:53103600-53104600	Active TSS	iPS-20b Cell Line	embryonic stem cell
40	chr19:53103600-53104800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr19:53103600-53105000	Active TSS	HUES48 Cell Line	embryonic stem cell
42	chr19:53103600-53105000	Active TSS	Colonic Mucosa	Colon
43	chr19:53103600-53105200	Active TSS	Primary T helper cells PMA-I stimulated	--
44	chr19:53103600-53105600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr19:53103600-53105800	Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr19:53103800-53104000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr19:53103800-53104000	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr19:53103800-53104000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr19:53103800-53104000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr19:53103800-53104000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood

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