Variant report

Variant	rs8109904
Chromosome Location	chr19:56115780-56115781
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	SP1	chr19:56115773-56118030	A549	lung:	n/a	chr19:56116015-56116025 chr19:56116530-56116544 chr19:56117056-56117070 chr19:56115982-56115994 chr19:56117707-56117714 chr19:56116691-56116700 chr19:56116998-56117007 chr19:56116533-56116545 chr19:56116515-56116524 chr19:56116997-56117009 chr19:56116015-56116025 chr19:56116690-56116700 chr19:56115982-56115994 chr19:56116689-56116701 chr19:56116691-56116700 chr19:56116515-56116524 chr19:56116513-56116525 chr19:56116690-56116699 chr19:56116514-56116524 chr19:56116670-56116680 chr19:56116535-56116544 chr19:56116533-56116545 chr19:56116686-56116700 chr19:56116670-56116680 chr19:56116534-56116544 chr19:56116997-56117009 chr19:56116690-56116700 chr19:56116689-56116701 chr19:56116535-56116544 chr19:56115984-56115993 chr19:56116514-56116524 chr19:56116514-56116523 chr19:56116991-56117000 chr19:56116994-56117008 chr19:56116513-56116525 chr19:56116534-56116544 chr19:56117444-56117453 chr19:56115979-56115993 chr19:56116510-56116524 chr19:56116534-56116543
2	SETDB1	chr19:56115640-56116152	U2OS	brain:	n/a	n/a
3	POLR2A	chr19:56115694-56117293	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr19:56115759-56118660	PANC-1	pancreas:	n/a	n/a
5	POLR2A	chr19:56115741-56118136	SK-N-MC	brain:	n/a	n/a
6	POLR2A	chr19:56115721-56118082	PANC-1	pancreas:	n/a	n/a
7	POLR2A	chr19:56115611-56117376	PFSK-1	brain:	n/a	n/a
8	SIX5	chr19:56115724-56116655	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:56115235..56119649-chr19:56131831..56136050,11	K562	blood:
2	chr19:56114907..56116947-chr19:56184542..56187154,2	K562	blood:
3	chr19:56115086..56118069-chr19:56150430..56156112,7	MCF-7	breast:
4	chr19:56089635..56093860-chr19:56114549..56117863,7	MCF-7	breast:
5	chr19:55987823..55989523-chr19:56114913..56117449,2	MCF-7	breast:
6	chr19:56090169..56092929-chr19:56114581..56116716,3	K562	blood:
7	chr19:56114376..56117189-chr19:56151962..56154337,3	K562	blood:
8	chr19:56113112..56115949-chr19:56151962..56154337,3	K562	blood:
9	chr19:55894932..55897598-chr19:56114798..56116891,2	MCF-7	breast:

Variant related genes	Relation type
FIZ1	TF binding region
ZNF865	TF binding region
ENSG00000233493	Chromatin interaction
ENSG00000108107	Chromatin interaction
ENSG00000218891	Chromatin interaction
ENSG00000197483	Chromatin interaction
ENSG00000179922	Chromatin interaction
ENSG00000173581	Chromatin interaction
ENSG00000213015	Chromatin interaction
ENSG00000063245	Chromatin interaction
ENSG00000267523	Chromatin interaction
ENSG00000269859	Chromatin interaction
ENSG00000171425	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1053817	1.00[ASN][1000 genomes]
rs11666636	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11667786	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11668752	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11669643	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11671353	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11671421	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11671545	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2902747	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4331432	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60547841	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73058305	1.00[ASN][1000 genomes]
rs73058308	1.00[ASN][1000 genomes]
rs73058310	1.00[ASN][1000 genomes]
rs73612853	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8100277	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912473	chr19:55874642-56145428	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
2	nsv912486	chr19:55977909-56145428	Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv912487	chr19:55977909-56215184	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv912494	chr19:56026072-56215184	Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
5	nsv912495	chr19:56033088-56132661	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv912496	chr19:56040051-56145428	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
7	nsv912497	chr19:56041848-56145428	Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
8	nsv912498	chr19:56041848-56215184	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
9	nsv828643	chr19:56059280-56154823	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
10	nsv912499	chr19:56071293-56132487	Flanking Active TSS Genic enhancers Active TSS Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
11	nsv912500	chr19:56078722-56175515	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers 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	86 gene(s)	inside rSNPs	diseases
12	nsv912501	chr19:56093365-56215184	Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
13	nsv912502	chr19:56099884-56138575	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 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	chr19:56111600-56116000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:56112200-56116000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr19:56112400-56116000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:56112400-56116000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr19:56112400-56116400	Weak transcription	Aorta	Aorta
6	chr19:56112600-56116000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr19:56112600-56116000	Weak transcription	Fetal Lung	lung
8	chr19:56112600-56116000	Weak transcription	HSMMtube	muscle
9	chr19:56112800-56115800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr19:56112800-56115800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr19:56112800-56115800	Weak transcription	Adipose Nuclei	Adipose
12	chr19:56112800-56115800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr19:56112800-56115800	Weak transcription	Fetal Brain Male	brain
14	chr19:56112800-56115800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr19:56112800-56115800	Weak transcription	HSMM	muscle
16	chr19:56112800-56116000	Weak transcription	Brain Angular Gyrus	brain
17	chr19:56112800-56116000	Weak transcription	Brain Anterior Caudate	brain
18	chr19:56112800-56116000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr19:56112800-56116000	Weak transcription	Fetal Kidney	kidney
20	chr19:56112800-56116000	Weak transcription	Left Ventricle	heart
21	chr19:56112800-56116000	Weak transcription	Psoas Muscle	Psoas
22	chr19:56112800-56116000	Weak transcription	Right Atrium	heart
23	chr19:56112800-56116000	Weak transcription	NH-A	brain
24	chr19:56113000-56115800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr19:56113000-56115800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr19:56113000-56115800	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr19:56113000-56115800	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr19:56113000-56115800	Weak transcription	HUVEC	blood vessel
29	chr19:56113000-56115800	Weak transcription	Osteobl	bone
30	chr19:56113000-56116000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr19:56113000-56116000	Weak transcription	Primary T cells from cord blood	blood
32	chr19:56113000-56116000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr19:56113000-56116000	Weak transcription	Brain Hippocampus Middle	brain
34	chr19:56113000-56116000	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr19:56113000-56116000	Weak transcription	Brain Substantia Nigra	brain
36	chr19:56113000-56116000	Weak transcription	Colon Smooth Muscle	Colon
37	chr19:56113000-56116000	Weak transcription	Fetal Heart	heart
38	chr19:56113000-56116000	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr19:56113000-56116000	Weak transcription	Rectal Smooth Muscle	rectum
40	chr19:56113000-56116000	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr19:56113000-56116000	Weak transcription	NHDF-Ad	bronchial
42	chr19:56113000-56116200	Weak transcription	Small Intestine	intestine
43	chr19:56113200-56115800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr19:56113200-56115800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr19:56113200-56115800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr19:56113200-56115800	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr19:56113200-56115800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr19:56113200-56115800	Weak transcription	Brain Germinal Matrix	brain
49	chr19:56113200-56115800	Weak transcription	A549	lung
50	chr19:56113200-56116000	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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