Variant report

Variant	rs56115240
Chromosome Location	chr19:56147382-56147383
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:42)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:42 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr19:56145622-56147578	K562	blood:	n/a	chr19:56146783-56146794
2	POLR2A	chr19:56146082-56149393	GM12892	blood:	n/a	n/a
3	POU2F2	chr19:56146705-56147845	GM12878	blood:	n/a	chr19:56146838-56146850 chr19:56146826-56146838
4	POLR2A	chr19:56146118-56147777	HL-60	blood:	n/a	n/a
5	POLR2A	chr19:56146100-56148322	GM19193	blood:	n/a	n/a
6	POLR2A	chr19:56146092-56148563	GM12878	blood:	n/a	n/a
7	POLR2A	chr19:56146070-56148494	GM12891	blood:	n/a	n/a
8	POLR2A	chr19:56146049-56148415	GM12891	blood:	n/a	n/a
9	SPI1	chr19:56146793-56147652	HL-60	blood:	n/a	chr19:56147283-56147296
10	HEY1	chr19:56147201-56147748	K562	blood:	n/a	n/a
11	POLR2A	chr19:56146057-56147761	GM12892	blood:	n/a	n/a
12	POLR2A	chr19:56147191-56147832	GM12878	blood:	n/a	n/a
13	POLR2A	chr19:56146108-56148514	GM12891	blood:	n/a	n/a
14	POLR2A	chr19:56146046-56148076	GM12892	blood:	n/a	n/a
15	POLR2A	chr19:56146066-56155822	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr19:56145990-56148670	PFSK-1	brain:	n/a	n/a
17	POLR2A	chr19:56146089-56148481	GM18505	blood:	n/a	n/a
18	POLR2A	chr19:56146054-56148535	GM12878	blood:	n/a	n/a
19	MTA3	chr19:56146054-56147560	GM12878	blood:	n/a	n/a
20	POLR2A	chr19:56146111-56148468	IMR90	lung:	n/a	n/a
21	POLR2A	chr19:56145947-56149686	SK-N-MC	brain:	n/a	n/a
22	POLR2A	chr19:56146054-56148734	GM12891	blood:	n/a	n/a
23	POLR2A	chr19:56146022-56147406	K562	blood:	n/a	n/a
24	POLR2A	chr19:56146113-56147861	K562	blood:	n/a	n/a
25	POLR2A	chr19:56146111-56148523	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr19:56146995-56149583	K562	blood:	n/a	n/a
27	POLR2A	chr19:56146114-56147752	PBDE	blood:	n/a	n/a
28	POLR2A	chr19:56145941-56148656	GM12892	blood:	n/a	n/a
29	POLR2A	chr19:56145999-56149668	GM12878	blood:	n/a	n/a
30	ESRRA	chr19:56145920-56147842	GM12878	blood:	n/a	n/a
31	POLR2A	chr19:56146128-56147876	GM12878	blood:	n/a	n/a
32	WRNIP1	chr19:56146112-56147393	GM12878	blood:	n/a	n/a
33	POLR2A	chr19:56147283-56147755	ECC-1	luminal epithelium:	n/a	n/a
34	POLR2A	chr19:56147323-56147973	HepG2	liver:	n/a	n/a
35	SPI1	chr19:56147298-56147467	K562	blood:	n/a	n/a
36	POLR2A	chr19:56146110-56148376	GM12891	blood:	n/a	n/a
37	SREBP2	chr19:56145955-56147719	GM12878	blood:	n/a	n/a
38	POLR2A	chr19:56146047-56148543	GM12892	blood:	n/a	n/a
39	SPI1	chr19:56147234-56147564	GM12878	blood:	n/a	chr19:56147283-56147296
40	POLR2A	chr19:56146014-56148713	PANC-1	pancreas:	n/a	n/a
41	POLR2A	chr19:56146039-56148828	GM12878	blood:	n/a	n/a
42	POLR2A	chr19:56147358-56148051	HepG2	liver:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:56143909..56147540-chr19:56180767..56182811,3	MCF-7	breast:
2	chr19:55895074..55897174-chr19:56145786..56148520,2	MCF-7	breast:
3	chr19:56109995..56114029-chr19:56145200..56149074,4	MCF-7	breast:
4	chr19:55917719..55921194-chr19:56143842..56149725,7	K562	blood:
5	chr19:56131862..56136924-chr19:56144839..56148352,5	MCF-7	breast:
6	chr19:56116639..56119326-chr19:56146420..56148377,2	K562	blood:
7	chr19:56134501..56137412-chr19:56145689..56149345,6	K562	blood:

No data

Variant related genes	Relation type
ZNF580	TF binding region
ENSG00000108107	Chromatin interaction
ENSG00000233493	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000179922	Chromatin interaction
ENSG00000179943	Chromatin interaction
ENSG00000267096	Chromatin interaction
ENSG00000261221	Chromatin interaction
ENSG00000171443	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs56250101	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56331023	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61736526	1.00[AMR][1000 genomes]
rs73933303	1.00[AMR][1000 genomes]
rs73933306	1.00[AMR][1000 genomes]
rs73933307	1.00[AMR][1000 genomes]
rs73933308	1.00[AMR][1000 genomes]
rs73934401	1.00[AMR][1000 genomes]
rs73934402	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73936310	1.00[AMR][1000 genomes]
rs73936311	1.00[AMR][1000 genomes]
rs73936315	1.00[AMR][1000 genomes]
rs73936316	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	nsv428026	chr19:56130849-56423514	Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	82 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56145600-56147400	Flanking Active TSS	Primary hematopoietic stem cells	blood
2	chr19:56145600-56147600	Flanking Active TSS	Primary B cells from cord blood	blood
3	chr19:56145600-56148200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr19:56145800-56148000	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr19:56146000-56147800	Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr19:56146000-56148200	Active TSS	H9 Cell Line	embryonic stem cell
7	chr19:56146200-56147400	Active TSS	Ovary	ovary
8	chr19:56146400-56147400	Active TSS	Aorta	Aorta
9	chr19:56146400-56147600	Flanking Active TSS	Brain Germinal Matrix	brain
10	chr19:56146400-56147800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr19:56146400-56147800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
12	chr19:56146400-56148200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr19:56146400-56148400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
14	chr19:56146600-56147400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
15	chr19:56146600-56147400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
16	chr19:56146600-56147400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
17	chr19:56146600-56147400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
18	chr19:56146600-56147400	Flanking Active TSS	Fetal Brain Male	brain
19	chr19:56146600-56147400	Flanking Active TSS	Fetal Brain Female	brain
20	chr19:56146600-56147400	Flanking Active TSS	Fetal Stomach	stomach
21	chr19:56146600-56147600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr19:56146600-56147600	Flanking Active TSS	Primary B cells from peripheral blood	blood
23	chr19:56146600-56147600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr19:56146600-56147600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
25	chr19:56146600-56147600	Flanking Active TSS	Fetal Muscle Trunk	muscle
26	chr19:56146600-56147600	Flanking Active TSS	Fetal Thymus	thymus
27	chr19:56146600-56147600	Flanking Active TSS	HUVEC	blood vessel
28	chr19:56146600-56147800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr19:56146600-56147800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
30	chr19:56146600-56147800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr19:56146600-56147800	Flanking Active TSS	Colonic Mucosa	Colon
32	chr19:56146600-56147800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
33	chr19:56146600-56148000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr19:56146600-56148200	Flanking Active TSS	Primary T cells from cord blood	blood
35	chr19:56146600-56148200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr19:56146600-56148200	Flanking Active TSS	Adipose Nuclei	Adipose
37	chr19:56146600-56148200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
38	chr19:56146600-56148400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
39	chr19:56146800-56147400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr19:56146800-56147400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
41	chr19:56146800-56147400	Flanking Active TSS	Fetal Muscle Leg	muscle
42	chr19:56146800-56147400	Flanking Active TSS	Placenta	Placenta
43	chr19:56146800-56147400	Flanking Active TSS	Stomach Mucosa	stomach
44	chr19:56146800-56147600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
45	chr19:56146800-56147600	Flanking Active TSS	Brain Angular Gyrus	brain
46	chr19:56146800-56147600	Flanking Active TSS	Fetal Lung	lung
47	chr19:56146800-56147600	Flanking Active TSS	Placenta Amnion	Placenta Amnion
48	chr19:56146800-56147600	Flanking Active TSS	Right Ventricle	heart
49	chr19:56146800-56147600	Flanking Active TSS	Thymus	Thymus
50	chr19:56146800-56147800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood

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