Variant report

Variant	rs644230
Chromosome Location	chr19:56147928-56147929
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:28)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:28 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:56146082-56149393	GM12892	blood:	n/a	n/a
2	POLR2A	chr19:56146100-56148322	GM19193	blood:	n/a	n/a
3	POLR2A	chr19:56146092-56148563	GM12878	blood:	n/a	n/a
4	POLR2A	chr19:56146070-56148494	GM12891	blood:	n/a	n/a
5	POLR2A	chr19:56146049-56148415	GM12891	blood:	n/a	n/a
6	POLR2A	chr19:56147905-56148481	GM12878	blood:	n/a	n/a
7	POLR2A	chr19:56147925-56148480	K562	blood:	n/a	n/a
8	POLR2A	chr19:56146108-56148514	GM12891	blood:	n/a	n/a
9	POLR2A	chr19:56146046-56148076	GM12892	blood:	n/a	n/a
10	POLR2A	chr19:56146066-56155822	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr19:56145990-56148670	PFSK-1	brain:	n/a	n/a
12	POLR2A	chr19:56146089-56148481	GM18505	blood:	n/a	n/a
13	POLR2A	chr19:56146054-56148535	GM12878	blood:	n/a	n/a
14	POLR2A	chr19:56146111-56148468	IMR90	lung:	n/a	n/a
15	POLR2A	chr19:56145947-56149686	SK-N-MC	brain:	n/a	n/a
16	POLR2A	chr19:56146054-56148734	GM12891	blood:	n/a	n/a
17	POLR2A	chr19:56146111-56148523	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr19:56146995-56149583	K562	blood:	n/a	n/a
19	POLR2A	chr19:56145941-56148656	GM12892	blood:	n/a	n/a
20	POLR2A	chr19:56145999-56149668	GM12878	blood:	n/a	n/a
21	POLR2A	chr19:56147876-56148438	GM12878	blood:	n/a	n/a
22	POLR2A	chr19:56147675-56148588	MCF10A-Er-Src	breast:	n/a	n/a
23	POLR2A	chr19:56147323-56147973	HepG2	liver:	n/a	n/a
24	POLR2A	chr19:56146110-56148376	GM12891	blood:	n/a	n/a
25	POLR2A	chr19:56146047-56148543	GM12892	blood:	n/a	n/a
26	POLR2A	chr19:56146014-56148713	PANC-1	pancreas:	n/a	n/a
27	POLR2A	chr19:56146039-56148828	GM12878	blood:	n/a	n/a
28	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	chr19:55895074..55897174-chr19:56145786..56148520,2	MCF-7	breast:
2	chr19:56109995..56114029-chr19:56145200..56149074,4	MCF-7	breast:
3	chr19:56135345..56138507-chr19:56147845..56151809,4	K562	blood:
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
CCDC106	TF binding region
ZNF581	TF binding region
ENSG00000179922	Chromatin interaction
ENSG00000261221	Chromatin interaction
ENSG00000108107	Chromatin interaction
ENSG00000233493	Chromatin interaction
ENSG00000171443	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000179943	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs310464	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs310465	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs310467	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs310470	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs310471	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs310474	0.89[EUR][1000 genomes]
rs504003	1.00[CHB][hapmap]
rs507498	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs520125	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs522669	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs553947	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs581023	0.84[EUR][1000 genomes]
rs612211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs636466	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs636467	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs637788	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[EUR][1000 genomes]
rs681433	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7246799	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7251872	0.86[ASN][1000 genomes]
rs889091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][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:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56145600-56148200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr19:56145800-56148000	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr19:56146000-56148200	Active TSS	H9 Cell Line	embryonic stem cell
4	chr19:56146400-56148200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr19:56146400-56148400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
6	chr19:56146600-56148000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr19:56146600-56148200	Flanking Active TSS	Primary T cells from cord blood	blood
8	chr19:56146600-56148200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
9	chr19:56146600-56148200	Flanking Active TSS	Adipose Nuclei	Adipose
10	chr19:56146600-56148200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
11	chr19:56146600-56148400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
12	chr19:56146800-56148000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr19:56146800-56148000	Flanking Active TSS	NH-A	brain
14	chr19:56146800-56148200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
15	chr19:56146800-56148200	Flanking Active TSS	Brain Hippocampus Middle	brain
16	chr19:56146800-56148200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
17	chr19:56146800-56148200	Flanking Active TSS	Hela-S3	cervix
18	chr19:56146800-56148400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr19:56146800-56148400	Flanking Active TSS	Duodenum Mucosa	Duodenum
20	chr19:56146800-56148400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
21	chr19:56146800-56148400	Flanking Active TSS	Stomach Smooth Muscle	stomach
22	chr19:56147000-56148000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
23	chr19:56147000-56148000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr19:56147000-56148000	Flanking Active TSS	NHEK	skin
25	chr19:56147000-56148200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr19:56147000-56148200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
27	chr19:56147000-56148200	Flanking Active TSS	Colon Smooth Muscle	Colon
28	chr19:56147000-56148200	Flanking Active TSS	NHDF-Ad	bronchial
29	chr19:56147000-56148200	Flanking Active TSS	Osteobl	bone
30	chr19:56147000-56148400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr19:56147000-56148400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr19:56147200-56148000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr19:56147200-56148400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr19:56147200-56148400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr19:56147200-56148400	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr19:56147200-56148400	Flanking Active TSS	HepG2	liver
37	chr19:56147200-56148600	Flanking Active TSS	GM12878-XiMat	blood
38	chr19:56147400-56148000	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr19:56147400-56148000	Enhancers	Fetal Brain Male	brain
40	chr19:56147400-56148000	Enhancers	Fetal Kidney	kidney
41	chr19:56147400-56148200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr19:56147400-56148200	Genic enhancers	Fetal Stomach	stomach
43	chr19:56147400-56148200	Enhancers	Small Intestine	intestine
44	chr19:56147400-56148200	Enhancers	Stomach Mucosa	stomach
45	chr19:56147400-56148400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr19:56147400-56148400	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr19:56147400-56148400	Enhancers	Aorta	Aorta
48	chr19:56147400-56148600	Enhancers	Primary neutrophils fromperipheralblood	blood
49	chr19:56147400-56148600	Enhancers	Placenta	Placenta
50	chr19:56147400-56149200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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