Variant report

Variant	rs2560875
Chromosome Location	chr19:52774175-52774176
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:52774064-52775003	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr19:52774024-52774379	HepG2	liver:	n/a	n/a
3	POLR2A	chr19:52774105-52775017	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr19:52772414-52775242	GM12878	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:52771242..52774496-chr19:52796154..52801198,5	MCF-7	breast:
2	chr19:52773000..52774618-chr19:52792454..52794386,2	K562	blood:
3	chr19:52772712..52774263-chr19:52799047..52800693,2	K562	blood:
4	chr19:52772026..52776261-chr19:52781637..52786393,5	K562	blood:
5	chr19:52771880..52774244-chr19:52838831..52841718,3	MCF-7	breast:
6	chr19:52772363..52775107-chr19:52799601..52802037,4	MCF-7	breast:
7	chr19:52772381..52778282-chr19:52778346..52783668,9	MCF-7	breast:
8	chr19:52771362..52774263-chr19:52797982..52800693,2	K562	blood:
9	chr19:52692994..52696358-chr19:52773094..52775949,3	MCF-7	breast:
10	chr19:52733004..52735653-chr19:52772074..52774471,2	MCF-7	breast:
11	chr19:52773231..52774853-chr19:52802417..52804914,2	MCF-7	breast:

No data

Variant related genes	Relation type
ZNF766	TF binding region
ENSG00000167554	Chromatin interaction
ENSG00000269102	Chromatin interaction
ENSG00000198464	Chromatin interaction
ENSG00000208002	Chromatin interaction
ENSG00000268015	Chromatin interaction
ENSG00000105568	Chromatin interaction
ENSG00000196214	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10426950	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2089275	0.81[AFR][1000 genomes]
rs2560871	0.81[AFR][1000 genomes]
rs2560873	0.81[AFR][1000 genomes]
rs2560877	0.82[AFR][1000 genomes]
rs2560904	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2560905	0.95[EUR][1000 genomes]
rs2657923	0.81[AFR][1000 genomes]
rs2657924	0.81[AFR][1000 genomes]
rs2657926	0.81[AFR][1000 genomes]
rs2657927	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2657928	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2657930	0.85[AFR][1000 genomes]
rs62110405	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6509630	0.90[AFR][1000 genomes]
rs8112349	0.87[AFR][1000 genomes]
rs9304727	0.90[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
2	esv3366000	chr19:52491073-52842946	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats 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 miRNA miRNA target site	49 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	chr19:52772200-52774200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:52772200-52774200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr19:52772200-52774200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr19:52772200-52774200	Active TSS	A549	lung
5	chr19:52772400-52774200	Active TSS	H9 Cell Line	embryonic stem cell
6	chr19:52772400-52774200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr19:52772400-52774200	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr19:52772400-52774200	Active TSS	Fetal Intestine Large	intestine
9	chr19:52772400-52774200	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr19:52772400-52774200	Active TSS	HSMMtube	muscle
11	chr19:52772400-52774200	Active TSS	NH-A	brain
12	chr19:52772400-52774400	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr19:52772400-52774400	Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr19:52772400-52774400	Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr19:52772400-52774400	Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr19:52772400-52774400	Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr19:52772400-52774400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr19:52772400-52774400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr19:52772400-52774400	Active TSS	HSMM	muscle
20	chr19:52772400-52774400	Active TSS	NHDF-Ad	bronchial
21	chr19:52772400-52774400	Active TSS	NHLF	lung
22	chr19:52772400-52774600	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr19:52772400-52774600	Active TSS	Fetal Kidney	kidney
24	chr19:52772400-52774600	Active TSS	GM12878-XiMat	blood
25	chr19:52772600-52774200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr19:52772600-52774400	Active TSS	HMEC	breast
27	chr19:52772600-52774400	Active TSS	Osteobl	bone
28	chr19:52773000-52774200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
29	chr19:52773200-52774200	Flanking Active TSS	Primary B cells from cord blood	blood
30	chr19:52773200-52774200	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr19:52773400-52774200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr19:52773400-52774600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
33	chr19:52773600-52774200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr19:52773600-52774200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr19:52773600-52774200	Flanking Active TSS	Liver	Liver
36	chr19:52773600-52774200	Flanking Active TSS	Brain Angular Gyrus	brain
37	chr19:52773600-52774200	Flanking Active TSS	Brain Anterior Caudate	brain
38	chr19:52773600-52774200	Flanking Active TSS	Brain Hippocampus Middle	brain
39	chr19:52773600-52774200	Flanking Active TSS	Colonic Mucosa	Colon
40	chr19:52773600-52774200	Flanking Active TSS	Fetal Muscle Trunk	muscle
41	chr19:52773600-52774200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
42	chr19:52773600-52774200	Flanking Active TSS	Rectal Smooth Muscle	rectum
43	chr19:52773600-52774200	Flanking Active TSS	Hela-S3	cervix
44	chr19:52773600-52774200	Flanking Active TSS	HUVEC	blood vessel
45	chr19:52773600-52774400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
46	chr19:52773600-52774400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr19:52773600-52774400	Flanking Active TSS	Fetal Stomach	stomach
48	chr19:52773600-52774400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
49	chr19:52773600-52774600	Flanking Active TSS	Primary hematopoietic stem cells	blood
50	chr19:52773600-52774600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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