Variant report

Variant	rs2560874
Chromosome Location	chr19:52774218-52774219
allele	C/T
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
ENSG00000268015	Chromatin interaction
ENSG00000105568	Chromatin interaction
ENSG00000167554	Chromatin interaction
ENSG00000196214	Chromatin interaction
ENSG00000198464	Chromatin interaction
ENSG00000269102	Chromatin interaction
ENSG00000208002	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2002322	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2002323	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2560876	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2657925	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2657929	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][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:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52772400-52774400	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr19:52772400-52774400	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr19:52772400-52774400	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr19:52772400-52774400	Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr19:52772400-52774400	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr19:52772400-52774400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr19:52772400-52774400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr19:52772400-52774400	Active TSS	HSMM	muscle
9	chr19:52772400-52774400	Active TSS	NHDF-Ad	bronchial
10	chr19:52772400-52774400	Active TSS	NHLF	lung
11	chr19:52772400-52774600	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr19:52772400-52774600	Active TSS	Fetal Kidney	kidney
13	chr19:52772400-52774600	Active TSS	GM12878-XiMat	blood
14	chr19:52772600-52774400	Active TSS	HMEC	breast
15	chr19:52772600-52774400	Active TSS	Osteobl	bone
16	chr19:52773400-52774600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr19:52773600-52774400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr19:52773600-52774400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr19:52773600-52774400	Flanking Active TSS	Fetal Stomach	stomach
20	chr19:52773600-52774400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr19:52773600-52774600	Flanking Active TSS	Primary hematopoietic stem cells	blood
22	chr19:52773600-52774600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr19:52773600-52774600	Flanking Active TSS	Stomach Smooth Muscle	stomach
24	chr19:52773800-52774400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
25	chr19:52773800-52774400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
26	chr19:52773800-52774400	Flanking Active TSS	Brain Germinal Matrix	brain
27	chr19:52773800-52774400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr19:52773800-52774400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
29	chr19:52773800-52774600	Flanking Active TSS	Primary T cells from cord blood	blood
30	chr19:52773800-52774600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr19:52773800-52774600	Enhancers	Stomach Mucosa	stomach
32	chr19:52773800-52774600	Enhancers	Spleen	Spleen
33	chr19:52773800-52774600	Flanking Active TSS	Dnd41	blood
34	chr19:52773800-52774800	Flanking Active TSS	Fetal Brain Female	brain
35	chr19:52774000-52774400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr19:52774000-52774400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr19:52774000-52774400	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr19:52774000-52774400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr19:52774000-52774400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
40	chr19:52774000-52774400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
41	chr19:52774000-52774400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr19:52774000-52774400	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr19:52774000-52774400	Active TSS	Sigmoid Colon	Sigmoid Colon
44	chr19:52774000-52774400	Weak transcription	K562	blood
45	chr19:52774000-52774600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr19:52774000-52774600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr19:52774000-52774600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr19:52774000-52774600	Enhancers	Primary B cells from peripheral blood	blood
49	chr19:52774000-52774600	Enhancers	Primary T cells fromperipheralblood	blood
50	chr19:52774000-52774600	Enhancers	Primary T helper naive cells from peripheral blood	blood

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