Variant report

Variant	rs2560876
Chromosome Location	chr19:52773587-52773588
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:66)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:66 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:52772457-52773698	MCF10A-Er-Src	breast:	n/a	n/a
2	RUNX3	chr19:52772468-52773650	GM12878	blood:	n/a	n/a
3	POLR2A	chr19:52772358-52773879	MCF-7	breast:	n/a	n/a
4	MAX	chr19:52772359-52773723	A549	lung:	n/a	n/a
5	POLR2A	chr19:52772492-52773884	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr19:52772454-52773872	GM18526	blood:	n/a	n/a
7	MAZ	chr19:52772597-52773669	K562	blood:	n/a	n/a
8	POLR2A	chr19:52772554-52773934	GM12891	blood:	n/a	n/a
9	POLR2A	chr19:52772263-52774060	SK-N-MC	brain:	n/a	n/a
10	POLR2A	chr19:52772359-52773963	GM12892	blood:	n/a	n/a
11	POLR2A	chr19:52773556-52773797	K562	blood:	n/a	n/a
12	MTA3	chr19:52772222-52773945	GM12878	blood:	n/a	n/a
13	POLR2A	chr19:52772300-52773934	U87	brain:	n/a	n/a
14	ELK1	chr19:52772585-52773611	GM12878	blood:	n/a	n/a
15	POLR2A	chr19:52772376-52773589	PFSK-1	brain:	n/a	n/a
16	POLR2A	chr19:52772251-52773893	H1-hESC	embryonic stem cell:	n/a	n/a
17	SIN3A	chr19:52772490-52773940	H1-hESC	embryonic stem cell:	n/a	chr19:52773131-52773144 chr19:52772824-52772835
18	POLR2A	chr19:52772400-52773965	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr19:52772430-52774012	H1-neurons	neurons:	n/a	n/a
20	POLR2A	chr19:52772480-52774033	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr19:52772367-52773768	PANC-1	pancreas:	n/a	n/a
22	POLR2A	chr19:52772455-52773619	HL-60	blood:	n/a	n/a
23	REST	chr19:52772460-52773639	HL-60	blood:	n/a	chr19:52772792-52772805
24	RELA	chr19:52772506-52773834	GM15510	blood:	n/a	n/a
25	ELF1	chr19:52773537-52773739	K562	blood:	n/a	chr19:52773630-52773643
26	ZNF263	chr19:52772744-52773926	HEK293-T-REx	kidney:	n/a	chr19:52773763-52773772
27	POLR2A	chr19:52772422-52774052	GM12878	blood:	n/a	n/a
28	TAF1	chr19:52772440-52773926	H1-hESC	embryonic stem cell:	n/a	n/a
29	HEY1	chr19:52773552-52773920	K562	blood:	n/a	n/a
30	POLR2A	chr19:52772336-52773973	HepG2	liver:	n/a	n/a
31	RELA	chr19:52772508-52773736	GM12891	blood:	n/a	n/a
32	POLR2A	chr19:52772447-52773588	H1-neurons	neurons:	n/a	n/a
33	RCOR1	chr19:52772519-52773665	GM12878	blood:	n/a	n/a
34	RELA	chr19:52772539-52773672	GM19099	blood:	n/a	n/a
35	POLR2A	chr19:52772368-52773843	GM12892	blood:	n/a	n/a
36	POLR2A	chr19:52772486-52773865	GM12878	blood:	n/a	n/a
37	RAD21	chr19:52772750-52773874	IMR90	lung:	n/a	chr19:52773580-52773589
38	IRF1	chr19:52773571-52773659	K562	blood:	n/a	chr19:52773616-52773627
39	SIN3AK20	chr19:52772351-52773609	MCF-7	breast:	n/a	n/a
40	POLR2A	chr19:52772465-52774017	IMR90	lung:	n/a	n/a
41	POLR2A	chr19:52772443-52773909	GM19099	blood:	n/a	n/a
42	POLR2A	chr19:52772468-52773929	GM19193	blood:	n/a	n/a
43	YY1	chr19:52772418-52773590	SK-N-SH	brain:	n/a	chr19:52773129-52773138 chr19:52773228-52773239
44	WRNIP1	chr19:52773425-52773935	GM12878	blood:	n/a	n/a
45	POLR2A	chr19:52772433-52773925	GM12891	blood:	n/a	n/a
46	TCF12	chr19:52772289-52773944	A549	lung:	n/a	n/a
47	POLR2A	chr19:52772471-52773873	GM18505	blood:	n/a	n/a
48	MXI1	chr19:52772315-52774164	SK-N-SH	brain:	n/a	n/a
49	TBP	chr19:52772438-52773675	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr19:52772465-52773743	HepG2	liver:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:52771242..52774496-chr19:52796154..52801198,5	MCF-7	breast:
2	chr19:52771473..52773658-chr19:52872286..52874915,2	MCF-7	breast:
3	chr19:52773000..52774618-chr19:52792454..52794386,2	K562	blood:
4	chr19:52772712..52774263-chr19:52799047..52800693,2	K562	blood:
5	chr19:52772026..52776261-chr19:52781637..52786393,5	K562	blood:
6	chr19:52771880..52774244-chr19:52838831..52841718,3	MCF-7	breast:
7	chr19:52772363..52775107-chr19:52799601..52802037,4	MCF-7	breast:
8	chr19:52772381..52778282-chr19:52778346..52783668,9	MCF-7	breast:
9	chr19:52772873..52773677-chr2:32390867..32391602,2	Hela-S3	cervix:
10	chr19:52771362..52774263-chr19:52797982..52800693,2	K562	blood:
11	chr19:52692994..52696358-chr19:52773094..52775949,3	MCF-7	breast:
12	chr19:52733004..52735653-chr19:52772074..52774471,2	MCF-7	breast:
13	chr19:52641013..52643402-chr19:52771783..52774070,3	MCF-7	breast:
14	chr19:52771196..52774040-chr19:52836837..52839956,3	MCF-7	breast:
15	chr19:52597459..52600188-chr19:52771516..52774031,2	MCF-7	breast:
16	chr19:52773231..52774853-chr19:52802417..52804914,2	MCF-7	breast:

No data

Variant related genes	Relation type
ZNF766	TF binding region
ENSG00000268015	Chromatin interaction
ENSG00000152683	Chromatin interaction
ENSG00000269102	Chromatin interaction
ENSG00000196214	Chromatin interaction
ENSG00000208002	Chromatin interaction
ENSG00000167554	Chromatin interaction
ENSG00000256087	Chromatin interaction
ENSG00000105568	Chromatin interaction
ENSG00000221923	Chromatin interaction
ENSG00000204611	Chromatin interaction
ENSG00000198464	Chromatin interaction
ENSG00000197608	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	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2002323	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2560874	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2657925	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2657929	1.00[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:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52772200-52773600	Active TSS	Brain Angular Gyrus	brain
2	chr19:52772200-52773600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr19:52772200-52773800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr19:52772200-52773800	Active TSS	Brain Germinal Matrix	brain
5	chr19:52772200-52773800	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr19:52772200-52773800	Active TSS	Esophagus	oesophagus
7	chr19:52772200-52773800	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr19:52772200-52774000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr19:52772200-52774000	Active TSS	Fetal Lung	lung
10	chr19:52772200-52774200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:52772200-52774200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr19:52772200-52774200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr19:52772200-52774200	Active TSS	A549	lung
14	chr19:52772400-52773600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr19:52772400-52773600	Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr19:52772400-52773600	Active TSS	Hela-S3	cervix
17	chr19:52772400-52773600	Active TSS	HUVEC	blood vessel
18	chr19:52772400-52773800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr19:52772400-52773800	Active TSS	H1 Cell Line	embryonic stem cell
20	chr19:52772400-52773800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr19:52772400-52773800	Active TSS	Colon Smooth Muscle	Colon
22	chr19:52772400-52773800	Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr19:52772400-52773800	Active TSS	Psoas Muscle	Psoas
24	chr19:52772400-52773800	Active TSS	Right Ventricle	heart
25	chr19:52772400-52773800	Active TSS	Thymus	Thymus
26	chr19:52772400-52773800	Active TSS	NHEK	skin
27	chr19:52772400-52774000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr19:52772400-52774000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr19:52772400-52774000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr19:52772400-52774000	Active TSS	Aorta	Aorta
31	chr19:52772400-52774000	Active TSS	Fetal Brain Male	brain
32	chr19:52772400-52774000	Active TSS	K562	blood
33	chr19:52772400-52774200	Active TSS	H9 Cell Line	embryonic stem cell
34	chr19:52772400-52774200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr19:52772400-52774200	Active TSS	HUES64 Cell Line	embryonic stem cell
36	chr19:52772400-52774200	Active TSS	Fetal Intestine Large	intestine
37	chr19:52772400-52774200	Active TSS	Pancreatic Islets	Pancreatic Islet
38	chr19:52772400-52774200	Active TSS	HSMMtube	muscle
39	chr19:52772400-52774200	Active TSS	NH-A	brain
40	chr19:52772400-52774400	Active TSS	HUES48 Cell Line	embryonic stem cell
41	chr19:52772400-52774400	Active TSS	HUES6 Cell Line	embryonic stem cell
42	chr19:52772400-52774400	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr19:52772400-52774400	Active TSS	iPS-18 Cell Line	embryonic stem cell
44	chr19:52772400-52774400	Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr19:52772400-52774400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr19:52772400-52774400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr19:52772400-52774400	Active TSS	HSMM	muscle
48	chr19:52772400-52774400	Active TSS	NHDF-Ad	bronchial
49	chr19:52772400-52774400	Active TSS	NHLF	lung
50	chr19:52772400-52774600	Active TSS	ES-I3 Cell Line	embryonic stem cell

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