Variant report

Variant	rs59544809
Chromosome Location	chr10:54078059-54078060
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TAF1	chr10:54077749-54078295	A549	lung:	n/a	n/a
2	GATA3	chr10:54077794-54078442	A549	lung:	n/a	chr10:54078228-54078238
3	POLR2A	chr10:54076930-54079438	HUVEC	blood vessel:	n/a	n/a
4	TCF12	chr10:54077620-54079502	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr10:54077088-54079315	HCT-116	colon:	n/a	n/a
6	EP300	chr10:54077674-54079535	A549	lung:	n/a	chr10:54078994-54079003 chr10:54078073-54078087 chr10:54078993-54079002 chr10:54079270-54079284
7	POLR2A	chr10:54077855-54078157	A549	lung:	n/a	n/a
8	BCL3	chr10:54077024-54080405	A549	lung:	n/a	chr10:54078994-54079003 chr10:54078993-54079002 chr10:54079324-54079331
9	GATA3	chr10:54077598-54079866	A549	lung:	n/a	chr10:54079532-54079549 chr10:54079529-54079542 chr10:54079531-54079538 chr10:54079320-54079336 chr10:54079323-54079333 chr10:54079320-54079336 chr10:54079531-54079540 chr10:54078228-54078238
10	JUND	chr10:54077626-54079472	HCT-116	colon:	n/a	chr10:54078993-54079002 chr10:54078994-54079001 chr10:54078993-54079003 chr10:54078994-54079003 chr10:54078992-54079003 chr10:54078994-54079002
11	JUN	chr10:54077722-54079293	Hela-S3	cervix:	n/a	chr10:54078993-54079002 chr10:54078994-54079001 chr10:54078993-54079003 chr10:54078994-54079003 chr10:54078994-54079002
12	PBX3	chr10:54077656-54079439	SK-N-SH	brain:	n/a	n/a
13	POLR2A	chr10:54077782-54078225	HUVEC	blood vessel:	n/a	n/a
14	PML	chr10:54077749-54078410	MCF-7	breast:	n/a	n/a
15	GATA3	chr10:54077665-54079534	SK-N-SH	brain:	n/a	chr10:54079320-54079336 chr10:54079323-54079333 chr10:54079320-54079336 chr10:54078228-54078238
16	EP300	chr10:54077663-54079654	A549	lung:	n/a	chr10:54078994-54079003 chr10:54079546-54079560 chr10:54078073-54078087 chr10:54078993-54079002 chr10:54079270-54079284
17	TCF12	chr10:54077592-54079442	SK-N-SH	brain:	n/a	n/a
18	TEAD4	chr10:54077680-54078388	SK-N-SH	brain:	n/a	n/a
19	EP300	chr10:54078036-54078350	SK-N-SH_RA	brain:	n/a	chr10:54078073-54078087
20	NR2C2	chr10:54077820-54078790	HepG2	liver:	n/a	n/a
21	SIN3AK20	chr10:54077786-54078260	SK-N-SH	brain:	n/a	n/a
22	REST	chr10:54077787-54079851	A549	lung:	n/a	n/a
23	POLR2A	chr10:54077809-54078172	HepG2	liver:	n/a	n/a
24	SIN3AK20	chr10:54077716-54079416	HCT-116	colon:	n/a	n/a
25	POLR2A	chr10:54073525-54079363	HUVEC	blood vessel:	n/a	n/a
26	FOS	chr10:54077821-54079373	MCF10A-Er-Src	breast:	n/a	chr10:54078993-54079002 chr10:54078994-54079001 chr10:54078993-54079003 chr10:54078994-54079003 chr10:54078992-54079003 chr10:54078994-54079002
27	POLR2A	chr10:54073092-54080655	SK-N-SH	brain:	n/a	n/a
28	ZBTB33	chr10:54077809-54079245	A549	lung:	n/a	n/a
29	POLR2A	chr10:54077328-54079239	HUVEC	blood vessel:	n/a	n/a
30	HEY1	chr10:54077753-54078185	HepG2	liver:	n/a	n/a
31	JUND	chr10:54077393-54080125	SK-N-SH	brain:	n/a	chr10:54078993-54079002 chr10:54078994-54079001 chr10:54078993-54079003 chr10:54078994-54079003 chr10:54078992-54079003 chr10:54078994-54079002
32	SP1	chr10:54077447-54079612	HCT-116	colon:	n/a	n/a
33	SP1	chr10:54077681-54079436	A549	lung:	n/a	n/a
34	TCF7L2	chr10:54077919-54078439	HCT-116	colon:	n/a	n/a
35	PBX3	chr10:54077876-54079286	A549	lung:	n/a	n/a
36	NFIC	chr10:54077616-54079455	SK-N-SH	brain:	n/a	n/a
37	POLR2A	chr10:54072864-54080901	ProgFib	skin:	n/a	n/a
38	TCF7L2	chr10:54077800-54079920	PANC-1	pancreas:	n/a	chr10:54078993-54079002 chr10:54079793-54079802
39	FOXA2	chr10:54077851-54078218	A549	lung:	n/a	n/a
40	MAX	chr10:54077812-54078369	SK-N-SH	brain:	n/a	n/a
41	POLR2A	chr10:54076964-54079358	MCF-7	breast:	n/a	n/a
42	JUND	chr10:54077705-54079327	A549	lung:	n/a	chr10:54078993-54079002 chr10:54078994-54079001 chr10:54078993-54079003 chr10:54078994-54079003 chr10:54078992-54079003 chr10:54078994-54079002
43	PBX3	chr10:54077720-54079321	SK-N-SH	brain:	n/a	n/a
44	USF1	chr10:54077679-54079585	A549	lung:	n/a	n/a
45	SP1	chr10:54077717-54079681	A549	lung:	n/a	n/a
46	POLR2A	chr10:54074945-54078566	HepG2	liver:	n/a	n/a
47	JUND	chr10:54077820-54078563	A549	lung:	n/a	n/a
48	SIX5	chr10:54077794-54079770	A549	lung:	n/a	chr10:54077991-54078000
49	FOSL1	chr10:54077622-54079510	HCT-116	colon:	n/a	chr10:54078993-54079002 chr10:54078994-54079001 chr10:54078993-54079003 chr10:54078994-54079003 chr10:54078994-54079002
50	FOSL2	chr10:54077232-54079564	A549	lung:	n/a	chr10:54078993-54079002 chr10:54078994-54079001 chr10:54078993-54079003 chr10:54078994-54079003 chr10:54078994-54079002

No.	Distal block	Cell Line	Cell type
1	chr10:54076999..54078873-chr10:54246852..54248689,2	MCF-7	breast:
2	chr10:54065577..54083492-chr10:54193846..54218961,120	MCF-7	breast:
3	chr10:54068229..54070730-chr10:54076005..54078630,2	K562	blood:
4	chr10:54077521..54079030-chr10:54180923..54182792,2	MCF-7	breast:
5	chr10:54077756..54080731-chr10:54080779..54082733,3	MCF-7	breast:
6	chr10:54071324..54082180-chr10:54192987..54217560,81	MCF-7	breast:
7	chr10:54077968..54079519-chr10:54235163..54236705,2	MCF-7	breast:
8	chr10:54068768..54071357-chr10:54075695..54080723,4	MCF-7	breast:
9	chr10:54076700..54078715-chr10:54233855..54235476,2	MCF-7	breast:

Variant related genes	Relation type
PRKG1-AS1	TF binding region
ENSG00000231131	Chromatin interaction

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

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

rs_ID	r²[population]
rs1528878	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1528879	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs16929708	0.89[AMR][1000 genomes]
rs60133922	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs73331254	0.85[AMR][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	nsv1045692	chr10:53301450-54086823	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv532194	chr10:53746620-54735550	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv895399	chr10:53900872-54219820	Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv895400	chr10:54073294-54094359	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:54075000-54078400	Transcr. at gene 5' and 3'	A549	lung
2	chr10:54075400-54078200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr10:54075800-54078200	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
4	chr10:54077000-54078600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr10:54077200-54078200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr10:54077200-54078800	Flanking Active TSS	HUVEC	blood vessel
7	chr10:54077400-54078800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr10:54077400-54078800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
9	chr10:54077600-54078200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr10:54077600-54078200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr10:54077600-54078200	Genic enhancers	NHLF	lung
12	chr10:54077600-54078400	Flanking Active TSS	NHEK	skin
13	chr10:54077600-54078600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr10:54077600-54080600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr10:54077800-54078200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr10:54077800-54078200	Flanking Active TSS	Osteobl	bone
17	chr10:54077800-54078400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr10:54077800-54078400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr10:54077800-54078400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr10:54077800-54078400	Flanking Active TSS	Hela-S3	cervix
21	chr10:54077800-54078400	Flanking Active TSS	HMEC	breast
22	chr10:54077800-54078400	Flanking Active TSS	NH-A	brain
23	chr10:54077800-54078800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr10:54077800-54080600	Enhancers	HSMMtube	muscle
25	chr10:54078000-54078200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr10:54078000-54078200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
27	chr10:54078000-54078200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr10:54078000-54078200	Enhancers	Spleen	Spleen
29	chr10:54078000-54078200	Enhancers	HepG2	liver
30	chr10:54078000-54078400	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr10:54078000-54078400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr10:54078000-54078400	Flanking Active TSS	HSMM	muscle
33	chr10:54078000-54078600	Enhancers	Placenta Amnion	Placenta Amnion
34	chr10:54078000-54078800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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