Variant report

Variant	rs57063593
Chromosome Location	chr19:56182087-56182088
allele	A/G
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	POLR2A	chr19:56177320-56182238	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr19:56181543-56182200	U87	brain:	n/a	n/a
3	REST	chr19:56181518-56182513	PANC-1	pancreas:	n/a	chr19:56182308-56182318 chr19:56182359-56182379
4	NR3C1	chr19:56181690-56182391	A549	lung:	n/a	chr19:56182237-56182244 chr19:56182267-56182274
5	NR3C1	chr19:56181558-56182445	A549	lung:	n/a	chr19:56182237-56182244 chr19:56182267-56182274
6	CEBPB	chr19:56181340-56182421	ECC-1	luminal epithelium:	n/a	n/a
7	FOXM1	chr19:56181527-56182583	ECC-1	luminal epithelium:	n/a	n/a
8	ZBTB7A	chr19:56181646-56182460	ECC-1	luminal epithelium:	n/a	n/a
9	SIX5	chr19:56181588-56182246	A549	lung:	n/a	n/a
10	GABPA	chr19:56181546-56182090	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr19:56181649-56182104	Gliobla	brain:	n/a	n/a
12	PBX3	chr19:56181537-56182516	A549	lung:	n/a	chr19:56182053-56182062
13	TEAD4	chr19:56181239-56182508	ECC-1	luminal epithelium:	n/a	n/a
14	GATA3	chr19:56181425-56182649	A549	lung:	n/a	n/a
15	NFIC	chr19:56181199-56182603	ECC-1	luminal epithelium:	n/a	n/a
16	POLR2A	chr19:56179437-56183102	Hela-S3	cervix:	n/a	n/a
17	FOXM1	chr19:56181471-56182617	ECC-1	luminal epithelium:	n/a	n/a
18	POLR2A	chr19:56181622-56182345	H1-neurons	neurons:	n/a	n/a
19	POLR2A	chr19:56180664-56183041	GM12878	blood:	n/a	n/a
20	TCF12	chr19:56181116-56182663	ECC-1	luminal epithelium:	n/a	chr19:56181359-56181369
21	EP300	chr19:56181499-56182512	A549	lung:	n/a	n/a
22	REST	chr19:56181653-56182430	PANC-1	pancreas:	n/a	chr19:56182308-56182318 chr19:56182359-56182379
23	BCL3	chr19:56181565-56182492	A549	lung:	n/a	n/a
24	POLR2A	chr19:56181527-56182335	Hela-S3	cervix:	n/a	n/a
25	MAX	chr19:56181847-56182418	NB4	blood:	n/a	chr19:56182394-56182403
26	POLR2A	chr19:56177383-56182464	GM12892	blood:	n/a	n/a
27	POLR2A	chr19:56181495-56182201	GM15510	blood:	n/a	n/a
28	POLR2A	chr19:56181551-56182279	ECC-1	luminal epithelium:	n/a	n/a
29	YY1	chr19:56181604-56182412	ECC-1	luminal epithelium:	n/a	chr19:56181953-56181964
30	POLR2A	chr19:56180025-56183224	HL-60	blood:	n/a	n/a
31	POLR2A	chr19:56181533-56182162	HUVEC	blood vessel:	n/a	n/a
32	ESR1	chr19:56181591-56182360	ECC-1	luminal epithelium:	n/a	n/a
33	EP300	chr19:56181132-56182561	ECC-1	luminal epithelium:	n/a	n/a
34	ESR1	chr19:56181356-56182470	ECC-1	luminal epithelium:	n/a	n/a
35	POLR2A	chr19:56180627-56183153	K562	blood:	n/a	n/a
36	POLR2A	chr19:56181399-56182335	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr19:56181621-56182459	A549	lung:	n/a	n/a
38	POLR2A	chr19:56180800-56182160	HepG2	liver:	n/a	n/a
39	POLR2A	chr19:56177227-56182460	K562	blood:	n/a	n/a
40	POLR2A	chr19:56181276-56182440	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr19:56180637-56182430	GM12892	blood:	n/a	n/a
42	POLR2A	chr19:56181509-56182594	GM12878	blood:	n/a	n/a
43	POLR2A	chr19:56180652-56182438	GM12878	blood:	n/a	n/a
44	TCF12	chr19:56181444-56182566	A549	lung:	n/a	n/a
45	POLR2A	chr19:56181391-56182229	GM12891	blood:	n/a	n/a
46	EP300	chr19:56181491-56182390	A549	lung:	n/a	n/a
47	POLR2A	chr19:56181048-56183283	PANC-1	pancreas:	n/a	n/a
48	NR3C1	chr19:56181681-56182410	ECC-1	luminal epithelium:	n/a	chr19:56182237-56182244 chr19:56182267-56182274
49	TEAD4	chr19:56181266-56182487	ECC-1	luminal epithelium:	n/a	n/a
50	ATF3	chr19:56181545-56182130	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:56181298..56183731-chr19:59054697..59056845,2	K562	blood:
2	chr19:56164975..56168855-chr19:56176069..56182259,9	MCF-7	breast:
3	chr19:55917418..55919506-chr19:56180430..56182148,2	K562	blood:
4	chr19:56143909..56147540-chr19:56180767..56182811,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EPN1-3	chr19:56181998-56182106	ENSG00000267096.1

Variant related genes	Relation type
EPN1	TF binding region
ENSG00000063244	Chromatin interaction
ENSG00000130726	Chromatin interaction
ENSG00000171425	Chromatin interaction
ENSG00000264910	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000213015	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11545669	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs310438	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs310439	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs310442	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs310443	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs310444	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs310470	0.83[EUR][1000 genomes]
rs310471	0.83[EUR][1000 genomes]
rs310474	0.83[EUR][1000 genomes]
rs507498	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs537728	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs581023	1.00[ASN][1000 genomes]
rs600106	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs630491	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs636466	0.83[EUR][1000 genomes]
rs636467	0.83[EUR][1000 genomes]
rs637788	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs679577	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs680444	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs681433	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7246799	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
5	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
6	nsv833882	chr19:56158633-56326564	Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv1061024	chr19:56167101-56217359	Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
8	esv3349569	chr19:56179960-56182791	Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 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	chr19:56170000-56184800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:56170200-56182200	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr19:56170200-56182400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
4	chr19:56170200-56182400	Strong transcription	Rectal Smooth Muscle	rectum
5	chr19:56170200-56184000	Strong transcription	Primary T cells from cord blood	blood
6	chr19:56170200-56185200	Strong transcription	Fetal Thymus	thymus
7	chr19:56170200-56185400	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr19:56170200-56185800	Strong transcription	Fetal Stomach	stomach
9	chr19:56170400-56182200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr19:56170400-56183000	Strong transcription	Sigmoid Colon	Sigmoid Colon
11	chr19:56170400-56185600	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr19:56170400-56185800	Strong transcription	Fetal Brain Female	brain
13	chr19:56170600-56182400	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr19:56170600-56182400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr19:56170800-56182600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr19:56170800-56182800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr19:56170800-56185400	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr19:56170800-56185800	Weak transcription	Psoas Muscle	Psoas
19	chr19:56170800-56186000	Weak transcription	Right Atrium	heart
20	chr19:56171000-56182800	Strong transcription	NHLF	lung
21	chr19:56171200-56182600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr19:56171200-56183000	Strong transcription	Primary B cells from cord blood	blood
23	chr19:56171200-56184600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr19:56171400-56185000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr19:56171400-56185400	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr19:56171600-56182400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr19:56172000-56182600	Strong transcription	Osteobl	bone
28	chr19:56172000-56185000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr19:56172200-56185000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr19:56172600-56186000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr19:56172800-56184800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr19:56175400-56185600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr19:56175800-56186000	Weak transcription	Fetal Kidney	kidney
34	chr19:56177200-56183200	Genic enhancers	Primary T cells fromperipheralblood	blood
35	chr19:56177400-56183200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr19:56177400-56183200	Genic enhancers	Gastric	stomach
37	chr19:56177600-56182200	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr19:56177600-56182600	Strong transcription	Primary hematopoietic stem cells	blood
39	chr19:56178000-56185800	Weak transcription	HSMMtube	muscle
40	chr19:56178600-56185800	Weak transcription	Fetal Brain Male	brain
41	chr19:56179800-56184800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr19:56179800-56185000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr19:56179800-56185400	Strong transcription	NHEK	skin
44	chr19:56180000-56183000	Strong transcription	Small Intestine	intestine
45	chr19:56180200-56185600	Genic enhancers	Dnd41	blood
46	chr19:56181200-56182600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
47	chr19:56181200-56183200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr19:56181200-56184200	Strong transcription	Hela-S3	cervix
49	chr19:56181400-56182200	Genic enhancers	Primary B cells from peripheral blood	blood
50	chr19:56181400-56182200	Genic enhancers	Primary T helper naive cells from peripheral blood	blood

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