Variant report

Variant	rs57696232
Chromosome Location	chr19:56183037-56183038
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:211)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:211 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr19:56182832-56183273	A549	lung:	n/a	n/a
2	POLR2A	chr19:56182592-56183218	K562	blood:	n/a	n/a
3	CTCF	chr19:56182980-56183206	GM10248	blood:	n/a	n/a
4	USF1	chr19:56182998-56183244	SK-N-SH_RA	brain:	n/a	n/a
5	CTCF	chr19:56183000-56183150	GM12873	blood:	n/a	n/a
6	CTCF	chr19:56183020-56183170	NHDF-neo	bronchial:	n/a	n/a
7	CTCF	chr19:56183020-56183170	HRPEpiC	eye:	n/a	n/a
8	RAD21	chr19:56182850-56183214	A549	lung:	n/a	chr19:56183025-56183037
9	RAD21	chr19:56182999-56183146	GM12878	blood:	n/a	chr19:56183025-56183037
10	CTCF	chr19:56183020-56183170	HBMEC	blood vessel:	n/a	n/a
11	USF1	chr19:56182986-56183274	H1-hESC	embryonic stem cell:	n/a	n/a
12	JUND	chr19:56182951-56183188	K562	blood:	n/a	n/a
13	CTCF	chr19:56183000-56183150	HMEC	breast:	n/a	n/a
14	BRCA1	chr19:56182971-56183130	HepG2	liver:	n/a	n/a
15	CTCF	chr19:56182948-56183199	HepG2	liver:	n/a	n/a
16	RAD21	chr19:56182903-56183284	ECC-1	luminal epithelium:	n/a	chr19:56183025-56183037
17	CTCF	chr19:56182931-56183210	H1-hESC	embryonic stem cell:	n/a	n/a
18	CTCF	chr19:56182959-56183210	LNCaP	prostate:	n/a	n/a
19	CTCF	chr19:56182980-56183130	GM12870	blood:	n/a	n/a
20	POLR2A	chr19:56182753-56183118	H1-hESC	embryonic stem cell:	n/a	n/a
21	GABPA	chr19:56182843-56183197	H1-hESC	embryonic stem cell:	n/a	n/a
22	CTCF	chr19:56182848-56183205	HepG2	liver:	n/a	n/a
23	POLR2A	chr19:56182778-56183182	Hela-S3	cervix:	n/a	n/a
24	CTCF	chr19:56183020-56183170	AG10803	skin:	n/a	n/a
25	CTCF	chr19:56182818-56183331	K562	blood:	n/a	n/a
26	CTCF	chr19:56182908-56183198	H1-hESC	embryonic stem cell:	n/a	n/a
27	CTCF	chr19:56182960-56183110	HFF-Myc	foreskin:	n/a	n/a
28	POLR2A	chr19:56182313-56183257	SK-N-MC	brain:	n/a	n/a
29	CTCF	chr19:56182959-56183209	MCF-7	breast:	n/a	n/a
30	CTCF	chr19:56183020-56183170	GM12865	blood:	n/a	n/a
31	CTCF	chr19:56183020-56183170	BJ	skin:	n/a	n/a
32	CTCF	chr19:56183014-56183195	GM20000	blood:	n/a	n/a
33	CTCF	chr19:56182980-56183130	GM12865	blood:	n/a	n/a
34	POLR2A	chr19:56182920-56183170	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr19:56182843-56183177	H1-hESC	embryonic stem cell:	n/a	n/a
36	CTCF	chr19:56183020-56183170	HVMF	connective:	n/a	n/a
37	POLR2A	chr19:56182869-56183075	GM12878	blood:	n/a	n/a
38	CTCF	chr19:56183020-56183170	HCM	heart:	n/a	n/a
39	CEBPB	chr19:56182958-56183370	H1-hESC	embryonic stem cell:	n/a	n/a
40	RAD21	chr19:56182942-56183195	K562	blood:	n/a	chr19:56183025-56183037
41	RAD21	chr19:56182908-56183215	H1-hESC	embryonic stem cell:	n/a	chr19:56183025-56183037
42	CTCF	chr19:56183000-56183150	GM12878	blood:	n/a	n/a
43	MXI1	chr19:56182921-56183199	H1-hESC	embryonic stem cell:	n/a	n/a
44	CTCF	chr19:56183020-56183170	HepG2	liver:	n/a	n/a
45	CTCF	chr19:56182929-56183195	SK-N-SH_RA	brain:	n/a	n/a
46	TBP	chr19:56182958-56183206	H1-hESC	embryonic stem cell:	n/a	n/a
47	CHD2	chr19:56182938-56183232	H1-hESC	embryonic stem cell:	n/a	n/a
48	JUND	chr19:56182932-56183250	H1-hESC	embryonic stem cell:	n/a	n/a
49	CTCF	chr19:56183004-56183192	LNCaP	prostate:	n/a	n/a
50	CTCF	chr19:56183000-56183150	HFF-Myc	foreskin:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:56181298..56183731-chr19:59054697..59056845,2	K562	blood:
2	chr19:56182120..56185364-chr19:56187275..56191666,5	MCF-7	breast:
3	chr19:56182358..56184024-chr19:56184712..56187207,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EPN1-3	chr19:56182743-56183435	ENSG00000267096.1

No data

Variant related genes	Relation type
EPN1	TF binding region
ENSG00000267523	Chromatin interaction
ENSG00000063245	Chromatin interaction
ENSG00000264910	Chromatin interaction
ENSG00000130726	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs16986466	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs310444	0.97[AFR][1000 genomes]
rs57728680	0.84[AFR][1000 genomes]
rs61736527	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73613290	0.87[AFR][1000 genomes]
rs73615076	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

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	chr19:56170200-56184000	Strong transcription	Primary T cells from cord blood	blood
3	chr19:56170200-56185200	Strong transcription	Fetal Thymus	thymus
4	chr19:56170200-56185400	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr19:56170200-56185800	Strong transcription	Fetal Stomach	stomach
6	chr19:56170400-56185600	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr19:56170400-56185800	Strong transcription	Fetal Brain Female	brain
8	chr19:56170800-56185400	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr19:56170800-56185800	Weak transcription	Psoas Muscle	Psoas
10	chr19:56170800-56186000	Weak transcription	Right Atrium	heart
11	chr19:56171200-56184600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr19:56171400-56185000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr19:56171400-56185400	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr19:56172000-56185000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr19:56172200-56185000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr19:56172600-56186000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr19:56172800-56184800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr19:56175400-56185600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr19:56175800-56186000	Weak transcription	Fetal Kidney	kidney
20	chr19:56177200-56183200	Genic enhancers	Primary T cells fromperipheralblood	blood
21	chr19:56177400-56183200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr19:56177400-56183200	Genic enhancers	Gastric	stomach
23	chr19:56178000-56185800	Weak transcription	HSMMtube	muscle
24	chr19:56178600-56185800	Weak transcription	Fetal Brain Male	brain
25	chr19:56179800-56184800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr19:56179800-56185000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr19:56179800-56185400	Strong transcription	NHEK	skin
28	chr19:56180200-56185600	Genic enhancers	Dnd41	blood
29	chr19:56181200-56183200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr19:56181200-56184200	Strong transcription	Hela-S3	cervix
31	chr19:56181600-56183200	Genic enhancers	Cortex derived primary cultured neurospheres	brain
32	chr19:56181600-56183200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr19:56181600-56184000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr19:56181600-56184000	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr19:56181600-56185800	Genic enhancers	Liver	Liver
36	chr19:56181800-56185400	Strong transcription	GM12878-XiMat	blood
37	chr19:56182000-56183200	Strong transcription	Pancreas	Pancrea
38	chr19:56182000-56183200	Genic enhancers	Spleen	Spleen
39	chr19:56182000-56183400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr19:56182000-56183600	Weak transcription	NH-A	brain
41	chr19:56182000-56183800	Weak transcription	HUVEC	blood vessel
42	chr19:56182000-56184000	Strong transcription	Colonic Mucosa	Colon
43	chr19:56182000-56184200	Strong transcription	Lung	lung
44	chr19:56182000-56184400	Strong transcription	HepG2	liver
45	chr19:56182000-56184800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr19:56182000-56184800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr19:56182000-56184800	Weak transcription	Fetal Lung	lung
48	chr19:56182000-56185200	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr19:56182000-56185200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr19:56182000-56185200	Strong transcription	Fetal Muscle Trunk	muscle

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