Variant report

Variant	rs56250101
Chromosome Location	chr19:56151167-56151168
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	chr19:56150319-56156666	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr19:56150228-56156269	GM12891	blood:	n/a	n/a
3	POLR2A	chr19:56150192-56156534	GM12878	blood:	n/a	n/a
4	POLR2A	chr19:56150380-56151264	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr19:56149778-56157300	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr19:56150010-56156634	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr19:56150270-56155844	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr19:56151135-56153336	K562	blood:	n/a	n/a
9	STAT5A	chr19:56151161-56153862	GM12878	blood:	n/a	chr19:56151811-56151818 chr19:56152748-56152760 chr19:56152799-56152807 chr19:56152675-56152687 chr19:56151740-56151752
10	POLR2A	chr19:56146066-56155822	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr19:56150509-56155890	PBDE	blood:	n/a	n/a
12	POLR2A	chr19:56150387-56157088	GM18505	blood:	n/a	n/a
13	CTCF	chr19:56150241-56153137	SK-N-SH	brain:	n/a	chr19:56152319-56152332 chr19:56152316-56152329
14	POLR2A	chr19:56149442-56155618	HepG2	liver:	n/a	n/a
15	JUN	chr19:56151135-56153473	K562	blood:	n/a	chr19:56153109-56153118 chr19:56153108-56153117
16	POLR2A	chr19:56151126-56156975	K562	blood:	n/a	n/a
17	POLR2A	chr19:56151159-56153976	PFSK-1	brain:	n/a	n/a
18	MXI1	chr19:56151126-56156192	SK-N-SH	brain:	n/a	chr19:56155427-56155436 chr19:56151538-56151547 chr19:56151540-56151549 chr19:56155425-56155434
19	POLR2A	chr19:56150136-56156336	K562	blood:	n/a	n/a
20	MTA3	chr19:56151145-56156293	GM12878	blood:	n/a	n/a
21	POLR2A	chr19:56151154-56155908	GM12892	blood:	n/a	n/a
22	POLR2A	chr19:56149741-56156388	SK-N-MC	brain:	n/a	n/a
23	MAX	chr19:56151151-56153107	K562	blood:	n/a	chr19:56151539-56151548 chr19:56151539-56151549 chr19:56151539-56151549 chr19:56151538-56151549

No.	Distal block	Cell Line	Cell type
1	chr19:55994990..55999125-chr19:56150596..56153745,4	K562	blood:
2	chr19:56111889..56113389-chr19:56150627..56153013,2	K562	blood:
3	chr19:56109576..56111086-chr19:56151064..56152602,2	K562	blood:
4	chr19:56133203..56138391-chr19:56150309..56156340,8	K562	blood:
5	chr19:56109287..56112853-chr19:56149861..56154883,7	MCF-7	breast:
6	chr19:56086664..56089219-chr19:56150784..56152646,2	MCF-7	breast:
7	chr19:55627842..55630893-chr19:56150877..56153462,3	MCF-7	breast:
8	chr19:56115086..56118069-chr19:56150430..56156112,7	MCF-7	breast:
9	chr19:55917594..55920802-chr19:56150613..56153734,3	K562	blood:
10	chr19:56135345..56138507-chr19:56147845..56151809,4	K562	blood:

Variant related genes	Relation type
CCDC106	TF binding region
ZNF581	TF binding region
ZNF580	TF binding region
ENSG00000261221	Chromatin interaction
ENSG00000090971	Chromatin interaction
ENSG00000125503	Chromatin interaction
ENSG00000171443	Chromatin interaction
ENSG00000179922	Chromatin interaction
ENSG00000267730	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000179943	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs56115240	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56331023	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61736526	1.00[AMR][1000 genomes]
rs73933303	1.00[AMR][1000 genomes]
rs73933306	1.00[AMR][1000 genomes]
rs73933307	1.00[AMR][1000 genomes]
rs73933308	1.00[AMR][1000 genomes]
rs73934393	0.81[AFR][1000 genomes]
rs73934395	0.81[AFR][1000 genomes]
rs73934401	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73934402	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73936310	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73936311	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73936315	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73936316	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv828643	chr19:56059280-56154823	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	nsv912500	chr19:56078722-56175515	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
6	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
7	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
8	nsv912503	chr19:56149077-56162776	Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
9	nsv912504	chr19:56149077-56170415	Flanking Active TSS Genic enhancers Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56147800-56151400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:56147800-56151400	Enhancers	Liver	Liver
3	chr19:56147800-56151400	Enhancers	Brain Substantia Nigra	brain
4	chr19:56147800-56151600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr19:56147800-56151600	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr19:56147800-56151600	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr19:56147800-56151600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr19:56147800-56151600	Weak transcription	Fetal Heart	heart
9	chr19:56147800-56151600	Enhancers	Pancreas	Pancrea
10	chr19:56147800-56151800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr19:56147800-56151800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr19:56148000-56151400	Enhancers	Duodenum Smooth Muscle	Duodenum
13	chr19:56148200-56151200	Weak transcription	Small Intestine	intestine
14	chr19:56148200-56151200	Weak transcription	HUVEC	blood vessel
15	chr19:56148200-56151400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr19:56148200-56151400	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr19:56148200-56151400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr19:56148200-56151400	Weak transcription	HMEC	breast
19	chr19:56148200-56151400	Weak transcription	HSMM	muscle
20	chr19:56148200-56151400	Weak transcription	HSMMtube	muscle
21	chr19:56148200-56151400	Weak transcription	NHEK	skin
22	chr19:56148200-56151600	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr19:56148200-56151600	Enhancers	Adipose Nuclei	Adipose
24	chr19:56148200-56151800	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr19:56148200-56151800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr19:56148400-56151200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr19:56148400-56151200	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr19:56148400-56151200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr19:56148400-56151200	Weak transcription	Colonic Mucosa	Colon
30	chr19:56148400-56151200	Weak transcription	Rectal Smooth Muscle	rectum
31	chr19:56148400-56151200	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr19:56148400-56151200	Weak transcription	NH-A	brain
33	chr19:56148400-56151200	Weak transcription	Osteobl	bone
34	chr19:56148400-56151400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr19:56148400-56151400	Weak transcription	Brain Anterior Caudate	brain
36	chr19:56148400-56151400	Weak transcription	Esophagus	oesophagus
37	chr19:56148400-56151400	Weak transcription	Fetal Lung	lung
38	chr19:56148400-56151400	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr19:56148400-56151400	Enhancers	Dnd41	blood
40	chr19:56148400-56151400	Weak transcription	NHLF	lung
41	chr19:56149000-56151200	Weak transcription	Duodenum Mucosa	Duodenum
42	chr19:56149200-56151400	Weak transcription	Primary B cells from cord blood	blood
43	chr19:56149200-56151400	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr19:56149200-56151600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr19:56149200-56151800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr19:56149400-56151200	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr19:56149400-56151400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr19:56149400-56151400	Weak transcription	Ovary	ovary
49	chr19:56149400-56151600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr19:56149400-56151800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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