Variant report

Variant	rs600106
Chromosome Location	chr19:56182472-56182473
allele	C/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	REST	chr19:56181518-56182513	PANC-1	pancreas:	n/a	chr19:56182308-56182318 chr19:56182359-56182379
2	FOXM1	chr19:56181527-56182583	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr19:56182313-56183257	SK-N-MC	brain:	n/a	n/a
4	PBX3	chr19:56181537-56182516	A549	lung:	n/a	chr19:56182053-56182062
5	POLR2A	chr19:56182131-56182714	PFSK-1	brain:	n/a	n/a
6	TEAD4	chr19:56181239-56182508	ECC-1	luminal epithelium:	n/a	n/a
7	GATA3	chr19:56181425-56182649	A549	lung:	n/a	n/a
8	NFIC	chr19:56181199-56182603	ECC-1	luminal epithelium:	n/a	n/a
9	POLR2A	chr19:56179437-56183102	Hela-S3	cervix:	n/a	n/a
10	FOXM1	chr19:56181471-56182617	ECC-1	luminal epithelium:	n/a	n/a
11	POLR2A	chr19:56180664-56183041	GM12878	blood:	n/a	n/a
12	TCF12	chr19:56181116-56182663	ECC-1	luminal epithelium:	n/a	chr19:56181359-56181369
13	EP300	chr19:56181499-56182512	A549	lung:	n/a	n/a
14	BCL3	chr19:56181565-56182492	A549	lung:	n/a	n/a
15	POLR2A	chr19:56180025-56183224	HL-60	blood:	n/a	n/a
16	EP300	chr19:56181132-56182561	ECC-1	luminal epithelium:	n/a	n/a
17	POLR2A	chr19:56180627-56183153	K562	blood:	n/a	n/a
18	POLR2A	chr19:56181509-56182594	GM12878	blood:	n/a	n/a
19	TCF12	chr19:56181444-56182566	A549	lung:	n/a	n/a
20	CTCF	chr19:56182451-56183303	A549	lung:	n/a	n/a
21	POLR2A	chr19:56181048-56183283	PANC-1	pancreas:	n/a	n/a
22	TEAD4	chr19:56181266-56182487	ECC-1	luminal epithelium:	n/a	n/a
23	MAX	chr19:56181525-56182584	A549	lung:	n/a	chr19:56182394-56182403
24	EP300	chr19:56181177-56182472	ECC-1	luminal epithelium:	n/a	n/a
25	TCF12	chr19:56181130-56182647	ECC-1	luminal epithelium:	n/a	chr19:56181359-56181369
26	POLR2A	chr19:56180772-56182630	K562	blood:	n/a	n/a
27	SIN3AK20	chr19:56181527-56182474	PANC-1	pancreas:	n/a	n/a
28	MAX	chr19:56181456-56182483	ECC-1	luminal epithelium:	n/a	chr19:56182394-56182403
29	BCL3	chr19:56181502-56182501	A549	lung:	n/a	n/a
30	POLR2A	chr19:56177574-56182562	GM12892	blood:	n/a	n/a
31	POLR2A	chr19:56177312-56183116	A549	lung:	n/a	n/a
32	TCF7L2	chr19:56181258-56182486	PANC-1	pancreas:	n/a	n/a
33	PBX3	chr19:56181646-56182482	A549	lung:	n/a	chr19:56182053-56182062
34	POLR2A	chr19:56179427-56183202	HepG2	liver:	n/a	n/a
35	NFIC	chr19:56181296-56182607	ECC-1	luminal epithelium:	n/a	n/a
36	POLR2A	chr19:56177127-56183356	PANC-1	pancreas:	n/a	n/a
37	POLR2A	chr19:56180390-56182758	GM12878	blood:	n/a	n/a
38	YY1	chr19:56181616-56182472	ECC-1	luminal epithelium:	n/a	chr19:56181953-56181964
39	MAX	chr19:56181325-56182477	ECC-1	luminal epithelium:	n/a	chr19:56182394-56182403
40	POLR2A	chr19:56181963-56182472	K562	blood:	n/a	n/a
41	MYC	chr19:56181786-56182613	NB4	blood:	n/a	chr19:56182394-56182403

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:
4	chr19:56143909..56147540-chr19:56180767..56182811,3	MCF-7	breast:

Variant related genes	Relation type
EPN1	TF binding region
ENSG00000063245	Chromatin interaction
ENSG00000264910	Chromatin interaction
ENSG00000130726	Chromatin interaction
ENSG00000267523	Chromatin interaction
ENSG00000171425	Chromatin interaction
ENSG00000213015	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11545669	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs310438	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs310439	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs310442	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs310443	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs310444	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs310470	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs310471	1.00[AFR][1000 genomes];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]
rs56038728	1.00[AFR][1000 genomes]
rs57063593	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs581023	1.00[ASN][1000 genomes]
rs630491	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs636466	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs636467	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs637788	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs679577	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs680444	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs681433	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7246799	1.00[AFR][1000 genomes];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	chr19:56170200-56184000	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	chr19:56170400-56183000	Strong transcription	Sigmoid Colon	Sigmoid Colon
7	chr19:56170400-56185600	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr19:56170400-56185800	Strong transcription	Fetal Brain Female	brain
9	chr19:56170800-56182600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr19:56170800-56182800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr19:56170800-56185400	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr19:56170800-56185800	Weak transcription	Psoas Muscle	Psoas
13	chr19:56170800-56186000	Weak transcription	Right Atrium	heart
14	chr19:56171000-56182800	Strong transcription	NHLF	lung
15	chr19:56171200-56182600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr19:56171200-56183000	Strong transcription	Primary B cells from cord blood	blood
17	chr19:56171200-56184600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr19:56171400-56185000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr19:56171400-56185400	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr19:56172000-56182600	Strong transcription	Osteobl	bone
21	chr19:56172000-56185000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr19:56172200-56185000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr19:56172600-56186000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr19:56172800-56184800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr19:56175400-56185600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr19:56175800-56186000	Weak transcription	Fetal Kidney	kidney
27	chr19:56177200-56183200	Genic enhancers	Primary T cells fromperipheralblood	blood
28	chr19:56177400-56183200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr19:56177400-56183200	Genic enhancers	Gastric	stomach
30	chr19:56177600-56182600	Strong transcription	Primary hematopoietic stem cells	blood
31	chr19:56178000-56185800	Weak transcription	HSMMtube	muscle
32	chr19:56178600-56185800	Weak transcription	Fetal Brain Male	brain
33	chr19:56179800-56184800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr19:56179800-56185000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr19:56179800-56185400	Strong transcription	NHEK	skin
36	chr19:56180000-56183000	Strong transcription	Small Intestine	intestine
37	chr19:56180200-56185600	Genic enhancers	Dnd41	blood
38	chr19:56181200-56182600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
39	chr19:56181200-56183200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr19:56181200-56184200	Strong transcription	Hela-S3	cervix
41	chr19:56181600-56182600	Enhancers	Fetal Heart	heart
42	chr19:56181600-56182600	Genic enhancers	Stomach Smooth Muscle	stomach
43	chr19:56181600-56183200	Genic enhancers	Cortex derived primary cultured neurospheres	brain
44	chr19:56181600-56183200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr19:56181600-56184000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr19:56181600-56184000	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr19:56181600-56185800	Genic enhancers	Liver	Liver
48	chr19:56181800-56182600	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr19:56181800-56183000	Genic enhancers	Brain Germinal Matrix	brain
50	chr19:56181800-56185400	Strong transcription	GM12878-XiMat	blood

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