Variant report

Variant	rs28385383
Chromosome Location	chr19:56194986-56194987
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:35)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:35 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BHLHE40	chr19:56194931-56195654	HepG2	liver:	n/a	n/a
2	TBP	chr19:56194953-56195593	HepG2	liver:	n/a	n/a
3	MBD4	chr19:56194934-56195417	HepG2	liver:	n/a	n/a
4	HNF4A	chr19:56194885-56195607	HepG2	liver:	n/a	chr19:56195141-56195156
5	FOXA1	chr19:56194926-56195773	HepG2	liver:	n/a	n/a
6	ELF1	chr19:56194917-56195279	HepG2	liver:	n/a	n/a
7	MYBL2	chr19:56194683-56195747	HepG2	liver:	n/a	n/a
8	HNF4A	chr19:56194913-56195571	HepG2	liver:	n/a	chr19:56195141-56195156
9	EP300	chr19:56194929-56195698	HepG2	liver:	n/a	n/a
10	FOXA1	chr19:56194909-56195727	HepG2	liver:	n/a	n/a
11	HEY1	chr19:56194867-56195804	HepG2	liver:	n/a	n/a
12	POLR2A	chr19:56194957-56195612	HepG2	liver:	n/a	n/a
13	HEY1	chr19:56194980-56195682	HepG2	liver:	n/a	n/a
14	MAX	chr19:56194984-56195453	HepG2	liver:	n/a	n/a
15	POLR2A	chr19:56194861-56195707	HepG2	liver:	n/a	n/a
16	ARID3A	chr19:56194927-56195558	HepG2	liver:	n/a	n/a
17	TEAD4	chr19:56194859-56195726	HepG2	liver:	n/a	n/a
18	MXI1	chr19:56194921-56195589	HepG2	liver:	n/a	n/a
19	ZEB1	chr19:56194610-56195789	HepG2	liver:	n/a	n/a
20	EP300	chr19:56194871-56195644	HepG2	liver:	n/a	n/a
21	HNF4G	chr19:56194898-56195584	HepG2	liver:	n/a	n/a
22	SP1	chr19:56194780-56195746	HepG2	liver:	n/a	n/a
23	NFIC	chr19:56194950-56195598	HepG2	liver:	n/a	n/a
24	POLR2A	chr19:56194937-56195727	HepG2	liver:	n/a	n/a
25	NFIC	chr19:56194941-56195622	HepG2	liver:	n/a	n/a
26	FOXA1	chr19:56194897-56195620	HepG2	liver:	n/a	n/a
27	POLR2A	chr19:56194937-56195654	HepG2	liver:	n/a	n/a
28	MYBL2	chr19:56194753-56195500	HepG2	liver:	n/a	n/a
29	POLR2A	chr19:56194695-56195777	HepG2	liver:	n/a	n/a
30	FOXA1	chr19:56194879-56195724	HepG2	liver:	n/a	n/a
31	HNF4G	chr19:56194839-56195563	HepG2	liver:	n/a	n/a
32	ELF1	chr19:56194935-56195289	HepG2	liver:	n/a	n/a
33	POLR2A	chr19:56194943-56195143	K562	blood:	n/a	n/a
34	MAX	chr19:56194844-56195695	HepG2	liver:	n/a	n/a
35	MYC	chr19:56194936-56195323	HepG2	liver:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:56185642..56190165-chr19:56193908..56196750,4	MCF-7	breast:
2	chr19:56194595..56204961-chr19:56206160..56210902,10	K562	blood:
3	chr19:56165703..56169980-chr19:56194386..56196896,5	MCF-7	breast:
4	chr19:56111104..56113443-chr19:56194551..56196136,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000211571	TF binding region
ENSG00000267018	Chromatin interaction
ENSG00000063245	Chromatin interaction
ENSG00000267183	Chromatin interaction
ENSG00000171443	Chromatin interaction
ENSG00000063244	Chromatin interaction
ENSG00000203305	Chromatin interaction
ENSG00000267523	Chromatin interaction
ENSG00000179943	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10402618	0.89[ASN][1000 genomes]
rs10403866	0.95[ASN][1000 genomes]
rs10408613	0.91[ASN][1000 genomes]
rs10410404	0.87[ASN][1000 genomes]
rs10410802	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10410886	0.86[ASN][1000 genomes]
rs10412050	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10415521	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10417539	0.96[ASN][1000 genomes]
rs10421319	0.86[ASN][1000 genomes]
rs11882031	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28595590	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28668166	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs310437	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs310441	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3745446	0.81[ASN][1000 genomes]
rs4801526	0.81[ASN][1000 genomes]
rs523509	0.85[ASN][1000 genomes]
rs57544196	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs584405	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60873246	0.92[ASN][1000 genomes]
rs617073	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs648651	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs681804	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7256441	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73613281	0.94[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs8100143	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104242	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8109983	0.98[ASN][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:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56188200-56218200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr19:56188400-56195000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr19:56188400-56211200	Strong transcription	Cortex derived primary cultured neurospheres	brain
4	chr19:56188400-56213600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr19:56188600-56210000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr19:56188600-56212400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:56188600-56215600	Weak transcription	Fetal Brain Male	brain
8	chr19:56188800-56199800	Weak transcription	HSMMtube	muscle
9	chr19:56188800-56212400	Strong transcription	Thymus	Thymus
10	chr19:56189000-56199600	Strong transcription	Fetal Stomach	stomach
11	chr19:56189000-56210000	Strong transcription	Fetal Brain Female	brain
12	chr19:56189200-56195200	Genic enhancers	Fetal Intestine Small	intestine
13	chr19:56189200-56195400	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr19:56189200-56199400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr19:56189200-56209400	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr19:56189200-56212600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr19:56189400-56198000	Strong transcription	Brain Inferior Temporal Lobe	brain
18	chr19:56189400-56199600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr19:56189400-56209400	Strong transcription	Fetal Thymus	thymus
20	chr19:56189400-56209400	Strong transcription	Dnd41	blood
21	chr19:56189400-56212400	Strong transcription	Brain Germinal Matrix	brain
22	chr19:56189600-56204600	Strong transcription	Brain Anterior Caudate	brain
23	chr19:56189600-56209400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr19:56189600-56209800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr19:56189600-56213200	Strong transcription	Primary T cells from cord blood	blood
26	chr19:56190000-56196800	Weak transcription	Primary hematopoietic stem cells	blood
27	chr19:56190000-56198400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr19:56190000-56212600	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr19:56190200-56210200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr19:56190200-56212400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr19:56190400-56197600	Strong transcription	Brain Angular Gyrus	brain
32	chr19:56190400-56198000	Strong transcription	Colon Smooth Muscle	Colon
33	chr19:56190600-56198800	Strong transcription	Fetal Muscle Leg	muscle
34	chr19:56190600-56198800	Weak transcription	Small Intestine	intestine
35	chr19:56191000-56212400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr19:56191400-56195000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr19:56191400-56195000	Weak transcription	Brain Substantia Nigra	brain
38	chr19:56191400-56204600	Weak transcription	NHDF-Ad	bronchial
39	chr19:56191600-56197200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr19:56191800-56196200	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr19:56191800-56199400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr19:56191800-56200200	Weak transcription	K562	blood
43	chr19:56191800-56201800	Strong transcription	NHEK	skin
44	chr19:56191800-56203000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr19:56191800-56218800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr19:56192000-56195400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr19:56192000-56198600	Strong transcription	Stomach Smooth Muscle	stomach
48	chr19:56192000-56214600	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr19:56192200-56195000	Weak transcription	HMEC	breast
50	chr19:56192200-56196800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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