Variant report

Variant	rs28799665
Chromosome Location	chr19:53435453-53435454
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	chr19:53434963-53435643	H1-hESC	embryonic stem cell:	n/a	n/a
2	USF1	chr19:53435434-53435725	H1-hESC	embryonic stem cell:	n/a	chr19:53435591-53435602
3	POLR2A	chr19:53435182-53435466	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:53434778..53437566-chr19:53444319..53447141,2	MCF-7	breast:
2	chr19:53424849..53427676-chr19:53433481..53436897,3	K562	blood:

Variant related genes	Relation type
ZNF816-ZNF321P	TF binding region
ENSG00000269646	Chromatin interaction
ENSG00000213793	Chromatin interaction
ENSG00000180257	Chromatin interaction
ENSG00000213801	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10412732	1.00[AMR][1000 genomes]
rs10420210	0.83[AMR][1000 genomes]
rs28520171	0.85[AFR][1000 genomes]
rs28683090	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912308	chr19:53092465-53436337	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv912309	chr19:53092465-53440653	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv912310	chr19:53092465-53451291	Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv912313	chr19:53103875-53436337	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv912317	chr19:53105547-53440653	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv1066762	chr19:53112568-53552217	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	nsv912318	chr19:53118278-53451291	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv432072	chr19:53144788-53554388	Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	esv3401212	chr19:53151131-53482063	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
10	nsv912321	chr19:53186836-53451291	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
11	nsv1058903	chr19:53193570-53489633	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
12	nsv1067280	chr19:53193570-53567287	Active TSS Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
13	nsv544062	chr19:53193570-53567287	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers 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	33 gene(s)	inside rSNPs	diseases
14	nsv580030	chr19:53194344-53547394	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
15	nsv1057118	chr19:53195426-53480449	Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
16	nsv530807	chr19:53210488-53695881	Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
17	nsv912323	chr19:53249347-53451291	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
18	esv3431689	chr19:53291230-53483998	Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
19	nsv912329	chr19:53317001-53440653	Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
20	nsv912330	chr19:53317001-53478109	Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
21	nsv1064234	chr19:53346827-53480449	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
22	esv3319159	chr19:53361167-53446431	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
23	esv3319160	chr19:53361308-53446343	ZNF genes & repeats Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
24	esv3326632	chr19:53371248-53697569	Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
25	nsv963071	chr19:53401720-53480869	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
26	esv2758506	chr19:53410459-53652575	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
27	esv2758769	chr19:53410459-53652575	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
28	nsv428370	chr19:53410459-53652575	Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53426600-53444800	Weak transcription	Fetal Heart	heart
2	chr19:53426800-53435600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr19:53426800-53444800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr19:53426800-53445000	Weak transcription	Small Intestine	intestine
5	chr19:53426800-53445200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr19:53426800-53445200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr19:53427000-53440200	Weak transcription	Aorta	Aorta
8	chr19:53427000-53442600	Weak transcription	Ovary	ovary
9	chr19:53427000-53444800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr19:53427200-53439600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr19:53427400-53444800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr19:53427400-53445000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr19:53427400-53445200	Weak transcription	Left Ventricle	heart
14	chr19:53427600-53439600	Weak transcription	Fetal Lung	lung
15	chr19:53427600-53440200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr19:53427600-53440200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr19:53427600-53442200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr19:53427600-53444600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr19:53427600-53444800	Weak transcription	NHDF-Ad	bronchial
20	chr19:53427800-53437200	Weak transcription	Hela-S3	cervix
21	chr19:53427800-53438200	Weak transcription	Stomach Mucosa	stomach
22	chr19:53427800-53438200	Weak transcription	Osteobl	bone
23	chr19:53427800-53440000	Weak transcription	Colonic Mucosa	Colon
24	chr19:53427800-53440200	Weak transcription	Spleen	Spleen
25	chr19:53427800-53444800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr19:53427800-53445200	Weak transcription	NHLF	lung
27	chr19:53428400-53440400	Weak transcription	NHEK	skin
28	chr19:53428600-53444800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr19:53430800-53436800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr19:53431600-53435600	Weak transcription	Fetal Stomach	stomach
31	chr19:53432000-53440200	Weak transcription	Thymus	Thymus
32	chr19:53432000-53444600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr19:53432000-53444800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr19:53432200-53439600	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr19:53432200-53439600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr19:53432200-53442200	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr19:53432400-53435800	Weak transcription	Primary B cells from peripheral blood	blood
38	chr19:53432400-53439200	Weak transcription	Fetal Kidney	kidney
39	chr19:53432400-53440200	Weak transcription	Stomach Smooth Muscle	stomach
40	chr19:53432400-53440800	Weak transcription	Dnd41	blood
41	chr19:53432400-53444800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr19:53432400-53444800	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr19:53432600-53435600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr19:53432600-53435600	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr19:53432600-53435800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr19:53432600-53437800	Weak transcription	Fetal Intestine Large	intestine
47	chr19:53432600-53439200	Weak transcription	HepG2	liver
48	chr19:53432600-53439600	Weak transcription	Esophagus	oesophagus
49	chr19:53432600-53439800	Weak transcription	Gastric	stomach
50	chr19:53432600-53440000	Weak transcription	H9 Cell Line	embryonic stem cell

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