Variant report

Variant	rs3794983
Chromosome Location	chr19:52096053-52096054
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:52095177-52098004	U87	brain:	n/a	n/a
2	POLR2A	chr19:52095947-52098295	K562	blood:	n/a	n/a
3	POLR2A	chr19:52095284-52097348	U87	brain:	n/a	n/a
4	POLR2A	chr19:52095276-52097905	K562	blood:	n/a	n/a
5	POLR2A	chr19:52095284-52097962	U87	brain:	n/a	n/a
6	POLR2A	chr19:52095901-52096417	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr19:52096002-52096926	K562	blood:	n/a	n/a
8	POLR2A	chr19:52095171-52098010	U87	brain:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:51914893..51917429-chr19:52094517..52097128,3	K562	blood:
2	chr19:52095454..52097791-chr19:52104410..52105932,2	K562	blood:
3	chr19:51915124..51917429-chr19:52094517..52096646,2	K562	blood:
4	chr19:52096005..52097791-chr19:52103717..52105932,2	K562	blood:
5	chr19:51897297..51899400-chr19:52095029..52099296,3	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC018755.11.1-1	chr19:52095036-52096304	NR_034159

No data

Variant related genes	Relation type
ENSG00000269388	TF binding region
ENSG00000268889	Chromatin interaction
ENSG00000269388	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11084092	0.96[EUR][1000 genomes]
rs3794982	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3794984	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4801881	0.96[EUR][1000 genomes]
rs4802822	0.96[EUR][1000 genomes]
rs62114984	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7252645	0.96[EUR][1000 genomes]
rs7252767	0.96[EUR][1000 genomes]
rs883979	0.95[EUR][1000 genomes];0.88[ASN][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	nsv1066308	chr19:51680133-52103974	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv544049	chr19:51680133-52103974	Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	nsv544051	chr19:51944903-52147459	Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	esv2758504	chr19:51991896-52266700	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	542 gene(s)	inside rSNPs	diseases
5	esv2758767	chr19:51991896-52604625	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	578 gene(s)	inside rSNPs	diseases
6	nsv469584	chr19:52001381-52151821	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv482654	chr19:52001381-52151821	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats 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	25 gene(s)	inside rSNPs	diseases
8	nsv579966	chr19:52075622-52131119	Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
9	nsv482909	chr19:52091735-52266700	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	533 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52075800-52096800	Weak transcription	HepG2	liver
2	chr19:52077000-52097000	Weak transcription	Hela-S3	cervix
3	chr19:52091200-52096200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr19:52091200-52096400	Weak transcription	Brain Substantia Nigra	brain
5	chr19:52091200-52096400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr19:52091200-52096600	Weak transcription	Right Ventricle	heart
7	chr19:52091200-52096800	Weak transcription	Small Intestine	intestine
8	chr19:52091400-52096200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr19:52091400-52096200	Weak transcription	Lung	lung
10	chr19:52091400-52096400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr19:52091400-52096400	Weak transcription	Brain Angular Gyrus	brain
12	chr19:52091400-52096400	Weak transcription	Brain Hippocampus Middle	brain
13	chr19:52091400-52096400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr19:52091400-52096400	Weak transcription	Fetal Intestine Large	intestine
15	chr19:52091400-52096400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr19:52091400-52096400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr19:52091400-52096600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr19:52091400-52096600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr19:52091400-52096600	Weak transcription	Colonic Mucosa	Colon
20	chr19:52091400-52096600	Weak transcription	Colon Smooth Muscle	Colon
21	chr19:52091400-52096800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr19:52091400-52096800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr19:52091400-52096800	Weak transcription	Rectal Smooth Muscle	rectum
24	chr19:52091600-52096200	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr19:52091600-52096200	Weak transcription	Spleen	Spleen
26	chr19:52091600-52096400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr19:52091600-52096400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr19:52091600-52096400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr19:52091600-52096400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr19:52091600-52096400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr19:52091600-52096400	Weak transcription	Esophagus	oesophagus
32	chr19:52091600-52096400	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr19:52091600-52096400	Weak transcription	Stomach Smooth Muscle	stomach
34	chr19:52091600-52096400	Weak transcription	Thymus	Thymus
35	chr19:52091600-52096600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr19:52091600-52096600	Weak transcription	Adipose Nuclei	Adipose
37	chr19:52091600-52096600	Weak transcription	Fetal Muscle Leg	muscle
38	chr19:52091600-52096600	Weak transcription	Fetal Thymus	thymus
39	chr19:52091600-52096600	Weak transcription	Left Ventricle	heart
40	chr19:52091600-52096600	Weak transcription	Ovary	ovary
41	chr19:52091600-52096600	Weak transcription	NHEK	skin
42	chr19:52091600-52096800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr19:52091600-52097000	Weak transcription	Aorta	Aorta
44	chr19:52091800-52096200	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr19:52091800-52096200	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr19:52091800-52096200	Weak transcription	Dnd41	blood
47	chr19:52091800-52096400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr19:52091800-52096400	Weak transcription	Duodenum Mucosa	Duodenum
49	chr19:52091800-52096400	Weak transcription	GM12878-XiMat	blood
50	chr19:52091800-52096600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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