Variant report

Variant	rs2303089
Chromosome Location	chr19:55964720-55964721
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:55952279..55955138-chr19:55963056..55965766,3	K562	blood:
2	chr19:55768403..55770603-chr19:55963034..55965781,2	K562	blood:
3	chr19:55956258..55958945-chr19:55964103..55966551,2	K562	blood:
4	chr19:55963302..55966247-chr19:56117122..56119582,2	K562	blood:
5	chr19:55962879..55966431-chr19:56013063..56017664,4	K562	blood:
6	chr19:55963237..55966425-chr19:55989269..55992485,3	K562	blood:
7	chr19:55683561..55685355-chr19:55963248..55964995,2	K562	blood:
8	chr19:55951925..55955138-chr19:55963056..55965766,4	K562	blood:
9	chr19:55894504..55900051-chr19:55962971..55968155,6	K562	blood:
10	chr19:55963041..55966300-chr19:55968298..55973344,6	MCF-7	breast:
11	chr19:55915948..55921315-chr19:55958410..55968133,14	K562	blood:
12	chr19:55962879..55966271-chr19:56014948..56017664,3	K562	blood:
13	chr19:55917232..55920888-chr19:55959942..55966428,7	K562	blood:
14	chr19:55962858..55966620-chr19:55998648..56002437,4	K562	blood:
15	chr19:55895254..55899821-chr19:55961359..55968155,8	K562	blood:
16	chr19:55962707..55966415-chr19:56152837..56156064,3	K562	blood:
17	chr19:55962858..55965792-chr19:55998648..56000316,2	K562	blood:
18	chr19:55964045..55966011-chr19:56013009..56014563,2	K562	blood:
19	chr19:55910368..55912840-chr19:55964651..55967610,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SHISA7-1	chr19:55964356-55964951	NONHSAT068040

No data

Variant related genes	Relation type
ENSG00000108107	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000213015	Chromatin interaction
ENSG00000171425	Chromatin interaction
ENSG00000105063	Chromatin interaction
ENSG00000233493	Chromatin interaction
ENSG00000179954	Chromatin interaction
ENSG00000267093	Chromatin interaction
ENSG00000187902	Chromatin interaction
ENSG00000063241	Chromatin interaction
ENSG00000129990	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10412033	1.00[TSI][hapmap]
rs12462602	0.97[ASN][1000 genomes]
rs62128233	0.97[ASN][1000 genomes]
rs7247719	1.00[ASW][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.83[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7253234	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[ASN][1000 genomes]
rs73606265	0.87[AMR][1000 genomes]
rs73606269	0.87[AMR][1000 genomes];0.81[EUR][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	nsv912457	chr19:55725410-56019597	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers 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 miRNA target site	228 gene(s)	inside rSNPs	diseases
2	nsv432086	chr19:55807586-56050844	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS 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	220 gene(s)	inside rSNPs	diseases
3	nsv912463	chr19:55845386-56004901	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
4	nsv912473	chr19:55874642-56145428	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
5	nsv912477	chr19:55936376-55972950	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv912478	chr19:55936376-56045522	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
7	nsv912479	chr19:55942456-55969746	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55960600-55966600	Weak transcription	Pancreas	Pancrea
2	chr19:55961800-55965000	Active TSS	Brain Angular Gyrus	brain
3	chr19:55962600-55964800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
4	chr19:55962800-55964800	Enhancers	Primary B cells from cord blood	blood
5	chr19:55963000-55964800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
6	chr19:55963000-55964800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr19:55963600-55964800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
8	chr19:55963800-55971000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr19:55964000-55964800	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
10	chr19:55964000-55964800	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
11	chr19:55964000-55964800	Active TSS	Brain Germinal Matrix	brain
12	chr19:55964000-55964800	Enhancers	Fetal Brain Male	brain
13	chr19:55964000-55964800	Active TSS	Fetal Brain Female	brain
14	chr19:55964000-55964800	Bivalent Enhancer	Fetal Intestine Large	intestine
15	chr19:55964000-55964800	Bivalent Enhancer	Fetal Muscle Leg	muscle
16	chr19:55964000-55965000	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
17	chr19:55964000-55965400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
18	chr19:55964000-55965400	Weak transcription	Adipose Nuclei	Adipose
19	chr19:55964000-55965600	Weak transcription	GM12878-XiMat	blood
20	chr19:55964000-55970400	Weak transcription	Fetal Lung	lung
21	chr19:55964000-55971200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr19:55964000-55971200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr19:55964000-55971200	Weak transcription	NHLF	lung
24	chr19:55964000-55971400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr19:55964000-55971800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr19:55964200-55964800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr19:55964200-55964800	Enhancers	Right Ventricle	heart
28	chr19:55964200-55965000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
29	chr19:55964200-55965400	Weak transcription	Esophagus	oesophagus
30	chr19:55964200-55965400	Enhancers	K562	blood
31	chr19:55964200-55965600	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr19:55964200-55965600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr19:55964200-55966600	Weak transcription	Colonic Mucosa	Colon
34	chr19:55964200-55966600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr19:55964200-55967000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr19:55964200-55967600	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr19:55964200-55968400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr19:55964200-55969200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr19:55964200-55971000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr19:55964200-55971000	Weak transcription	Colon Smooth Muscle	Colon
41	chr19:55964200-55971000	Weak transcription	Left Ventricle	heart
42	chr19:55964200-55971000	Weak transcription	Rectal Smooth Muscle	rectum
43	chr19:55964200-55971200	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr19:55964200-55971200	Weak transcription	Osteobl	bone
45	chr19:55964200-55971400	Weak transcription	HUVEC	blood vessel
46	chr19:55964200-55971600	Weak transcription	NHEK	skin
47	chr19:55964200-55972200	Weak transcription	Small Intestine	intestine
48	chr19:55964400-55964800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr19:55964400-55964800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
50	chr19:55964400-55964800	Bivalent Enhancer	Fetal Intestine Small	intestine

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