Variant report

Variant	rs11880346
Chromosome Location	chr19:55758535-55758536
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:55758533-55758864	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:55758193-55758690	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:55756546..55759225-chr19:55768234..55771187,4	MCF-7	breast:
2	chr19:55756340..55759161-chr19:55791491..55793386,3	K562	blood:
3	chr19:55749108..55754176-chr19:55757011..55758995,4	MCF-7	breast:
4	chr19:55752155..55754012-chr19:55755401..55758757,4	K562	blood:
5	chr19:55757527..55760012-chr19:55894968..55896931,2	MCF-7	breast:
6	chr19:55758319..55759930-chr19:55790512..55793308,2	MCF-7	breast:

No data

Variant related genes	Relation type
PPP6R1	TF binding region
ENSG00000133265	Chromatin interaction
ENSG00000108107	Chromatin interaction
ENSG00000233493	Chromatin interaction
ENSG00000105063	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11881572	0.86[AFR][1000 genomes]
rs28682430	1.00[EUR][1000 genomes]
rs61737174	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7249693	1.00[EUR][1000 genomes]
rs7507792	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1816335	chr19:55683977-55901099	Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv1065760	chr19:55721521-55929740	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
3	nsv912454	chr19:55725410-55783552	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
4	nsv912455	chr19:55725410-55879872	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv912456	chr19:55725410-55925500	Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
6	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

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55729400-55766200	Weak transcription	Fetal Brain Male	brain
2	chr19:55733800-55758600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr19:55734600-55759800	Strong transcription	Brain Anterior Caudate	brain
4	chr19:55734800-55758600	Strong transcription	Primary T cells fromperipheralblood	blood
5	chr19:55735000-55762400	Strong transcription	Thymus	Thymus
6	chr19:55735200-55762200	Strong transcription	Fetal Thymus	thymus
7	chr19:55736800-55760000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr19:55736800-55764200	Strong transcription	Dnd41	blood
9	chr19:55737000-55758600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:55737000-55758800	Strong transcription	Placenta	Placenta
11	chr19:55737000-55759000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr19:55737000-55760000	Strong transcription	Brain Germinal Matrix	brain
13	chr19:55737000-55760600	Strong transcription	Primary T cells from cord blood	blood
14	chr19:55737200-55758800	Strong transcription	Brain Inferior Temporal Lobe	brain
15	chr19:55737200-55759200	Strong transcription	Brain Hippocampus Middle	brain
16	chr19:55737200-55759800	Strong transcription	Lung	lung
17	chr19:55737400-55758600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr19:55737400-55758600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr19:55737400-55758600	Strong transcription	Fetal Muscle Leg	muscle
20	chr19:55737400-55758600	Strong transcription	Skeletal Muscle Male	skeletal muscle
21	chr19:55737400-55758800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr19:55737400-55759000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr19:55737400-55759800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr19:55737400-55760000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr19:55737600-55758600	Strong transcription	Adipose Nuclei	Adipose
26	chr19:55737600-55758800	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr19:55737600-55759000	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr19:55737800-55758600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr19:55737800-55758800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr19:55737800-55759200	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr19:55737800-55760000	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr19:55738000-55758600	Strong transcription	Ovary	ovary
33	chr19:55738000-55760000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
34	chr19:55738200-55758600	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr19:55738200-55758800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr19:55738600-55758600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr19:55738600-55758600	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr19:55740400-55758600	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr19:55740400-55758600	Strong transcription	Stomach Smooth Muscle	stomach
40	chr19:55740400-55766000	Strong transcription	Fetal Stomach	stomach
41	chr19:55740600-55759000	Weak transcription	Right Atrium	heart
42	chr19:55740800-55758600	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr19:55741000-55758600	Strong transcription	Duodenum Mucosa	Duodenum
44	chr19:55741200-55758800	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr19:55741400-55758600	Strong transcription	A549	lung
46	chr19:55741800-55758800	Strong transcription	Rectal Smooth Muscle	rectum
47	chr19:55742000-55758800	Strong transcription	Primary B cells from cord blood	blood
48	chr19:55742400-55759200	Strong transcription	Brain Angular Gyrus	brain
49	chr19:55742600-55758600	Strong transcription	Primary T killer memory cells from peripheral blood	blood
50	chr19:55742600-55759000	Strong transcription	Liver	Liver

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