Variant report

Variant	rs10854193
Chromosome Location	chr20:52328338-52328339
allele	A/G
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:59482922..59485740-chr20:52327701..52330610,2	MCF-7	breast:
2	chr20:52278028..52279035-chr20:52327271..52328369,11	MCF-7	breast:
3	chr20:47538326..47539861-chr20:52328073..52331013,2	MCF-7	breast:
4	chr20:52327822..52329367-chr8:102505228..102507771,2	MCF-7	breast:
5	chr20:52327570..52329244-chr7:156255388..156257052,2	MCF-7	breast:
6	chr20:52327864..52329489-chr6:58775870..58778258,2	MCF-7	breast:
7	chr20:52278079..52279035-chr20:52327271..52328369,9	MCF-7	breast:
8	chr20:52327738..52329665-chr20:55839158..55840882,2	MCF-7	breast:
9	chr20:52309398..52311832-chr20:52327074..52329815,2	K562	blood:
10	chr17:57918348..57920574-chr20:52327129..52329556,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000101144	Chromatin interaction
ENSG00000124198	Chromatin interaction
ENSG00000199004	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11086435	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4811452	0.80[CEU][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4811453	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4811454	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4811455	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4811456	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56055743	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs57351418	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6013764	0.82[ASN][1000 genomes]
rs6022682	0.82[ASN][1000 genomes]
rs60762133	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8125426	0.81[EUR][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	nsv1055342	chr20:52126973-52352323	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	214 gene(s)	inside rSNPs	diseases
2	esv3412883	chr20:52176349-52393416	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	250 gene(s)	inside rSNPs	diseases
3	nsv834007	chr20:52213864-52404557	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	174 gene(s)	inside rSNPs	diseases
4	nsv912935	chr20:52221906-52337118	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	101 gene(s)	inside rSNPs	diseases
5	nsv912936	chr20:52250876-52344962	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
6	nsv912937	chr20:52251863-52344962	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
7	esv34060	chr20:52251863-52702186	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	296 gene(s)	inside rSNPs	diseases
8	nsv912938	chr20:52276452-52328338	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
9	nsv437185	chr20:52300359-52330053	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52316200-52330400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr20:52323600-52328800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr20:52324200-52329200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr20:52324400-52328400	Weak transcription	Fetal Heart	heart
5	chr20:52325000-52328400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr20:52325000-52328800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr20:52325000-52330400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr20:52325200-52328400	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr20:52325200-52328400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr20:52325200-52328400	Weak transcription	Fetal Kidney	kidney
11	chr20:52325200-52328600	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr20:52325200-52328600	Weak transcription	Osteobl	bone
13	chr20:52325200-52334600	Weak transcription	Fetal Muscle Leg	muscle
14	chr20:52325600-52328800	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr20:52325800-52329400	Enhancers	GM12878-XiMat	blood
16	chr20:52326200-52333000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr20:52327400-52329200	Enhancers	Primary B cells from peripheral blood	blood
18	chr20:52327600-52330000	Enhancers	Fetal Thymus	thymus
19	chr20:52327800-52328400	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr20:52327800-52328800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr20:52327800-52329000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr20:52327800-52329200	Enhancers	A549	lung
23	chr20:52327800-52329400	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr20:52327800-52329600	Enhancers	Liver	Liver
25	chr20:52327800-52330800	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr20:52327800-52331200	Enhancers	Placenta	Placenta
27	chr20:52328000-52328400	Enhancers	Thymus	Thymus
28	chr20:52328000-52328600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr20:52328000-52328600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
30	chr20:52328000-52328800	Enhancers	Primary T cells from cord blood	blood
31	chr20:52328000-52328800	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr20:52328000-52329000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr20:52328000-52329000	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr20:52328000-52329000	Enhancers	Primary B cells from cord blood	blood
35	chr20:52328000-52329200	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr20:52328000-52329400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr20:52328000-52329600	Enhancers	Pancreas	Pancrea
38	chr20:52328000-52329600	Flanking Active TSS	HepG2	liver
39	chr20:52328000-52330800	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr20:52328000-52331400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr20:52328200-52328800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr20:52328200-52328800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr20:52328200-52328800	Enhancers	Primary T cells fromperipheralblood	blood
44	chr20:52328200-52328800	Enhancers	Duodenum Mucosa	Duodenum
45	chr20:52328200-52328800	Enhancers	Monocytes-CD14+_RO01746	blood
46	chr20:52328200-52329000	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr20:52328200-52329000	Enhancers	Ovary	ovary
48	chr20:52328200-52329200	Enhancers	Fetal Lung	lung
49	chr20:52328200-52329400	Enhancers	Spleen	Spleen
50	chr20:52328200-52330400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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