Variant report

Variant	rs11699573
Chromosome Location	chr20:52491761-52491762
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr17:58601420..58603983-chr20:52490138..52492332,2	MCF-7	breast:
2	chr17:57919005..57920769-chr20:52489404..52491830,2	MCF-7	breast:
3	chr20:52490662..52493657-chr3:155587949..155590436,2	MCF-7	breast:
4	chr20:52491204..52492000-chr6:70763728..70764531,2	MCF-7	breast:
5	chr20:19738102..19740026-chr20:52490721..52492491,2	MCF-7	breast:
6	chr20:52491297..52491798-chr7:122756625..122757125,2	MCF-7	breast:
7	chr20:52369283..52371652-chr20:52490163..52491937,2	K562	blood:
8	chr1:144930770..144933506-chr20:52490207..52493077,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000259349	Chromatin interaction
ENSG00000163655	Chromatin interaction
ENSG00000062725	Chromatin interaction
ENSG00000268628	Chromatin interaction
ENSG00000178104	Chromatin interaction
ENSG00000233895	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11086444	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11697016	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11906676	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13037872	0.96[ASN][1000 genomes]
rs13038143	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1859902	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35507231	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6064013	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6064016	0.86[EUR][1000 genomes]
rs6068699	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6068702	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7352529	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8114312	0.85[EUR][1000 genomes];0.97[ASN][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	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
2	nsv834008	chr20:52368660-52533410	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	185 gene(s)	inside rSNPs	diseases
3	nsv834009	chr20:52386050-52590795	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	182 gene(s)	inside rSNPs	diseases
4	nsv1060372	chr20:52409008-52502100	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	122 gene(s)	inside rSNPs	diseases
5	esv1831516	chr20:52437245-52514913	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	98 gene(s)	inside rSNPs	diseases
6	nsv586222	chr20:52473679-52506380	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	74 gene(s)	inside rSNPs	diseases
7	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52482800-52492000	Weak transcription	Gastric	stomach
2	chr20:52483400-52495000	Weak transcription	Spleen	Spleen
3	chr20:52485000-52493000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr20:52487400-52495000	Weak transcription	Small Intestine	intestine
5	chr20:52487400-52495400	Weak transcription	K562	blood
6	chr20:52489000-52493200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr20:52489000-52494600	Weak transcription	Liver	Liver
8	chr20:52489200-52491800	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr20:52490000-52494000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr20:52490000-52494400	Weak transcription	Fetal Kidney	kidney
11	chr20:52490000-52494800	Weak transcription	A549	lung
12	chr20:52490000-52495000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr20:52490200-52491800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr20:52490200-52491800	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr20:52490200-52492000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr20:52490200-52492000	Weak transcription	Brain Germinal Matrix	brain
17	chr20:52490200-52493200	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr20:52490200-52493800	Weak transcription	HepG2	liver
19	chr20:52490200-52494800	Weak transcription	Duodenum Mucosa	Duodenum
20	chr20:52490200-52494800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr20:52490200-52495000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr20:52490200-52495200	Weak transcription	Fetal Lung	lung
23	chr20:52490200-52495400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr20:52490200-52495400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr20:52490200-52495400	Weak transcription	Fetal Muscle Leg	muscle
26	chr20:52490200-52496600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr20:52490200-52499800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr20:52490200-52501200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr20:52490200-52502400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr20:52490400-52491800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr20:52490400-52493200	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr20:52490400-52493400	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr20:52490400-52494600	Weak transcription	Fetal Intestine Small	intestine
34	chr20:52490400-52495000	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr20:52490400-52495400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr20:52490400-52495600	Weak transcription	Fetal Thymus	thymus
37	chr20:52490600-52495400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr20:52490600-52497800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr20:52491000-52494800	Weak transcription	Fetal Intestine Large	intestine
40	chr20:52491000-52495000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr20:52491000-52495600	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr20:52491200-52492800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
43	chr20:52491400-52492200	Active TSS	Primary B cells from cord blood	blood

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