Variant report

Variant	rs290445
Chromosome Location	chr20:52684627-52684628
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:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:56706894..56712075-chr20:52682647..52687928,11	MCF-7	breast:
2	chr20:52205396..52212193-chr20:52682424..52689159,12	MCF-7	breast:
3	chr20:46412807..46415546-chr20:52683653..52686507,2	MCF-7	breast:
4	chr20:46413324..46415448-chr20:52682941..52685877,2	MCF-7	breast:
5	chr20:52684089..52684879-chr20:52701289..52702251,3	MCF-7	breast:
6	chr17:56734557..56739323-chr20:52682038..52691817,18	MCF-7	breast:
7	chr20:52554098..52560340-chr20:52684210..52688448,9	MCF-7	breast:
8	chr20:52684180..52684700-chr20:52739750..52740710,2	MCF-7	breast:
9	chr20:52682759..52688435-chr20:55837866..55842743,7	MCF-7	breast:
10	chr20:52682551..52687365-chr20:55839673..55842619,5	MCF-7	breast:
11	chr11:20042762..20044450-chr20:52683643..52686513,2	MCF-7	breast:
12	chr20:52683952..52684959-chr20:52701399..52702153,3	MCF-7	breast:
13	chr17:56755655..56758495-chr20:52684394..52686862,2	MCF-7	breast:
14	chr17:56734742..56736763-chr20:52683079..52685534,3	MCF-7	breast:
15	chr17:59488630..59491909-chr20:52682988..52685576,3	MCF-7	breast:
16	chr20:52684414..52687124-chr6:151977348..151979114,2	MCF-7	breast:
17	chr17:57914792..57916494-chr20:52684237..52686091,2	MCF-7	breast:
18	chr17:56706875..56710932-chr20:52683217..52688645,17	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000196562	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000266826	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000187013	Chromatin interaction
ENSG00000091831	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000166833	Chromatin interaction
ENSG00000236352	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000171940	Chromatin interaction
ENSG00000200997	Chromatin interaction
ENSG00000062716	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs103926	1.00[ASN][1000 genomes]
rs290391	0.95[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs290392	0.95[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs290393	0.95[CHB][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs290399	0.86[ASN][1000 genomes]
rs290430	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs290431	0.92[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs290432	0.82[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap]
rs290436	0.94[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs290441	0.99[ASN][1000 genomes]
rs290444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs290446	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs290448	1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs290449	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs458674	0.85[ASN][1000 genomes]
rs459113	0.94[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs460317	0.85[ASN][1000 genomes]
rs460470	0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs462174	0.95[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs463420	0.90[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs463722	0.90[ASN][1000 genomes]
rs467267	0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs467321	0.85[ASN][1000 genomes]
rs756021	0.89[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
3	esv2756743	chr20:52679137-52685208	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region miRNA	20 gene(s)	inside rSNPs	diseases
4	esv2758801	chr20:52679137-52685208	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region miRNA	20 gene(s)	inside rSNPs	diseases
5	nsv912944	chr20:52681759-52693614	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region miRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs290445	BCAS1	Cis_1M	lymphoblastoid	RTeQTL
rs290445	BCAS1	cis	lymphoblastoid	seeQTL
rs290445	TMEM189	cis	cerebellum	SCAN
rs290445	BCAS1	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52681600-52684800	Enhancers	GM12878-XiMat	blood
2	chr20:52682000-52685000	Enhancers	Fetal Intestine Large	intestine
3	chr20:52682400-52686800	Weak transcription	Placenta	Placenta
4	chr20:52683000-52684800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr20:52683000-52687600	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr20:52683200-52685000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr20:52683200-52685400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr20:52683400-52684800	Flanking Active TSS	HepG2	liver
9	chr20:52683400-52685000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr20:52683400-52687400	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr20:52683600-52685200	Enhancers	Lung	lung
12	chr20:52683600-52685400	Enhancers	Pancreas	Pancrea
13	chr20:52683800-52684800	Enhancers	NHEK	skin
14	chr20:52683800-52685000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
15	chr20:52683800-52685000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr20:52683800-52685000	Enhancers	Fetal Heart	heart
17	chr20:52683800-52687200	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr20:52684000-52684800	Enhancers	Fetal Kidney	kidney
19	chr20:52684000-52687400	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr20:52684000-52687600	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr20:52684000-52687600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr20:52684200-52685200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr20:52684200-52687200	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr20:52684200-52687200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr20:52684200-52687600	Enhancers	H1 Cell Line	embryonic stem cell
26	chr20:52684400-52684800	Flanking Active TSS	Colonic Mucosa	Colon
27	chr20:52684400-52684800	Flanking Active TSS	Hela-S3	cervix
28	chr20:52684400-52685000	Flanking Active TSS	Duodenum Mucosa	Duodenum
29	chr20:52684400-52685000	Active TSS	Fetal Stomach	stomach
30	chr20:52684400-52685000	Active TSS	Gastric	stomach
31	chr20:52684400-52685200	Enhancers	Esophagus	oesophagus
32	chr20:52684400-52685200	Flanking Active TSS	A549	lung
33	chr20:52684400-52685400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
34	chr20:52684400-52687200	Active TSS	Stomach Mucosa	stomach
35	chr20:52684400-52687400	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr20:52684600-52685000	Flanking Active TSS	Fetal Intestine Small	intestine
37	chr20:52684600-52685200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr20:52684600-52685200	Active TSS	Rectal Smooth Muscle	rectum
39	chr20:52684600-52686000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr20:52684600-52686400	Weak transcription	K562	blood
41	chr20:52684600-52686800	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr20:52684600-52687000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr20:52684600-52687400	Enhancers	iPS-20b Cell Line	embryonic stem cell

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