Variant report

Variant	rs290446
Chromosome Location	chr20:52685084-52685085
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HA-E2F1	chr20:52683942-52685406	MCF-7	breast:	n/a	n/a
2	GATA3	chr20:52683759-52685486	A549	lung:	n/a	n/a
3	TEAD4	chr20:52683721-52688026	A549	lung:	n/a	chr20:52684379-52684388
4	USF1	chr20:52685078-52685464	H1-hESC	embryonic stem cell:	n/a	chr20:52685271-52685282
5	JUND	chr20:52683918-52685101	T-47D	breast:	n/a	chr20:52684337-52684347 chr20:52684336-52684347 chr20:52684337-52684347
6	CTCF	chr20:52684980-52685130	HepG2	liver:	n/a	n/a
7	GATA3	chr20:52684016-52685406	T-47D	breast:	n/a	n/a
8	TCF7L2	chr20:52684108-52685211	PANC-1	pancreas:	n/a	n/a
9	NR2F2	chr20:52683737-52688780	MCF-7	breast:	n/a	n/a
10	NR2F2	chr20:52682851-52688769	MCF-7	breast:	n/a	n/a
11	EP300	chr20:52684662-52685189	T-47D	breast:	n/a	n/a
12	MAX	chr20:52682798-52688785	MCF-7	breast:	n/a	chr20:52685611-52685621
13	RCOR1	chr20:52685072-52685143	HepG2	liver:	n/a	n/a
14	MAX	chr20:52683872-52685186	A549	lung:	n/a	n/a
15	MEF2A	chr20:52683834-52685458	SK-N-SH	brain:	n/a	chr20:52684181-52684197 chr20:52684181-52684196
16	GATA3	chr20:52683960-52685400	T-47D	breast:	n/a	n/a

No data

(count:15 , 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	chr17:56734557..56739323-chr20:52682038..52691817,18	MCF-7	breast:
6	chr20:52554098..52560340-chr20:52684210..52688448,9	MCF-7	breast:
7	chr20:52682759..52688435-chr20:55837866..55842743,7	MCF-7	breast:
8	chr20:52682551..52687365-chr20:55839673..55842619,5	MCF-7	breast:
9	chr11:20042762..20044450-chr20:52683643..52686513,2	MCF-7	breast:
10	chr17:56755655..56758495-chr20:52684394..52686862,2	MCF-7	breast:
11	chr17:56734742..56736763-chr20:52683079..52685534,3	MCF-7	breast:
12	chr17:59488630..59491909-chr20:52682988..52685576,3	MCF-7	breast:
13	chr20:52684414..52687124-chr6:151977348..151979114,2	MCF-7	breast:
14	chr17:57914792..57916494-chr20:52684237..52686091,2	MCF-7	breast:
15	chr17:56706875..56710932-chr20:52683217..52688645,17	MCF-7	breast:

No data

Variant related genes	Relation type
MIR4756	TF binding region
ENSG00000236352	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000200997	Chromatin interaction
ENSG00000166833	Chromatin interaction
ENSG00000196562	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000091831	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000266826	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000171940	Chromatin interaction
ENSG00000187013	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs103926	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1531485	0.84[YRI][hapmap];0.85[AFR][1000 genomes]
rs290391	0.88[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];0.90[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs290392	0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs290393	0.95[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs290399	0.86[ASN][1000 genomes]
rs290430	0.83[ASN][1000 genomes]
rs290431	0.90[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs290432	0.88[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs290436	0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs290440	0.85[AFR][1000 genomes]
rs290441	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs290444	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs290445	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs290447	0.84[ASW][hapmap];0.89[LWK][hapmap];0.83[MKK][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes]
rs290448	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs290449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs458674	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs459113	0.92[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs460317	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs460470	0.92[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs462083	0.82[YRI][hapmap]
rs462174	0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.84[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs463420	0.88[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs463722	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs467267	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.84[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs467321	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6068765	0.83[YRI][hapmap];0.86[AFR][1000 genomes]
rs756021	0.96[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs290446	BCAS1	cis	lymphoblastoid	seeQTL
rs290446	BCAS1	cis	multi-tissue	Pritchard
rs290446	BCAS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52682400-52686800	Weak transcription	Placenta	Placenta
2	chr20:52683000-52687600	Enhancers	HUES6 Cell Line	embryonic stem cell
3	chr20:52683200-52685400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr20:52683400-52687400	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr20:52683600-52685200	Enhancers	Lung	lung
6	chr20:52683600-52685400	Enhancers	Pancreas	Pancrea
7	chr20:52683800-52687200	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr20:52684000-52687400	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr20:52684000-52687600	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr20:52684000-52687600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr20:52684200-52685200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr20:52684200-52687200	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr20:52684200-52687200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr20:52684200-52687600	Enhancers	H1 Cell Line	embryonic stem cell
15	chr20:52684400-52685200	Enhancers	Esophagus	oesophagus
16	chr20:52684400-52685200	Flanking Active TSS	A549	lung
17	chr20:52684400-52685400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
18	chr20:52684400-52687200	Active TSS	Stomach Mucosa	stomach
19	chr20:52684400-52687400	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr20:52684600-52685200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr20:52684600-52685200	Active TSS	Rectal Smooth Muscle	rectum
22	chr20:52684600-52686000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr20:52684600-52686400	Weak transcription	K562	blood
24	chr20:52684600-52686800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr20:52684600-52687000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr20:52684600-52687400	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr20:52684800-52685800	Enhancers	Hela-S3	cervix
28	chr20:52684800-52686200	Enhancers	HepG2	liver
29	chr20:52685000-52685200	Active TSS	Duodenum Mucosa	Duodenum
30	chr20:52685000-52685200	Flanking Active TSS	Fetal Intestine Large	intestine
31	chr20:52685000-52685200	Bivalent Enhancer	Stomach Smooth Muscle	stomach
32	chr20:52685000-52685400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr20:52685000-52685400	Flanking Active TSS	Colonic Mucosa	Colon
34	chr20:52685000-52685400	Enhancers	Gastric	stomach
35	chr20:52685000-52686000	Weak transcription	Fetal Stomach	stomach
36	chr20:52685000-52686000	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr20:52685000-52686600	Active TSS	Fetal Intestine Small	intestine
38	chr20:52685000-52686800	Enhancers	H9 Cell Line	embryonic stem cell

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