Variant report

Variant	rs290391
Chromosome Location	chr20:52687186-52687187
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:44)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:44 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr20:52686825-52687297	HepG2	liver:	n/a	n/a
2	TEAD4	chr20:52683721-52688026	A549	lung:	n/a	chr20:52684379-52684388
3	EP300	chr20:52686789-52687229	HepG2	liver:	n/a	chr20:52687140-52687150
4	CTCF	chr20:52687080-52687230	HepG2	liver:	n/a	n/a
5	FOXA1	chr20:52686840-52687375	HepG2	liver:	n/a	n/a
6	RXRA	chr20:52686427-52687361	HepG2	liver:	n/a	n/a
7	FOXA2	chr20:52686852-52687305	HepG2	liver:	n/a	n/a
8	EP300	chr20:52686912-52687489	T-47D	breast:	n/a	chr20:52687140-52687150
9	ESR1	chr20:52687084-52687507	T-47D	breast:	n/a	n/a
10	EP300	chr20:52686863-52687566	T-47D	breast:	n/a	chr20:52687140-52687150
11	MAZ	chr20:52686716-52687189	HepG2	liver:	n/a	n/a
12	FOXA1	chr20:52686882-52687443	T-47D	breast:	n/a	n/a
13	HNF4A	chr20:52686826-52687311	HepG2	liver:	n/a	chr20:52687092-52687107
14	ESR1	chr20:52686989-52687510	T-47D	breast:	n/a	n/a
15	ESR1	chr20:52687068-52687585	T-47D	breast:	n/a	n/a
16	HNF4A	chr20:52686967-52687191	HepG2	liver:	n/a	chr20:52687092-52687107
17	FOXA1	chr20:52686801-52687348	HepG2	liver:	n/a	n/a
18	TCF12	chr20:52686506-52687428	A549	lung:	n/a	n/a
19	GATA3	chr20:52686845-52687572	T-47D	breast:	n/a	n/a
20	NR2F2	chr20:52683737-52688780	MCF-7	breast:	n/a	n/a
21	MYBL2	chr20:52686525-52687471	HepG2	liver:	n/a	n/a
22	NFIC	chr20:52686587-52687339	HepG2	liver:	n/a	n/a
23	NR2F2	chr20:52682851-52688769	MCF-7	breast:	n/a	n/a
24	ESR1	chr20:52687005-52687578	T-47D	breast:	n/a	n/a
25	ARID3A	chr20:52686806-52687301	HepG2	liver:	n/a	n/a
26	MAX	chr20:52682798-52688785	MCF-7	breast:	n/a	chr20:52685611-52685621
27	MAFF	chr20:52686963-52687353	HepG2	liver:	n/a	n/a
28	MEF2A	chr20:52686784-52687725	SK-N-SH	brain:	n/a	n/a
29	SMC3	chr20:52687119-52687200	HepG2	liver:	n/a	n/a
30	POLR2A	chr20:52686854-52687412	ProgFib	skin:	n/a	n/a
31	ESR1	chr20:52687167-52687576	T-47D	breast:	n/a	n/a
32	MAX	chr20:52686552-52687429	HepG2	liver:	n/a	n/a
33	RAD21	chr20:52686927-52687254	HepG2	liver:	n/a	n/a
34	FOXA2	chr20:52686894-52687397	A549	lung:	n/a	n/a
35	FOXA1	chr20:52686946-52687547	T-47D	breast:	n/a	n/a
36	MYBL2	chr20:52686568-52687416	HepG2	liver:	n/a	n/a
37	MAX	chr20:52687013-52687191	HepG2	liver:	n/a	n/a
38	FOXA1	chr20:52686799-52687406	HepG2	liver:	n/a	n/a
39	CTCF	chr20:52687080-52687230	MCF-7	breast:	n/a	n/a
40	HDAC2	chr20:52686639-52687355	HepG2	liver:	n/a	n/a
41	TBP	chr20:52686968-52687278	HepG2	liver:	n/a	n/a
42	CTCF	chr20:52687040-52687190	Caco-2	colon:	n/a	n/a
43	MAFK	chr20:52687096-52687198	HepG2	liver:	n/a	n/a
44	FOXA2	chr20:52686784-52687397	A549	lung:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:56706894..56712075-chr20:52682647..52687928,11	MCF-7	breast:
2	chr17:56734849..56737585-chr20:52685762..52689219,5	MCF-7	breast:
3	chr20:52205396..52212193-chr20:52682424..52689159,12	MCF-7	breast:
4	chr20:46130482..46132590-chr20:52685698..52688265,2	MCF-7	breast:
5	chr1:114472848..114474894-chr20:52685682..52687660,2	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	chr20:45946563..45948166-chr20:52686092..52688175,2	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	chr1:149222502..149226607-chr20:52685912..52688117,3	MCF-7	breast:
12	chr20:52643673..52645639-chr20:52687051..52688962,2	MCF-7	breast:
13	chr17:56706875..56710932-chr20:52683217..52688645,17	MCF-7	breast:

No data

Variant related genes	Relation type
BCAS1	TF binding region
MIR4756	TF binding region
ENSG00000202077	Chromatin interaction
ENSG00000266826	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000171940	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000236352	Chromatin interaction
ENSG00000064787	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000163349	Chromatin interaction
ENSG00000124151	Chromatin interaction
ENSG00000267882	Chromatin interaction
ENSG00000206737	Chromatin interaction
ENSG00000101040	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs103926	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1531485	0.84[YRI][hapmap];0.82[AFR][1000 genomes]
rs290392	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs290393	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs290399	0.90[ASN][1000 genomes]
rs290431	0.85[CHB][hapmap];0.80[ASN][1000 genomes]
rs290436	0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs290441	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs290444	0.94[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs290445	0.95[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs290446	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]
rs290447	0.82[LWK][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes]
rs290448	0.88[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.87[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]
rs290449	0.88[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs458674	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs459113	0.80[CEU][hapmap];0.87[CHB][hapmap];0.81[ASN][1000 genomes]
rs460317	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs460470	0.83[CEU][hapmap];0.88[CHB][hapmap];0.83[JPT][hapmap];0.93[YRI][hapmap];0.81[ASN][1000 genomes]
rs462083	0.82[YRI][hapmap]
rs462174	0.81[CEU][hapmap];0.90[CHB][hapmap];0.84[YRI][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs463420	0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs463722	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs467267	0.81[CEU][hapmap];0.90[CHB][hapmap];0.84[YRI][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs467321	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6068765	0.83[YRI][hapmap];0.80[AFR][1000 genomes]
rs756021	0.84[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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
rs290391	BCAS1	Cis_1M	lymphoblastoid	RTeQTL
rs290391	BCAS1	cis	lymphoblastoid	seeQTL
rs290391	BCAS1	cis	multi-tissue	Pritchard

Chromatin state (count:35 , 50 per page) page: 1

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

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