Variant report

Variant	rs55663904
Chromosome Location	chr20:22544090-22544091
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:5)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SP1	chr20:22543633-22544214	HepG2	liver:	n/a	n/a
2	POLR2A	chr20:22542551-22545334	HepG2	liver:	n/a	n/a
3	EP300	chr20:22543641-22544246	HepG2	liver:	n/a	n/a
4	FOXA1	chr20:22543722-22544211	HepG2	liver:	n/a	n/a
5	SP1	chr20:22543868-22544293	H1-hESC	embryonic stem cell:	n/a	n/a
6	FOSL2	chr20:22543713-22544740	HepG2	liver:	n/a	n/a
7	FOXA1	chr20:22543666-22544272	HepG2	liver:	n/a	n/a
8	MYBL2	chr20:22543636-22544434	HepG2	liver:	n/a	n/a
9	RXRA	chr20:22543732-22544243	HepG2	liver:	n/a	n/a
10	POLR2A	chr20:22539124-22546431	HepG2	liver:	n/a	n/a
11	HDAC2	chr20:22543745-22544133	HepG2	liver:	n/a	n/a
12	FOXA2	chr20:22543783-22544162	HepG2	liver:	n/a	n/a
13	POLR2A	chr20:22543786-22545151	HepG2	liver:	n/a	n/a
14	NANOG	chr20:22543992-22544258	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr20:22539677-22547334	HepG2	liver:	n/a	n/a
16	FOXA1	chr20:22543664-22544235	HepG2	liver:	n/a	n/a
17	FOXA1	chr20:22543756-22544266	HepG2	liver:	n/a	n/a
18	ARID3A	chr20:22543753-22544124	HepG2	liver:	n/a	n/a
19	NFIC	chr20:22543669-22544483	HepG2	liver:	n/a	n/a
20	MBD4	chr20:22543455-22545081	HepG2	liver:	n/a	n/a
21	MYBL2	chr20:22543574-22544392	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FOXA2-2	chr20:22541191-22545754	ENSG00000225074
2	lnc-FOXA2-2	chr20:22541194-22545754	XLOC_013684
3	lnc-FOXA2-2	chr20:22540989-22545754	NONHSAT078989
4	lnc-FOXA2-2	chr20:22541216-22545754	NONHSAT078994
5	lnc-FOXA2-2	chr20:22541192-22545754	NR_001558

No data

Variant related genes	Relation type
LINC00261	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1157319	1.00[AMR][1000 genomes]
rs12624528	1.00[AMR][1000 genomes]
rs1415812	1.00[AMR][1000 genomes]
rs16984026	1.00[AMR][1000 genomes]
rs16984047	1.00[AMR][1000 genomes]
rs1933205	1.00[AMR][1000 genomes]
rs3920804	1.00[AMR][1000 genomes]
rs55643169	1.00[AMR][1000 genomes]
rs55789916	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55848868	1.00[AMR][1000 genomes]
rs58225430	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60516763	1.00[AMR][1000 genomes]
rs6106535	1.00[AMR][1000 genomes]
rs61590736	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72470560	1.00[AMR][1000 genomes]
rs7270376	1.00[AMR][1000 genomes]
rs7270463	1.00[AMR][1000 genomes]
rs73900505	1.00[AMR][1000 genomes]
rs73900511	1.00[AMR][1000 genomes]
rs73900515	1.00[AMR][1000 genomes]
rs73900516	1.00[AMR][1000 genomes]
rs73900531	1.00[AMR][1000 genomes]
rs73900532	1.00[AMR][1000 genomes]
rs73900535	1.00[AMR][1000 genomes]
rs73902812	1.00[AMR][1000 genomes]
rs73902816	1.00[AMR][1000 genomes]
rs73902820	1.00[AMR][1000 genomes]
rs73902823	1.00[AMR][1000 genomes]
rs73902824	1.00[AMR][1000 genomes]
rs73902838	1.00[AMR][1000 genomes]
rs73902839	1.00[AMR][1000 genomes]
rs73902840	1.00[AMR][1000 genomes]
rs73902841	1.00[AMR][1000 genomes]
rs73902843	1.00[AMR][1000 genomes]
rs73902845	1.00[AMR][1000 genomes]
rs73902848	1.00[AMR][1000 genomes]
rs73902849	1.00[AMR][1000 genomes]
rs73902851	1.00[AMR][1000 genomes]
rs73902855	1.00[AMR][1000 genomes]
rs73902857	1.00[AMR][1000 genomes]
rs73902859	1.00[AMR][1000 genomes]
rs73902863	1.00[AMR][1000 genomes]
rs73902864	1.00[AMR][1000 genomes]
rs73902865	1.00[AMR][1000 genomes]
rs73902866	1.00[AMR][1000 genomes]
rs73902868	1.00[AMR][1000 genomes]
rs73902874	1.00[AMR][1000 genomes]
rs73902880	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73902891	0.95[AFR][1000 genomes]
rs73902892	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73902897	0.95[AFR][1000 genomes]
rs73902898	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73902900	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73902901	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73902902	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73904103	1.00[AFR][1000 genomes]
rs73904105	1.00[AFR][1000 genomes]
rs73904107	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8118829	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428690	chr20:22528757-22649625	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:22515000-22544200	Weak transcription	Pancreas	Pancrea
2	chr20:22536200-22544800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
3	chr20:22536800-22545200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
4	chr20:22539400-22545200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
5	chr20:22540000-22548800	Weak transcription	Gastric	stomach
6	chr20:22541200-22545000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
7	chr20:22541400-22544200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
8	chr20:22541400-22545200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr20:22542400-22544200	Enhancers	HepG2	liver
10	chr20:22542800-22544400	Enhancers	Pancreatic Islets	Pancreatic Islet
11	chr20:22542800-22544600	Enhancers	Liver	Liver
12	chr20:22542800-22544800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
13	chr20:22542800-22545000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
14	chr20:22543200-22544400	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
15	chr20:22543200-22548000	Weak transcription	K562	blood
16	chr20:22543400-22545200	Enhancers	Stomach Mucosa	stomach
17	chr20:22543600-22547800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr20:22544000-22544200	Bivalent Enhancer	Fetal Intestine Small	intestine
19	chr20:22544000-22544400	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
20	chr20:22544000-22544400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr20:22544000-22544400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
22	chr20:22544000-22545200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell

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