Variant report

Variant	rs16998896
Chromosome Location	chr20:52687027-52687028
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:45)
CpG islands
(count:61)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:45 , 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	FOXA1	chr20:52686840-52687375	HepG2	liver:	n/a	n/a
5	RXRA	chr20:52686427-52687361	HepG2	liver:	n/a	n/a
6	FOXA2	chr20:52686852-52687305	HepG2	liver:	n/a	n/a
7	EP300	chr20:52686912-52687489	T-47D	breast:	n/a	chr20:52687140-52687150
8	POLR2A	chr20:52686985-52687166	MCF-7	breast:	n/a	n/a
9	EP300	chr20:52686863-52687566	T-47D	breast:	n/a	chr20:52687140-52687150
10	MAZ	chr20:52686716-52687189	HepG2	liver:	n/a	n/a
11	FOXA1	chr20:52686882-52687443	T-47D	breast:	n/a	n/a
12	HNF4A	chr20:52686826-52687311	HepG2	liver:	n/a	chr20:52687092-52687107
13	RAD21	chr20:52686947-52687182	HepG2	liver:	n/a	n/a
14	ESR1	chr20:52686989-52687510	T-47D	breast:	n/a	n/a
15	USF2	chr20:52686739-52687091	HepG2	liver:	n/a	n/a
16	CHD2	chr20:52686637-52687140	HepG2	liver:	n/a	n/a
17	HNF4A	chr20:52686967-52687191	HepG2	liver:	n/a	chr20:52687092-52687107
18	POLR2A	chr20:52686961-52687140	A549	lung:	n/a	n/a
19	RFX5	chr20:52686939-52687181	HepG2	liver:	n/a	n/a
20	POLR2A	chr20:52687003-52687156	MCF-7	breast:	n/a	n/a
21	FOXA1	chr20:52686801-52687348	HepG2	liver:	n/a	n/a
22	TCF12	chr20:52686506-52687428	A549	lung:	n/a	n/a
23	GATA3	chr20:52686845-52687572	T-47D	breast:	n/a	n/a
24	NR2F2	chr20:52683737-52688780	MCF-7	breast:	n/a	n/a
25	MYBL2	chr20:52686525-52687471	HepG2	liver:	n/a	n/a
26	NFIC	chr20:52686587-52687339	HepG2	liver:	n/a	n/a
27	HEY1	chr20:52686869-52687182	HepG2	liver:	n/a	n/a
28	NR2F2	chr20:52682851-52688769	MCF-7	breast:	n/a	n/a
29	ESR1	chr20:52687005-52687578	T-47D	breast:	n/a	n/a
30	ARID3A	chr20:52686806-52687301	HepG2	liver:	n/a	n/a
31	MAX	chr20:52682798-52688785	MCF-7	breast:	n/a	chr20:52685611-52685621
32	MAFF	chr20:52686963-52687353	HepG2	liver:	n/a	n/a
33	MEF2A	chr20:52686784-52687725	SK-N-SH	brain:	n/a	n/a
34	POLR2A	chr20:52686854-52687412	ProgFib	skin:	n/a	n/a
35	MAX	chr20:52686552-52687429	HepG2	liver:	n/a	n/a
36	RAD21	chr20:52686927-52687254	HepG2	liver:	n/a	n/a
37	FOXA2	chr20:52686894-52687397	A549	lung:	n/a	n/a
38	FOXA1	chr20:52686946-52687547	T-47D	breast:	n/a	n/a
39	MYBL2	chr20:52686568-52687416	HepG2	liver:	n/a	n/a
40	MAX	chr20:52687013-52687191	HepG2	liver:	n/a	n/a
41	FOXA1	chr20:52686799-52687406	HepG2	liver:	n/a	n/a
42	HDAC2	chr20:52686639-52687355	HepG2	liver:	n/a	n/a
43	TBP	chr20:52686968-52687278	HepG2	liver:	n/a	n/a
44	RCOR1	chr20:52686574-52687181	HepG2	liver:	n/a	n/a
45	FOXA2	chr20:52686784-52687397	A549	lung:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr20:52687007-52687057	HCF	heart:	n/a
2	chr20:52687007-52687057	HepG2	liver:	n/a
3	chr20:52687007-52687057	NH-A	brain:	n/a
4	chr20:52687007-52687057	SK-N-SH	brain:	n/a
5	chr20:52687007-52687057	CMK	blood:	n/a
6	chr20:52687007-52687057	U87	brain:	n/a
7	chr20:52687007-52687057	MCF10A-Er-Src	breast:	n/a
8	chr20:52687007-52687057	HNPCEpiC	eye:	n/a
9	chr20:52687007-52687057	HEEpiC	esophagus:	n/a
10	chr20:52687007-52687057	H1-hESC	embryonic stem cell:	embryo
11	chr20:52687007-52687057	PANC-1	pancreas:	n/a
12	chr20:52687007-52687057	SAEC	small airway:	n/a
13	chr20:52687007-52687057	RPTEC	kidney:	n/a
14	chr20:52687007-52687057	SKMC	muscle:	n/a
15	chr20:52687007-52687057	LNCaP	prostate:	n/a
16	chr20:52687007-52687057	HEK293	kidney:	embryo
17	chr20:52687007-52687057	AG10803	skin:	n/a
18	chr20:52687007-52687057	AG09309	skin:	n/a
19	chr20:52687007-52687057	IMR90	lung:	fetal
20	chr20:52687007-52687057	Caco-2	colon:	n/a
21	chr20:52687007-52687057	HRPEpiC	eye:	n/a
22	chr20:52687007-52687057	PFSK-1	brain:	n/a
23	chr20:52687007-52687057	Jurkat	blood:	n/a
24	chr20:52687007-52687057	BJ	skin:	n/a
25	chr20:52687007-52687057	NT2-D1	testis:	n/a
26	chr20:52687007-52687057	AG04449	skin:	fetal
27	chr20:52687007-52687057	HCPEpiC	choroid plexus:	n/a
28	chr20:52687007-52687057	BE2_C	brain:	n/a
29	chr20:52687007-52687057	GM12891	blood:	n/a
30	chr20:52687007-52687057	HMEC	breast:	n/a
31	chr20:52687007-52687057	GM12892	blood:	n/a
32	chr20:52687007-52687057	HIPEpiC	eye:	n/a
33	chr20:52687007-52687057	NHDF-neo	bronchial:	n/a
34	chr20:52687007-52687057	HRCEpiC	kidney:	n/a
35	chr20:52687007-52687057	T-47D	breast:	n/a
36	chr20:52687007-52687057	ECC-1	luminal epithelium:	n/a
37	chr20:52687007-52687057	Hepatocyte	liver:	n/a
38	chr20:52687007-52687057	NHBE	bronchial:	n/a
39	chr20:52687007-52687057	GM19239	blood:	n/a
40	chr20:52687007-52687057	AG04450	lung:	fetal
41	chr20:52687007-52687057	MCF-7	breast:	n/a
42	chr20:52687007-52687057	HRE	kidney:	n/a
43	chr20:52687007-52687057	GM12878	blood:	n/a
44	chr20:52687007-52687057	ProgFib	skin:	n/a
45	chr20:52687007-52687057	PrEC	prostate:	n/a
46	chr20:52687007-52687057	HAEpiC	amniotic membrane:	n/a
47	chr20:52687007-52687057	HL-60	blood:	n/a
48	chr20:52687007-52687057	HCT-116	colon:	n/a
49	chr20:52687007-52687057	HCM	heart:	n/a
50	chr20:52687007-52687057	GM06990	blood:	n/a

(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	chr20:52684414..52687124-chr6:151977348..151979114,2	MCF-7	breast:
13	chr17:56706875..56710932-chr20:52683217..52688645,17	MCF-7	breast:

No data

Variant related genes	Relation type
MIR4756	TF binding region
MIR4756	CpG island
ENSG00000101144	Chromatin interaction
ENSG00000236352	Chromatin interaction
ENSG00000267882	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000266826	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000171940	Chromatin interaction
ENSG00000124151	Chromatin interaction
ENSG00000206737	Chromatin interaction
ENSG00000163349	Chromatin interaction
ENSG00000101040	Chromatin interaction
ENSG00000091831	Chromatin interaction
ENSG00000212195	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12625718	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs368195	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs377887	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs383469	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs388759	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs391906	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs392236	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6013885	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6123357	1.00[EUR][1000 genomes]
rs6127091	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6127092	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6127093	1.00[EUR][1000 genomes];0.88[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

No data

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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