Variant report

Variant	rs4253396
Chromosome Location	chr4:187186879-187186880
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr4:187186702-187187485	HepG2	liver:	n/a	n/a
2	HEY1	chr4:187186751-187187810	HepG2	liver:	n/a	n/a
3	POLR2A	chr4:187186762-187187487	HepG2	liver:	n/a	n/a
4	NFIC	chr4:187186741-187187275	HepG2	liver:	n/a	chr4:187187115-187187143
5	ARID3A	chr4:187186808-187187453	HepG2	liver:	n/a	n/a
6	FOXA1	chr4:187186834-187187179	HepG2	liver:	n/a	n/a
7	SP1	chr4:187186827-187187360	HepG2	liver:	n/a	n/a
8	FOXA1	chr4:187186747-187187536	HepG2	liver:	n/a	n/a
9	POLR2A	chr4:187186795-187187221	HepG2	liver:	n/a	n/a
10	REST	chr4:187186798-187187299	HepG2	liver:	n/a	n/a
11	TBP	chr4:187186784-187187439	HepG2	liver:	n/a	n/a
12	NFIC	chr4:187186713-187188022	HepG2	liver:	n/a	chr4:187187115-187187143
13	FOXA1	chr4:187186748-187187286	HepG2	liver:	n/a	n/a
14	HNF4A	chr4:187186772-187187174	HepG2	liver:	n/a	chr4:187186929-187186944
15	POLR2A	chr4:187186710-187188266	HepG2	liver:	n/a	n/a
16	POLR2A	chr4:187186843-187187104	H1-hESC	embryonic stem cell:	n/a	n/a
17	HNF4G	chr4:187186783-187187172	HepG2	liver:	n/a	chr4:187186930-187186945
18	MYBL2	chr4:187186672-187188355	HepG2	liver:	n/a	n/a
19	POLR2A	chr4:187186831-187188252	HepG2	liver:	n/a	n/a
20	FOXA1	chr4:187186763-187187209	HepG2	liver:	n/a	n/a
21	MBD4	chr4:187186729-187187444	HepG2	liver:	n/a	n/a
22	HDAC2	chr4:187186783-187187244	HepG2	liver:	n/a	chr4:187186816-187186830 chr4:187186813-187186827 chr4:187186817-187186831 chr4:187186820-187186834
23	MBD4	chr4:187186743-187187279	HepG2	liver:	n/a	n/a
24	MYBL2	chr4:187186672-187187345	HepG2	liver:	n/a	n/a
25	TEAD4	chr4:187186749-187187630	HepG2	liver:	n/a	n/a
26	HNF4A	chr4:187186777-187187178	HepG2	liver:	n/a	chr4:187186929-187186944
27	HNF4G	chr4:187186726-187187158	HepG2	liver:	n/a	chr4:187186930-187186945
28	EP300	chr4:187186763-187187218	HepG2	liver:	n/a	n/a
29	FOXA2	chr4:187186836-187187238	HepG2	liver:	n/a	n/a
30	HEY1	chr4:187186733-187187653	HepG2	liver:	n/a	n/a
31	POLR2A	chr4:187186819-187188230	HepG2	liver:	n/a	n/a
32	MAX	chr4:187186772-187187293	HepG2	liver:	n/a	n/a
33	SP1	chr4:187186779-187187179	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr4:187186828-187186953	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
F11	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs4253331	0.81[EUR][1000 genomes]
rs4253406	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4253408	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028146	chr4:186503899-187338335	Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv530178	chr4:186659940-187478310	Bivalent Enhancer Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv931977	chr4:186912987-187364756	Active TSS Strong transcription Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv869299	chr4:186958290-187192748	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv1033203	chr4:186990348-187333476	Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv537431	chr4:186990348-187333476	Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	nsv461864	chr4:187006806-187257004	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv596392	chr4:187006806-187257004	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv461865	chr4:187072383-187366649	Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	nsv596401	chr4:187072383-187366649	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
11	nsv881472	chr4:187152142-187187005	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv1034638	chr4:187185385-187213477	Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4253396	F11	cis	brain	BrainEAC

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:187150200-187187200	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr4:187151000-187187200	Weak transcription	Colon Smooth Muscle	Colon
3	chr4:187177400-187191800	Weak transcription	Right Atrium	heart
4	chr4:187182200-187187600	Weak transcription	Fetal Lung	lung
5	chr4:187185200-187187000	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr4:187185400-187187000	Enhancers	H9 Cell Line	embryonic stem cell
7	chr4:187185400-187187000	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr4:187186000-187187000	Enhancers	Pancreas	Pancrea
9	chr4:187186000-187187200	Enhancers	Fetal Intestine Large	intestine
10	chr4:187186000-187187600	Enhancers	Fetal Intestine Small	intestine
11	chr4:187186000-187188200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr4:187186200-187187000	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr4:187186400-187187000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr4:187186400-187188200	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr4:187186600-187188600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr4:187186800-187187000	Flanking Active TSS	Liver	Liver
17	chr4:187186800-187187000	Flanking Active TSS	HepG2	liver
18	chr4:187186800-187187400	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr4:187186800-187187800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
20	chr4:187186800-187188000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr4:187186800-187188200	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr4:187186800-187188400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr4:187186800-187188400	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr4:187186800-187188600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr4:187186800-187188600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
26	chr4:187186800-187188600	Enhancers	Rectal Mucosa Donor 31	rectum

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