Variant report

Variant	rs73839049
Chromosome Location	chr4:106819537-106819538
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	FOXA1	chr4:106819441-106819766	T-47D	breast:	n/a	n/a
2	HNF4A	chr4:106819441-106819749	HepG2	liver:	n/a	chr4:106819642-106819655 chr4:106819642-106819655
3	GATA3	chr4:106819366-106819763	T-47D	breast:	n/a	chr4:106819423-106819434
4	HNF4A	chr4:106819484-106819714	HepG2	liver:	n/a	chr4:106819642-106819655 chr4:106819642-106819655
5	JUND	chr4:106819321-106819748	HepG2	liver:	n/a	n/a
6	FOXA1	chr4:106819414-106819810	T-47D	breast:	n/a	n/a
7	GATA3	chr4:106819389-106819737	MCF-7	breast:	n/a	chr4:106819423-106819434
8	NFIC	chr4:106819426-106819895	HepG2	liver:	n/a	n/a
9	JUND	chr4:106819428-106819716	T-47D	breast:	n/a	n/a
10	JUND	chr4:106819336-106819588	H1-hESC	embryonic stem cell:	n/a	n/a
11	GATA3	chr4:106819091-106819907	MCF-7	breast:	n/a	chr4:106819423-106819434
12	FOXA1	chr4:106819273-106819925	HepG2	liver:	n/a	n/a
13	HDAC2	chr4:106819394-106819778	HepG2	liver:	n/a	n/a
14	FOXA1	chr4:106819368-106819867	HepG2	liver:	n/a	n/a
15	FOXA1	chr4:106819323-106819908	HepG2	liver:	n/a	n/a
16	EP300	chr4:106819430-106819777	HepG2	liver:	n/a	n/a
17	REST	chr4:106819462-106819754	HepG2	liver:	n/a	n/a
18	GATA3	chr4:106819261-106819659	MCF-7	breast:	n/a	chr4:106819423-106819434
19	MYBL2	chr4:106819458-106819818	HepG2	liver:	n/a	n/a
20	GATA3	chr4:106819424-106819733	T-47D	breast:	n/a	n/a
21	MYBL2	chr4:106819339-106819880	HepG2	liver:	n/a	n/a
22	KAP1	chr4:106819159-106819897	HEK293	kidney:	n/a	n/a
23	MBD4	chr4:106819389-106819831	HepG2	liver:	n/a	n/a
24	ZZZ3	chr4:106819302-106819569	Hela-S3	cervix:	n/a	n/a
25	GATA3	chr4:106819406-106819627	SH-SY5Y	brain:	n/a	chr4:106819423-106819434
26	FOXA2	chr4:106819463-106819784	HepG2	liver:	n/a	n/a
27	NFIC	chr4:106819465-106819794	HepG2	liver:	n/a	n/a
28	GATA2	chr4:106819372-106819668	SH-SY5Y	brain:	n/a	chr4:106819423-106819434
29	GATA3	chr4:106819310-106819787	MCF-7	breast:	n/a	chr4:106819423-106819434
30	FOXA1	chr4:106819312-106819772	HepG2	liver:	n/a	n/a
31	FOXA2	chr4:106819156-106820175	HepG2	liver:	n/a	n/a
32	EP300	chr4:106819535-106819735	HepG2	liver:	n/a	n/a
33	TEAD4	chr4:106819401-106819886	HepG2	liver:	n/a	n/a
34	HNF4G	chr4:106819461-106819758	HepG2	liver:	n/a	chr4:106819641-106819656 chr4:106819642-106819655 chr4:106819642-106819655
35	RXRA	chr4:106819421-106819703	HepG2	liver:	n/a	chr4:106819642-106819655 chr4:106819642-106819655

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:106817938..106820838-chr4:106829455..106833276,3	MCF-7	breast:

Variant related genes	Relation type
INTS12	TF binding region
ENSG00000168743	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10000995	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10001493	0.97[EUR][1000 genomes]
rs10004951	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10006990	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10008593	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10013403	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10027191	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10033978	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10470990	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11726457	0.97[EUR][1000 genomes]
rs11731982	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17036356	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17036363	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28369208	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28465019	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28481382	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28544485	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28557167	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6850909	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9992491	0.92[AMR][1000 genomes];0.91[EUR][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	nsv1014993	chr4:106796019-106980727	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv2418320	chr4:106819289-106819690	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
3	esv1383700	chr4:106819535-106819537	Weak transcription Bivalent Enhancer Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106818000-106824400	Weak transcription	Small Intestine	intestine
2	chr4:106818000-106844800	Weak transcription	Psoas Muscle	Psoas
3	chr4:106818200-106820200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
4	chr4:106818200-106830400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr4:106818400-106819600	Enhancers	Fetal Heart	heart
6	chr4:106819200-106819600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
7	chr4:106819200-106819800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
8	chr4:106819200-106820000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
9	chr4:106819200-106821400	Weak transcription	HSMMtube	muscle
10	chr4:106819200-106836200	Weak transcription	Aorta	Aorta
11	chr4:106819200-106844600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr4:106819400-106819600	Bivalent Enhancer	Fetal Intestine Large	intestine
13	chr4:106819400-106819600	Bivalent Enhancer	Stomach Mucosa	stomach
14	chr4:106819400-106820000	Enhancers	Fetal Intestine Small	intestine
15	chr4:106819400-106820200	Enhancers	GM12878-XiMat	blood
16	chr4:106819400-106820600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
17	chr4:106819400-106820800	Enhancers	Pancreas	Pancrea
18	chr4:106819400-106820800	Enhancers	HepG2	liver
19	chr4:106819400-106823400	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr4:106819400-106825400	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr4:106819400-106830600	Weak transcription	Duodenum Mucosa	Duodenum

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