Variant report

Variant	rs2072233
Chromosome Location	chr11:17519864-17519865
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	TCF7L2	chr11:17519673-17519873	Hela-S3	cervix:	n/a	n/a
2	BHLHE40	chr11:17519723-17520008	HepG2	liver:	n/a	n/a
3	CTCF	chr11:17519752-17519878	GM12892	blood:	n/a	n/a
4	GTF2F1	chr11:17519652-17520007	Hela-S3	cervix:	n/a	n/a
5	USF1	chr11:17519699-17520016	ECC-1	luminal epithelium:	n/a	n/a
6	RFX5	chr11:17519674-17519992	Hela-S3	cervix:	n/a	chr11:17519835-17519844
7	NFYB	chr11:17519614-17520004	Hela-S3	cervix:	n/a	chr11:17519835-17519845 chr11:17519832-17519847 chr11:17519832-17519847 chr11:17519834-17519849 chr11:17519834-17519847 chr11:17519836-17519848
8	MAZ	chr11:17519648-17519939	Hela-S3	cervix:	n/a	chr11:17519687-17519697
9	USF1	chr11:17519707-17519955	H1-hESC	embryonic stem cell:	n/a	n/a
10	RAD21	chr11:17519603-17519958	Hela-S3	cervix:	n/a	chr11:17519644-17519657
11	MAX	chr11:17519652-17519995	MCF-7	breast:	n/a	chr11:17519687-17519697 chr11:17519860-17519870
12	CTCF	chr11:17519725-17519917	MCF-7	breast:	n/a	n/a
13	CTCF	chr11:17519725-17519908	MCF-7	breast:	n/a	n/a
14	JUND	chr11:17519740-17520334	H1-hESC	embryonic stem cell:	n/a	chr11:17519834-17519843
15	CHD2	chr11:17519630-17519990	Hela-S3	cervix:	n/a	n/a
16	CEBPB	chr11:17519549-17520016	MCF-7	breast:	n/a	n/a
17	NFYB	chr11:17519701-17519900	K562	blood:	n/a	chr11:17519835-17519845 chr11:17519832-17519847 chr11:17519832-17519847 chr11:17519834-17519849 chr11:17519834-17519847 chr11:17519836-17519848
18	NFYB	chr11:17519768-17519924	GM12878	blood:	n/a	chr11:17519835-17519845 chr11:17519832-17519847 chr11:17519832-17519847 chr11:17519834-17519849 chr11:17519834-17519847 chr11:17519836-17519848
19	CTCF	chr11:17519715-17519921	MCF-7	breast:	n/a	n/a
20	USF1	chr11:17519602-17520078	H1-hESC	embryonic stem cell:	n/a	n/a
21	MAX	chr11:17519591-17520045	ECC-1	luminal epithelium:	n/a	chr11:17519687-17519697 chr11:17519860-17519870
22	CEBPB	chr11:17519671-17519920	A549	lung:	n/a	n/a
23	USF2	chr11:17519747-17519956	H1-hESC	embryonic stem cell:	n/a	n/a
24	CEBPB	chr11:17519686-17519980	H1-hESC	embryonic stem cell:	n/a	n/a
25	CTCF	chr11:17519789-17519888	GM12891	blood:	n/a	n/a
26	CEBPB	chr11:17519582-17520194	Hela-S3	cervix:	n/a	n/a
27	CTCF	chr11:17519731-17519898	Hela-S3	cervix:	n/a	n/a
28	CTCF	chr11:17519720-17519870	SAEC	small airway:	n/a	n/a
29	CTCF	chr11:17519732-17519907	MCF-7	breast:	n/a	n/a
30	CTCF	chr11:17519800-17519950	HEEpiC	esophagus:	n/a	n/a
31	NFYA	chr11:17519626-17519980	Hela-S3	cervix:	n/a	chr11:17519835-17519845 chr11:17519832-17519847 chr11:17519832-17519847 chr11:17519834-17519847 chr11:17519836-17519848
32	RCOR1	chr11:17519602-17519866	Hela-S3	cervix:	n/a	n/a
33	USF2	chr11:17519618-17520086	Hela-S3	cervix:	n/a	n/a
34	RAD21	chr11:17519642-17520423	H1-hESC	embryonic stem cell:	n/a	chr11:17519644-17519657
35	CTCF	chr11:17519720-17519870	Hela-S3	cervix:	n/a	n/a
36	ELK1	chr11:17519666-17519930	Hela-S3	cervix:	n/a	n/a
37	CTCF	chr11:17519740-17519890	WERI-Rb-1	eye:	n/a	n/a
38	CTCF	chr11:17519742-17519877	H1-hESC	embryonic stem cell:	n/a	n/a
39	CEBPB	chr11:17519669-17519957	HepG2	liver:	n/a	n/a
40	MYC	chr11:17519622-17520119	NB4	blood:	n/a	chr11:17519687-17519697 chr11:17519860-17519870
41	MAX	chr11:17519622-17520043	Hela-S3	cervix:	n/a	chr11:17519687-17519697 chr11:17519860-17519870
42	MAX	chr11:17519628-17520334	NB4	blood:	n/a	chr11:17519687-17519697 chr11:17519860-17519870
43	USF1	chr11:17519642-17519991	ECC-1	luminal epithelium:	n/a	n/a
44	CTCF	chr11:17519735-17519919	MCF-7	breast:	n/a	n/a
45	SMC3	chr11:17519589-17520046	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:17513527..17517514-chr11:17518816..17522718,5	K562	blood:
2	chr11:17405333..17406124-chr11:17519578..17520279,2	MCF-7	breast:
3	chr11:17094293..17097227-chr11:17519286..17521617,2	K562	blood:
4	chr11:17410518..17411123-chr11:17519560..17520298,2	MCF-7	breast:

Variant related genes	Relation type
USH1C	TF binding region
ENSG00000110700	Chromatin interaction
ENSG00000221322	Chromatin interaction
ENSG00000272034	Chromatin interaction
ENSG00000187486	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12576915	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2072224	0.82[AMR][1000 genomes]
rs2072226	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2072231	0.82[CEU][hapmap];1.00[CHB][hapmap];0.80[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2072232	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2355020	0.82[AMR][1000 genomes]
rs4756894	0.80[AMR][1000 genomes]
rs4756896	0.82[AMR][1000 genomes]
rs4756897	0.82[AMR][1000 genomes]
rs4757533	0.80[AMR][1000 genomes]
rs4757536	0.82[AMR][1000 genomes]
rs57527755	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58158338	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6486372	0.80[ASN][1000 genomes]
rs6486374	0.80[AMR][1000 genomes]
rs6486375	0.80[AMR][1000 genomes]
rs6486376	0.80[AMR][1000 genomes]
rs6486377	0.80[AMR][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	nsv469895	chr11:17368270-17584220	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv467714	chr11:17513147-17521825	Weak transcription Bivalent Enhancer Enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv553585	chr11:17513147-17521825	Bivalent Enhancer Weak transcription Strong transcription Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17511200-17526000	Weak transcription	Brain Substantia Nigra	brain
2	chr11:17512600-17530000	Weak transcription	Right Atrium	heart
3	chr11:17513600-17530600	Strong transcription	Fetal Intestine Small	intestine
4	chr11:17514800-17522800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:17515000-17523600	Weak transcription	Dnd41	blood
6	chr11:17515600-17524600	Strong transcription	Fetal Intestine Large	intestine
7	chr11:17516000-17523000	Strong transcription	Duodenum Mucosa	Duodenum
8	chr11:17516800-17529600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr11:17516800-17553000	Weak transcription	Stomach Mucosa	stomach
10	chr11:17518000-17522800	Strong transcription	Rectal Mucosa Donor 31	rectum
11	chr11:17519000-17521200	Weak transcription	Colonic Mucosa	Colon
12	chr11:17519000-17521800	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr11:17519400-17520200	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr11:17519600-17520000	Enhancers	Gastric	stomach
15	chr11:17519600-17520200	Enhancers	H1 Cell Line	embryonic stem cell
16	chr11:17519800-17520000	Enhancers	Brain Germinal Matrix	brain
17	chr11:17519800-17520000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
18	chr11:17519800-17520200	Enhancers	Esophagus	oesophagus
19	chr11:17519800-17520200	Bivalent Enhancer	Placenta	Placenta
20	chr11:17519800-17520200	Enhancers	Hela-S3	cervix

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