Variant report

Variant	rs13140290
Chromosome Location	chr4:165856679-165856680
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:120)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:120 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr4:165856656-165856744	GM20000	blood:	n/a	n/a
2	CTCF	chr4:165856640-165856790	HMF	breast:	n/a	n/a
3	RAD21	chr4:165856549-165856838	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr4:165856620-165856770	RPTEC	kidney:	n/a	n/a
5	CTCF	chr4:165856640-165856790	A549	lung:	n/a	n/a
6	CTCF	chr4:165856580-165856730	HEK293	kidney:	n/a	n/a
7	CTCF	chr4:165856639-165856827	K562	blood:	n/a	n/a
8	CTCF	chr4:165856580-165856730	HFF-Myc	foreskin:	n/a	n/a
9	CTCF	chr4:165856580-165856730	HAc	cerebellar:	n/a	n/a
10	USF1	chr4:165856518-165856874	HCT-116	colon:	n/a	n/a
11	USF1	chr4:165856472-165856774	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTCF	chr4:165856652-165856824	Gliobla	brain:	n/a	n/a
13	CTCF	chr4:165856660-165856810	GM12872	blood:	n/a	n/a
14	CTCF	chr4:165856620-165856770	HCPEpiC	choroid plexus:	n/a	n/a
15	CTCF	chr4:165856629-165856817	HepG2	liver:	n/a	n/a
16	RAD21	chr4:165856538-165856902	H1-hESC	embryonic stem cell:	n/a	n/a
17	ZNF143	chr4:165856498-165856888	GM12878	blood:	n/a	n/a
18	CTCF	chr4:165856620-165856770	WERI-Rb-1	eye:	n/a	n/a
19	CTCF	chr4:165856660-165856810	BE2_C	brain:	n/a	n/a
20	SMC3	chr4:165856581-165856873	HepG2	liver:	n/a	n/a
21	CTCF	chr4:165856537-165856875	H1-hESC	embryonic stem cell:	n/a	n/a
22	CTCF	chr4:165856628-165856836	GM12878	blood:	n/a	n/a
23	CTCF	chr4:165856653-165856894	GM19238	blood:	n/a	n/a
24	MTA3	chr4:165856559-165857761	GM12878	blood:	n/a	n/a
25	CTCF	chr4:165856640-165856790	GM12872	blood:	n/a	n/a
26	CTCF	chr4:165856640-165856790	Hela-S3	cervix:	n/a	n/a
27	CTCF	chr4:165856640-165856790	HPAF	blood vessel:	n/a	n/a
28	CTCF	chr4:165856600-165856750	MCF-7	breast:	n/a	n/a
29	CTCF	chr4:165856491-165856832	MCF-7	breast:	n/a	n/a
30	CTCF	chr4:165856640-165856790	GM12865	blood:	n/a	n/a
31	CTCF	chr4:165856660-165856810	GM12867	blood:	n/a	n/a
32	CTCF	chr4:165856620-165856770	GM06990	blood:	n/a	n/a
33	CTCF	chr4:165856600-165856750	GM12869	blood:	n/a	n/a
34	ZNF384	chr4:165855908-165856780	GM12878	blood:	n/a	n/a
35	CTCF	chr4:165856597-165856907	H1-hESC	embryonic stem cell:	n/a	n/a
36	CTCF	chr4:165856659-165856784	GM19240	blood:	n/a	n/a
37	CTCF	chr4:165856619-165856853	MCF-7	breast:	n/a	n/a
38	RAD21	chr4:165856570-165856804	HepG2	liver:	n/a	n/a
39	CTCF	chr4:165856600-165856750	HBMEC	blood vessel:	n/a	n/a
40	POLR2A	chr4:165856475-165858391	GM12891	blood:	n/a	n/a
41	POLR2A	chr4:165856518-165858362	GM19193	blood:	n/a	n/a
42	CTCF	chr4:165856644-165856806	MCF-7	breast:	n/a	n/a
43	CTCF	chr4:165856620-165856770	HCT-116	colon:	n/a	n/a
44	CTCF	chr4:165856592-165856782	K562	blood:	n/a	n/a
45	MXI1	chr4:165856544-165857862	GM12878	blood:	n/a	n/a
46	CTCF	chr4:165856640-165856790	HMEC	breast:	n/a	n/a
47	CTCF	chr4:165856600-165856750	HPF	lung:	n/a	n/a
48	CTCF	chr4:165856640-165856790	NB4	blood:	n/a	n/a
49	RAD21	chr4:165856424-165856943	H1-hESC	embryonic stem cell:	n/a	n/a
50	CTCF	chr4:165856654-165856773	Hela-S3	cervix:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:165856166..165858715-chr4:165877906..165879898,2	MCF-7	breast:
2	chr4:165699281..165700032-chr4:165856272..165857241,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000270960	TF binding region
ENSG00000250486	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11100583	0.82[ASN][1000 genomes]
rs12507869	0.81[ASN][1000 genomes]
rs13110309	0.81[ASN][1000 genomes]
rs13134940	0.81[ASN][1000 genomes]
rs13144590	0.81[ASN][1000 genomes]
rs17623445	0.81[ASN][1000 genomes]
rs28543022	0.91[ASN][1000 genomes]
rs28580702	0.91[ASN][1000 genomes]
rs3733419	0.81[ASN][1000 genomes]
rs3889248	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4234889	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4395461	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4691137	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61641856	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6834073	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72631697	0.86[ASN][1000 genomes]
rs7656863	0.82[ASN][1000 genomes]
rs7657444	0.81[ASN][1000 genomes]
rs8180162	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461821	chr4:165402309-165859951	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv596037	chr4:165402309-165859951	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1019150	chr4:165505585-165907924	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv1026152	chr4:165622244-166027447	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv537336	chr4:165622244-166027447	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
6	nsv1022210	chr4:165792630-166251612	Genic enhancers Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
7	nsv537337	chr4:165792630-166251612	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
8	nsv880382	chr4:165793001-165964290	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
9	esv2757965	chr4:165801816-165976350	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
10	esv2759299	chr4:165801816-165976350	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
11	nsv528686	chr4:165814359-165930168	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
12	nsv967697	chr4:165843736-165889668	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv1015970	chr4:165852926-165973078	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
14	nsv1021905	chr4:165852926-166212878	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
15	nsv830140	chr4:165855999-165956612	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:165853400-165856800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:165853600-165857800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr4:165854200-165858600	Weak transcription	HSMMtube	muscle
4	chr4:165855200-165858800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr4:165855600-165856800	Enhancers	GM12878-XiMat	blood
6	chr4:165855800-165857200	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr4:165856600-165858000	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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