Variant report

Variant	rs3113662
Chromosome Location	chr4:54487418-54487419
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:77)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:77 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr4:54487340-54487490	HCPEpiC	choroid plexus:	n/a	n/a
2	CTCF	chr4:54487202-54487570	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr4:54487340-54487490	NHEK	skin:	n/a	n/a
4	CTCF	chr4:54487282-54487504	MCF-7	breast:	n/a	n/a
5	CTCF	chr4:54487320-54487470	HMF	breast:	n/a	n/a
6	CTCF	chr4:54487360-54487510	HCT-116	colon:	n/a	n/a
7	CTCF	chr4:54487300-54487450	HRE	kidney:	n/a	n/a
8	CTCF	chr4:54487363-54487506	MCF-7	breast:	n/a	n/a
9	CTCF	chr4:54487300-54487450	GM12878	blood:	n/a	n/a
10	CTCF	chr4:54487240-54487612	MCF-7	breast:	n/a	n/a
11	CTCF	chr4:54487280-54487430	HCFaa	heart:	n/a	n/a
12	CTCF	chr4:54487360-54487510	GM12871	blood:	n/a	n/a
13	CTCF	chr4:54487300-54487510	RPTEC	kidney:	n/a	n/a
14	CTCF	chr4:54487400-54487550	BE2_C	brain:	n/a	n/a
15	CTCF	chr4:54487180-54487430	HMF	breast:	n/a	n/a
16	CTCF	chr4:54487360-54487510	GM12864	blood:	n/a	n/a
17	CTCF	chr4:54487280-54487430	HVMF	connective:	n/a	n/a
18	CTCF	chr4:54487342-54487442	Hela-S3	cervix:	n/a	n/a
19	CTCF	chr4:54487280-54487430	HRPEpiC	eye:	n/a	n/a
20	CTCF	chr4:54487265-54487526	MCF-7	breast:	n/a	n/a
21	CTCF	chr4:54487320-54487470	AoAF	blood vessel:	n/a	n/a
22	CTCF	chr4:54487360-54487510	HA-sp	spinal cord:	n/a	n/a
23	CTCF	chr4:54487300-54487590	HFF-Myc	foreskin:	n/a	n/a
24	CTCF	chr4:54487280-54487430	GM12873	blood:	n/a	n/a
25	CTCF	chr4:54487320-54487470	HCT-116	colon:	n/a	n/a
26	CTCF	chr4:54487300-54487450	HVMF	connective:	n/a	n/a
27	CTCF	chr4:54487300-54487450	GM12868	blood:	n/a	n/a
28	CTCF	chr4:54487280-54487430	RPTEC	kidney:	n/a	n/a
29	CTCF	chr4:54487321-54487466	K562	blood:	n/a	n/a
30	CTCF	chr4:54487300-54487450	HBMEC	blood vessel:	n/a	n/a
31	CTCF	chr4:54487300-54487450	HEK293	kidney:	n/a	n/a
32	CTCF	chr4:54487340-54487490	GM12872	blood:	n/a	n/a
33	CTCF	chr4:54487320-54487470	AG04449	skin:	n/a	n/a
34	CTCF	chr4:54487300-54487450	HMEC	breast:	n/a	n/a
35	CTCF	chr4:54487300-54487450	GM12864	blood:	n/a	n/a
36	CTCF	chr4:54487340-54487490	MCF-7	breast:	n/a	n/a
37	CTCF	chr4:54487300-54487450	SK-N-SH_RA	brain:	n/a	n/a
38	CTCF	chr4:54487240-54487527	K562	blood:	n/a	n/a
39	CTCF	chr4:54487373-54487434	HepG2	liver:	n/a	n/a
40	RAD21	chr4:54487265-54487557	H1-hESC	embryonic stem cell:	n/a	n/a
41	CTCF	chr4:54487300-54487450	GM12866	blood:	n/a	n/a
42	CTCF	chr4:54487367-54487452	A549	lung:	n/a	n/a
43	CTCF	chr4:54487280-54487430	GM06990	blood:	n/a	n/a
44	RAD21	chr4:54487164-54487514	H1-hESC	embryonic stem cell:	n/a	n/a
45	CTCF	chr4:54487280-54487430	GM12872	blood:	n/a	n/a
46	CTCF	chr4:54487199-54487579	MCF-7	breast:	n/a	n/a
47	CTCF	chr4:54487300-54487450	HepG2	liver:	n/a	n/a
48	CTCF	chr4:54487380-54487530	HBMEC	blood vessel:	n/a	n/a
49	CTCF	chr4:54487352-54487424	GM12878	blood:	n/a	n/a
50	CTCF	chr4:54487320-54487470	AG09309	skin:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:54487031..54487605-chr4:55099358..55100201,3	MCF-7	breast:
2	chr4:54486968..54487480-chr4:54567881..54568820,2	MCF-7	breast:

No data

Variant related genes	Relation type
LNX1	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1022187	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11945428	0.89[CEU][hapmap]
rs1546527	0.97[ASN][1000 genomes]
rs2412470	0.81[ASN][1000 genomes]
rs2572292	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2572300	0.97[ASN][1000 genomes]
rs2590770	0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2590771	0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2590773	0.95[ASN][1000 genomes]
rs2590778	0.95[ASN][1000 genomes]
rs2590779	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2590809	0.81[ASN][1000 genomes]
rs2590810	0.81[ASN][1000 genomes]
rs2616383	0.81[ASN][1000 genomes]
rs2616387	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2616388	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2616389	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2616425	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2668522	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2668523	0.93[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2668525	0.95[ASN][1000 genomes]
rs2668526	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2668527	0.95[ASN][1000 genomes]
rs2668528	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2668550	0.95[ASN][1000 genomes]
rs2668551	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2668552	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2668567	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs750545	0.81[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	nsv829936	chr4:54367783-54556123	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1004253	chr4:54471388-54494983	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1010881	chr4:54471545-54494983	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54484800-54487800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr4:54485200-54505800	Weak transcription	Esophagus	oesophagus
3	chr4:54486800-54489600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr4:54487200-54487600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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