Variant report

Variant	rs4776197
Chromosome Location	chr15:54269075-54269076
allele	A/G
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	CTCF	chr15:54268911-54269511	MCF-7	breast:	n/a	n/a
2	CTCF	chr15:54268886-54269343	A549	lung:	n/a	n/a
3	BHLHE40	chr15:54269065-54269371	GM12878	blood:	n/a	n/a
4	CTCF	chr15:54268992-54269422	GM12878	blood:	n/a	n/a
5	CTCF	chr15:54269060-54269210	HRPEpiC	eye:	n/a	n/a
6	CTCF	chr15:54269072-54269438	MCF-7	breast:	n/a	n/a
7	RAD21	chr15:54269005-54269448	A549	lung:	n/a	chr15:54269204-54269217
8	RAD21	chr15:54269035-54269410	H1-hESC	embryonic stem cell:	n/a	chr15:54269204-54269217
9	CTCF	chr15:54269069-54269428	H1-hESC	embryonic stem cell:	n/a	n/a
10	RAD21	chr15:54269032-54269447	GM12878	blood:	n/a	chr15:54269204-54269217
11	RAD21	chr15:54268912-54269478	H1-hESC	embryonic stem cell:	n/a	chr15:54269204-54269217
12	CTCF	chr15:54268877-54269526	SK-N-SH	brain:	n/a	n/a
13	CTCF	chr15:54269060-54269210	HMF	breast:	n/a	n/a
14	SMC3	chr15:54269072-54269370	HepG2	liver:	n/a	n/a
15	RAD21	chr15:54269066-54269399	H1-hESC	embryonic stem cell:	n/a	chr15:54269204-54269217
16	SMC3	chr15:54269027-54269505	GM12878	blood:	n/a	n/a
17	RAD21	chr15:54268927-54269534	MCF-7	breast:	n/a	chr15:54269204-54269217
18	FOXA1	chr15:54269072-54269336	T-47D	breast:	n/a	n/a
19	RAD21	chr15:54269021-54269448	A549	lung:	n/a	chr15:54269204-54269217
20	CTCF	chr15:54269020-54269365	H1-hESC	embryonic stem cell:	n/a	n/a
21	RAD21	chr15:54269062-54269417	HepG2	liver:	n/a	chr15:54269204-54269217
22	ZNF143	chr15:54269052-54269417	GM12878	blood:	n/a	n/a
23	RAD21	chr15:54268945-54269512	MCF-7	breast:	n/a	chr15:54269204-54269217
24	GATA3	chr15:54269056-54269362	T-47D	breast:	n/a	chr15:54269147-54269159 chr15:54269149-54269158
25	CTCF	chr15:54269040-54269190	A549	lung:	n/a	n/a
26	RAD21	chr15:54268905-54269437	SK-N-SH	brain:	n/a	chr15:54269204-54269217
27	RAD21	chr15:54269067-54269391	HepG2	liver:	n/a	chr15:54269204-54269217

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:54266407..54270072-chr15:55486535..55491034,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-WDR72-1	chr15:54268965-54269105	ENSG00000259669.1

Variant related genes	Relation type
ENSG00000259669	TF binding region
ENSG00000137876	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11857334	0.82[AMR][1000 genomes]
rs1478177	0.84[EUR][1000 genomes]
rs1478218	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17551796	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2414277	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4145152	0.85[EUR][1000 genomes]
rs4776196	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7175118	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72736943	0.85[EUR][1000 genomes]
rs8024617	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904223	chr15:53665247-54340070	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1052235	chr15:53677524-54618723	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv542388	chr15:53677524-54618723	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv904226	chr15:53883244-54458310	Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv457144	chr15:53890362-54455757	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv569440	chr15:53890362-54455757	ZNF genes & repeats Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv569441	chr15:53890362-54456754	Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv457145	chr15:53890393-54456754	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv569442	chr15:53890393-54456754	Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv949528	chr15:54041154-54281981	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv817539	chr15:54132584-55095235	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
12	nsv833011	chr15:54226235-54421567	Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv569491	chr15:54260920-54397493	Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv904229	chr15:54267610-54340070	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:54267400-54269600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links