Variant report

Variant	rs56228709
Chromosome Location	chr7:3534557-3534558
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:3528452..3531258-chr7:3533365..3536191,2	MCF-7	breast:

Extended variants
information (count: 146 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs10499339	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11971344	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11971403	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11972647	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11972733	1.00[ASN][1000 genomes]
rs11972798	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11973104	1.00[ASN][1000 genomes]
rs11973367	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11973741	1.00[ASN][1000 genomes]
rs11973763	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11975595	1.00[ASN][1000 genomes]
rs11975833	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11978310	1.00[ASN][1000 genomes]
rs11978422	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11979623	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11979985	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11981004	1.00[ASN][1000 genomes]
rs11981125	1.00[ASN][1000 genomes]
rs11981422	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11982674	1.00[ASN][1000 genomes]
rs11983288	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11983341	1.00[ASN][1000 genomes]
rs11984433	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1522503	1.00[ASN][1000 genomes]
rs17133260	1.00[ASN][1000 genomes]
rs17133277	1.00[ASN][1000 genomes]
rs17133284	1.00[ASN][1000 genomes]
rs17133303	1.00[ASN][1000 genomes]
rs17133309	1.00[ASN][1000 genomes]
rs17133324	1.00[ASN][1000 genomes]
rs17133354	1.00[ASN][1000 genomes]
rs17133377	1.00[ASN][1000 genomes]
rs17133394	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17133406	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17133423	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17133429	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17133437	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17133448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17133485	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17133545	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17133548	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17150661	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17741019	1.00[ASN][1000 genomes]
rs17741730	1.00[ASN][1000 genomes]
rs2090941	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2178629	1.00[ASN][1000 genomes]
rs2222407	1.00[ASN][1000 genomes]
rs2222408	1.00[ASN][1000 genomes]
rs28528961	1.00[ASN][1000 genomes]
rs4358699	1.00[ASN][1000 genomes]
rs55716539	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55936101	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55944002	1.00[ASN][1000 genomes]
rs56138263	1.00[ASN][1000 genomes]
rs56175518	1.00[ASN][1000 genomes]
rs56217543	1.00[ASN][1000 genomes]
rs56331655	1.00[ASN][1000 genomes]
rs58297549	1.00[ASN][1000 genomes]
rs59076306	1.00[ASN][1000 genomes]
rs59971325	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60243572	1.00[ASN][1000 genomes]
rs60418263	1.00[ASN][1000 genomes]
rs66492969	1.00[ASN][1000 genomes]
rs66540307	1.00[ASN][1000 genomes]
rs66546301	1.00[ASN][1000 genomes]
rs66664718	1.00[ASN][1000 genomes]
rs66665337	1.00[ASN][1000 genomes]
rs66790405	1.00[ASN][1000 genomes]
rs66941572	1.00[ASN][1000 genomes]
rs67179422	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67498702	1.00[ASN][1000 genomes]
rs67691723	1.00[ASN][1000 genomes]
rs67806403	1.00[ASN][1000 genomes]
rs67924867	1.00[ASN][1000 genomes]
rs68165343	1.00[ASN][1000 genomes]
rs6942774	1.00[ASN][1000 genomes]
rs6945265	1.00[ASN][1000 genomes]
rs6945914	1.00[ASN][1000 genomes]
rs6948557	1.00[ASN][1000 genomes]
rs6952184	1.00[ASN][1000 genomes]
rs6959134	1.00[ASN][1000 genomes]
rs6959489	1.00[ASN][1000 genomes]
rs6962043	1.00[ASN][1000 genomes]
rs6963043	1.00[ASN][1000 genomes]
rs6969044	1.00[ASN][1000 genomes]
rs6969455	1.00[ASN][1000 genomes]
rs6969711	1.00[ASN][1000 genomes]
rs6974121	1.00[ASN][1000 genomes]
rs6977110	1.00[ASN][1000 genomes]
rs73034713	1.00[ASN][1000 genomes]
rs73034779	1.00[ASN][1000 genomes]
rs73035928	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73035931	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73035936	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73035941	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73035942	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73035975	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73035985	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73036002	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73036706	1.00[ASN][1000 genomes]
rs73036757	1.00[ASN][1000 genomes]
rs73036762	1.00[ASN][1000 genomes]
rs73036799	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73038513	1.00[ASN][1000 genomes]
rs73038551	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73038553	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73038557	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73038581	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73038584	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73048700	1.00[ASN][1000 genomes]
rs73050200	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73050503	1.00[ASN][1000 genomes]
rs73050538	1.00[ASN][1000 genomes]
rs73050542	1.00[ASN][1000 genomes]
rs73051831	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73052642	1.00[ASN][1000 genomes]
rs7778916	1.00[ASN][1000 genomes]
rs7785207	1.00[ASN][1000 genomes]
rs7786415	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7794138	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs882921	0.92[EUR][1000 genomes]
rs9771086	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018173	chr7:3258989-3879848	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv538660	chr7:3258989-3879848	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv2758100	chr7:3286625-3560229	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv2759500	chr7:3286625-3560229	Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1016555	chr7:3298478-3872512	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv538661	chr7:3298478-3872512	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1020764	chr7:3348458-3554820	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv538662	chr7:3348458-3554820	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	esv2764026	chr7:3365002-3618361	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1015296	chr7:3381813-3560401	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	nsv916071	chr7:3423207-3697428	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv528715	chr7:3451251-3598581	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	nsv605902	chr7:3464896-3598581	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	nsv887333	chr7:3475716-3542488	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	nsv869723	chr7:3482682-3566293	Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv464270	chr7:3490865-3581357	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
17	nsv605904	chr7:3490865-3581357	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
18	nsv1027426	chr7:3506255-3556395	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
19	nsv538672	chr7:3506255-3556395	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
20	nsv1034716	chr7:3512406-3616155	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
21	esv1801470	chr7:3521000-3541046	Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
22	nsv1030469	chr7:3521036-3554820	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
23	nsv538673	chr7:3521036-3554820	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
24	nsv887334	chr7:3531275-3635105	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:3528600-3535000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr7:3528600-3535600	Weak transcription	Aorta	Aorta
3	chr7:3532800-3534800	Enhancers	HSMM	muscle
4	chr7:3533000-3534800	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr7:3533000-3534800	Enhancers	Pancreatic Islets	Pancreatic Islet
6	chr7:3533000-3535000	Weak transcription	Pancreas	Pancrea
7	chr7:3533000-3538600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr7:3533400-3536600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr7:3533600-3534600	Weak transcription	HSMMtube	muscle
10	chr7:3533600-3534800	Enhancers	Muscle Satellite Cultured Cells	--
11	chr7:3533600-3535200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr7:3533600-3535400	Weak transcription	Fetal Lung	lung
13	chr7:3533800-3535200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr7:3534400-3535800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr7:3534400-3536000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links