Variant report

Variant	rs6536880
Chromosome Location	chr4:165866613-165866614
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:165866322..165867965-chr4:165877072..165879577,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000250486	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10005938	0.86[ASN][1000 genomes]
rs10006119	0.86[ASN][1000 genomes]
rs10008027	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10011162	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10030484	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1077469	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11932635	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13142518	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17487295	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28402229	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3889246	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3889247	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3892134	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4073344	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4370095	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4425332	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4443238	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4541460	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4690795	0.92[ASN][1000 genomes]
rs4690796	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4691136	0.90[ASN][1000 genomes]
rs5027301	0.92[ASN][1000 genomes]
rs5027302	0.84[ASN][1000 genomes]
rs59634154	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6536879	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6536881	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6814345	0.86[ASN][1000 genomes]
rs6816770	0.92[ASN][1000 genomes]
rs7340843	0.92[ASN][1000 genomes]
rs7656256	0.86[ASN][1000 genomes]
rs7656698	0.86[ASN][1000 genomes]
rs7663683	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7673129	0.86[ASN][1000 genomes]
rs7676510	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7678154	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7678388	0.86[ASN][1000 genomes]
rs7678414	0.86[ASN][1000 genomes]
rs7678536	0.86[ASN][1000 genomes]
rs7681048	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7694572	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9762579	0.82[ASN][1000 genomes]
rs9917978	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	nsv517554	chr4:165859951-165878335	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
15	esv4358	chr4:165861368-165869440	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
16	esv2760876	chr4:165861386-165893486	Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
17	esv20237	chr4:165861441-165883885	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
18	nsv10607	chr4:165861465-165886549	Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
19	esv3467721	chr4:165862102-165867000	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
20	esv3467722	chr4:165862102-165867000	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:165859200-165869200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:165864600-165869200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:165864800-165869000	Weak transcription	Fetal Muscle Leg	muscle
4	chr4:165864800-165869200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:165865800-165867000	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr4:165866200-165866800	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr4:165866200-165866800	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr4:165866600-165866800	Enhancers	HMEC	breast
9	chr4:165866600-165868400	Weak transcription	iPS-15b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links