Variant report

Variant	rs58349531
Chromosome Location	chr6:29674943-29674944
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:29673901..29676614-chr6:29690934..29692528,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000204642	Chromatin interaction
ENSG00000225864	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10484548	0.81[EUR][1000 genomes]
rs11962004	0.81[EUR][1000 genomes]
rs11964095	0.81[EUR][1000 genomes]
rs11966844	0.81[EUR][1000 genomes]
rs17177823	0.81[EUR][1000 genomes]
rs29264	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs29270	0.86[ASN][1000 genomes]
rs3025660	0.81[EUR][1000 genomes]
rs3025667	0.81[EUR][1000 genomes]
rs362541	0.81[EUR][1000 genomes]
rs362542	0.81[EUR][1000 genomes]
rs55866912	0.81[EUR][1000 genomes]
rs56918232	0.80[ASN][1000 genomes]
rs57245255	0.86[ASN][1000 genomes]
rs57637386	0.86[ASN][1000 genomes]
rs6911622	0.80[ASN][1000 genomes]
rs6912636	0.81[EUR][1000 genomes]
rs6934884	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6935895	0.81[EUR][1000 genomes]
rs73402766	0.81[EUR][1000 genomes]
rs73402774	0.81[EUR][1000 genomes]
rs73404743	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73404745	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73404770	0.86[ASN][1000 genomes]
rs73404772	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73406513	0.80[ASN][1000 genomes]
rs73406600	0.80[ASN][1000 genomes]
rs73410967	0.80[ASN][1000 genomes]
rs9461531	0.81[EUR][1000 genomes]
rs9461532	0.81[EUR][1000 genomes]
rs9461533	0.81[EUR][1000 genomes]
rs9468550	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883530	chr6:29645038-29677641	Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv20940	chr6:29653954-29923410	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv970675	chr6:29657036-29692268	Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv428475	chr6:29659525-29763392	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv428139	chr6:29659525-29892317	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv427749	chr6:29659525-29975144	Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	nsv508397	chr6:29663132-29761448	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	esv1821077	chr6:29670915-29726207	Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	esv1794141	chr6:29670915-29765814	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29664000-29690600	Weak transcription	Right Atrium	heart
2	chr6:29670200-29678200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:29670800-29678200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:29673200-29675800	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr6:29673200-29676200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr6:29673200-29676400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr6:29673200-29677000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr6:29673400-29676000	Enhancers	Primary T cells fromperipheralblood	blood
9	chr6:29673400-29676200	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr6:29673400-29676200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr6:29673400-29676400	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr6:29673400-29678600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:29673600-29675400	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr6:29673600-29676000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr6:29673600-29676200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr6:29673600-29676400	Enhancers	Primary T cells from cord blood	blood
17	chr6:29673600-29676800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr6:29674000-29676000	Weak transcription	Primary B cells from peripheral blood	blood
19	chr6:29674200-29676000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr6:29674200-29676600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr6:29674800-29677200	Weak transcription	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links