Variant report

Variant	rs56026497
Chromosome Location	chr9:79166953-79166954
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	POLR2A	chr9:79166940-79167064	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:79073145..79075649-chr9:79165420..79167913,3	MCF-7	breast:
2	chr9:79166569..79168474-chr9:79175522..79177682,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000219149	TF binding region
ENSG00000187210	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10119518	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10121652	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10123325	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10521473	1.00[EUR][1000 genomes]
rs11144991	1.00[EUR][1000 genomes]
rs11144993	1.00[EUR][1000 genomes]
rs12336287	1.00[EUR][1000 genomes]
rs12337785	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12340696	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12342460	1.00[EUR][1000 genomes]
rs12344065	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12345816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12351220	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1346041	1.00[EUR][1000 genomes]
rs17062959	1.00[EUR][1000 genomes]
rs17062964	1.00[EUR][1000 genomes]
rs17062967	1.00[EUR][1000 genomes]
rs17081141	1.00[EUR][1000 genomes]
rs17081142	1.00[EUR][1000 genomes]
rs2015354	1.00[EUR][1000 genomes]
rs28470485	1.00[EUR][1000 genomes]
rs28576740	1.00[EUR][1000 genomes]
rs28587388	1.00[EUR][1000 genomes]
rs28635278	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55725331	1.00[EUR][1000 genomes]
rs55825540	1.00[EUR][1000 genomes]
rs56143215	1.00[EUR][1000 genomes]
rs56145880	1.00[EUR][1000 genomes]
rs56679509	1.00[EUR][1000 genomes]
rs57802610	1.00[EUR][1000 genomes]
rs60467484	1.00[EUR][1000 genomes]
rs6560530	1.00[EUR][1000 genomes]
rs7044442	1.00[EUR][1000 genomes]
rs73449878	1.00[EUR][1000 genomes]
rs73449890	1.00[EUR][1000 genomes]
rs73449896	1.00[EUR][1000 genomes]
rs73452104	1.00[EUR][1000 genomes]
rs73454158	1.00[EUR][1000 genomes]
rs73650254	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73650286	1.00[EUR][1000 genomes]
rs73650287	1.00[EUR][1000 genomes]
rs73650987	1.00[EUR][1000 genomes]
rs73650989	1.00[EUR][1000 genomes]
rs73650990	1.00[EUR][1000 genomes]
rs73650991	1.00[EUR][1000 genomes]
rs73650992	1.00[EUR][1000 genomes]
rs73650994	1.00[EUR][1000 genomes]
rs73650996	1.00[EUR][1000 genomes]
rs73650997	1.00[EUR][1000 genomes]
rs73650998	1.00[EUR][1000 genomes]
rs73650999	1.00[EUR][1000 genomes]
rs73651000	1.00[EUR][1000 genomes]
rs73651001	1.00[EUR][1000 genomes]
rs7848842	1.00[EUR][1000 genomes]
rs7850310	1.00[EUR][1000 genomes]
rs7855826	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7867080	1.00[EUR][1000 genomes]
rs7875591	1.00[EUR][1000 genomes]
rs867646	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv893479	chr9:78971253-79275226	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv949417	chr9:79078703-79282589	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv893480	chr9:79115844-79222584	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79137200-79173600	Weak transcription	Primary B cells from cord blood	blood
2	chr9:79154200-79171400	Weak transcription	Osteobl	bone
3	chr9:79154200-79172400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr9:79154400-79171600	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr9:79165200-79167400	Enhancers	Fetal Intestine Large	intestine
6	chr9:79165400-79167800	Enhancers	Duodenum Mucosa	Duodenum
7	chr9:79165400-79172400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr9:79165600-79167800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr9:79165600-79175600	Weak transcription	Gastric	stomach
10	chr9:79166200-79167000	Weak transcription	Stomach Mucosa	stomach
11	chr9:79166400-79167800	Enhancers	Fetal Intestine Small	intestine
12	chr9:79166800-79168600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links