Variant report

Variant	rs6539127
Chromosome Location	chr12:104576695-104576696
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104570742..104573318-chr12:104574956..104577002,2	K562	blood:
2	chr12:104566313..104569865-chr12:104572688..104576807,3	K562	blood:
3	chr12:104530299..104532759-chr12:104575223..104579205,3	MCF-7	breast:
4	chr12:104575420..104578369-chr12:104681215..104683180,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000120837	Chromatin interaction
ENSG00000198431	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11111911	0.84[AMR][1000 genomes]
rs11111937	1.00[ASN][1000 genomes]
rs11111942	1.00[ASN][1000 genomes]
rs11111969	1.00[ASN][1000 genomes]
rs11112015	1.00[ASN][1000 genomes]
rs12809773	1.00[ASN][1000 genomes]
rs12812451	1.00[ASN][1000 genomes]
rs12813601	1.00[ASN][1000 genomes]
rs12819539	1.00[ASN][1000 genomes]
rs12826196	1.00[ASN][1000 genomes]
rs12828655	1.00[ASN][1000 genomes]
rs34309392	1.00[ASN][1000 genomes]
rs34811234	1.00[ASN][1000 genomes]
rs34863477	1.00[ASN][1000 genomes]
rs35392305	1.00[ASN][1000 genomes]
rs35453744	1.00[ASN][1000 genomes]
rs35473944	1.00[ASN][1000 genomes]
rs35653685	1.00[ASN][1000 genomes]
rs35822062	1.00[ASN][1000 genomes]
rs35844634	1.00[ASN][1000 genomes]
rs35945288	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964733	1.00[ASN][1000 genomes]
rs4964778	1.00[ASN][1000 genomes]
rs66554757	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71466293	1.00[ASN][1000 genomes]
rs71466302	1.00[ASN][1000 genomes]
rs7294701	1.00[ASN][1000 genomes]
rs7305137	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311508	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7313536	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7978310	1.00[ASN][1000 genomes]
rs7979945	1.00[ASN][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	nsv1045725	chr12:104524153-104614108	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	n/a
2	nsv541586	chr12:104524153-104614108	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	n/a
3	esv1842062	chr12:104531180-104638773	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	n/a
4	nsv899493	chr12:104548613-104703228	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv899494	chr12:104561521-104806232	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104573600-104576800	Enhancers	Colon Smooth Muscle	Colon
2	chr12:104574000-104576800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr12:104574200-104576800	Enhancers	Muscle Satellite Cultured Cells	--
4	chr12:104574200-104576800	Enhancers	NHLF	lung
5	chr12:104574200-104577000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr12:104574200-104577000	Enhancers	Osteobl	bone
7	chr12:104574400-104576800	Enhancers	Rectal Smooth Muscle	rectum
8	chr12:104574400-104577000	Enhancers	Adipose Nuclei	Adipose
9	chr12:104574800-104576800	Enhancers	Placenta	Placenta
10	chr12:104575000-104577400	Enhancers	Pancreas	Pancrea
11	chr12:104575200-104576800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr12:104575200-104576800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr12:104575400-104576800	Enhancers	A549	lung
14	chr12:104575400-104577200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr12:104576000-104577400	Enhancers	Aorta	Aorta
16	chr12:104576200-104576800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr12:104576600-104576800	Weak transcription	Stomach Smooth Muscle	stomach
18	chr12:104576600-104577000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:104576600-104577600	Enhancers	Hela-S3	cervix
20	chr12:104576600-104578200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links