Variant report

Variant	rs12486399
Chromosome Location	chr3:178842822-178842823
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	chr3:178842346..178844303-chr3:179040865..179042396,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000121864	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10936993	0.94[EUR][1000 genomes]
rs12497857	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13320527	0.94[EUR][1000 genomes]
rs1517585	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2865084	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28697961	0.94[EUR][1000 genomes]
rs45455192	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4854906	0.94[EUR][1000 genomes]
rs4854940	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4854955	0.94[EUR][1000 genomes]
rs4854976	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855094	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60713157	0.84[EUR][1000 genomes]
rs61404287	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61796464	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61796465	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61796466	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61796467	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61798205	0.84[EUR][1000 genomes]
rs61798206	0.84[EUR][1000 genomes]
rs61798207	0.84[EUR][1000 genomes]
rs61798211	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61798213	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6443623	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6791215	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6804195	0.84[EUR][1000 genomes]
rs73051979	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73054091	0.90[EUR][1000 genomes]
rs7374077	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7615259	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs950486	0.94[EUR][1000 genomes]
rs9758036	0.84[EUR][1000 genomes]
rs9812252	0.94[EUR][1000 genomes]
rs9819654	0.94[EUR][1000 genomes]
rs9823044	0.94[EUR][1000 genomes]
rs9833206	0.94[EUR][1000 genomes]
rs9860843	0.96[EUR][1000 genomes]
rs9872959	0.94[EUR][1000 genomes]
rs9878005	0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv461026	chr3:178661814-178886609	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv592649	chr3:178661814-178886609	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers 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 miRNA target site	22 gene(s)	inside rSNPs	diseases
5	esv1792927	chr3:178734558-178877169	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	esv1841799	chr3:178739594-178884337	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv878037	chr3:178825910-178871906	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	esv3354111	chr3:178833305-179156908	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:0 , 50 per page) page:

No data

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links