Variant report

Variant	rs12494261
Chromosome Location	chr3:161010285-161010286
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:161009125..161010878-chr3:161045912..161048528,2	MCF-7	breast:
2	chr3:161000404..161005732-chr3:161006848..161011862,5	MCF-7	breast:
3	chr3:160818828..160822903-chr3:161006753..161012586,7	MCF-7	breast:
4	chr3:161009145..161011846-chr3:161137237..161140694,4	MCF-7	breast:
5	chr3:161006306..161018540-chr3:161080036..161092321,36	MCF-7	breast:
6	chr3:161008825..161011229-chr3:161019509..161021871,2	MCF-7	breast:
7	chr3:161006869..161011120-chr3:161039575..161043501,7	MCF-7	breast:
8	chr3:161006300..161011924-chr3:161012842..161019057,8	MCF-7	breast:
9	chr3:160990275..160995115-chr3:161003197..161013240,19	MCF-7	breast:
10	chr3:160985097..160988877-chr3:161008569..161012184,4	MCF-7	breast:
11	chr3:161009005..161010540-chr3:161015594..161017754,2	MCF-7	breast:
12	chr3:161003253..161016100-chr3:161121496..161137189,33	MCF-7	breast:
13	chr3:161006401..161012112-chr3:161031973..161037314,13	MCF-7	breast:
14	chr3:161009839..161012160-chr3:161055660..161057581,2	MCF-7	breast:
15	chr3:161009978..161012586-chr3:161040587..161043038,3	MCF-7	breast:
16	chr3:161004827..161016513-chr3:161081728..161095319,56	MCF-7	breast:
17	chr3:161001819..161012846-chr3:161052557..161065154,32	MCF-7	breast:
18	chr3:161009100..161011704-chr3:161125007..161126945,2	MCF-7	breast:
19	chr3:160995830..160998585-chr3:161007446..161010411,2	MCF-7	breast:
20	chr3:161007104..161011008-chr3:161031241..161034660,5	MCF-7	breast:
21	chr3:161007555..161015806-chr3:161127103..161142651,19	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000169251	Chromatin interaction
ENSG00000196542	Chromatin interaction
ENSG00000243838	Chromatin interaction
ENSG00000169255	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs12488318	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1471440	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1478567	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs163138	0.88[ASN][1000 genomes]
rs336544	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs336545	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs336546	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs336564	0.88[ASN][1000 genomes]
rs336565	0.88[ASN][1000 genomes]
rs336566	0.88[ASN][1000 genomes]
rs336571	0.86[ASN][1000 genomes]
rs336573	0.87[ASN][1000 genomes]
rs336574	0.87[ASN][1000 genomes]
rs336576	0.87[ASN][1000 genomes]
rs336581	0.88[ASN][1000 genomes]
rs336584	0.88[ASN][1000 genomes]
rs336587	0.88[ASN][1000 genomes]
rs336588	0.88[ASN][1000 genomes]
rs336592	0.88[ASN][1000 genomes]
rs419703	0.84[ASN][1000 genomes]
rs4429651	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4487256	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs455739	0.86[ASN][1000 genomes]
rs458197	0.85[ASN][1000 genomes]
rs459067	0.85[ASN][1000 genomes]
rs461616	0.86[ASN][1000 genomes]
rs462081	0.86[ASN][1000 genomes]
rs57201455	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62278055	0.92[ASN][1000 genomes]
rs62279860	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62279861	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62279862	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62279892	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73160351	0.86[ASN][1000 genomes]
rs73160362	0.93[ASN][1000 genomes]
rs73162530	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9290072	0.86[ASN][1000 genomes]
rs9290075	0.99[ASN][1000 genomes]
rs978933	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9811833	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9812083	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9827833	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9828189	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9828231	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9831725	0.90[ASN][1000 genomes]
rs9836094	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9839404	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9857946	0.86[ASN][1000 genomes]
rs9859045	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9876553	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1015063	chr3:160918307-161024070	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv829770	chr3:160989573-161069223	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160994600-161016800	Weak transcription	Right Ventricle	heart
2	chr3:161009800-161013000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:161009800-161016600	Weak transcription	Pancreas	Pancrea
4	chr3:161010000-161013000	Weak transcription	Stomach Mucosa	stomach
5	chr3:161010000-161015000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:161010200-161013000	Weak transcription	Esophagus	oesophagus
7	chr3:161010200-161013000	Weak transcription	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links