Variant report

Variant	rs12247470
Chromosome Location	chr10:6362679-6362680
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:6362567..6365351-chr10:6373129..6375526,2	MCF-7	breast:
2	chr10:6244843..6247041-chr10:6362405..6364804,2	MCF-7	breast:
3	chr10:6337823..6339767-chr10:6360899..6362837,2	MCF-7	breast:
4	chr10:6241505..6246812-chr10:6355218..6363190,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170525	Chromatin interaction
ENSG00000213994	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1005762	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1005763	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1005764	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12098455	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12241717	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12243287	0.91[AFR][1000 genomes]
rs12249235	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12250330	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12250469	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1557104	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1557106	0.96[AFR][1000 genomes]
rs1557107	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1054044	chr10:6155144-6487217	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv894836	chr10:6246678-6435374	Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv430123	chr10:6309402-6448384	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv430125	chr10:6322167-6477267	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv1053440	chr10:6354798-6669469	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6349400-6369800	Weak transcription	Adipose Nuclei	Adipose
2	chr10:6354200-6369200	Weak transcription	Brain Hippocampus Middle	brain
3	chr10:6355000-6363600	Weak transcription	Brain Cingulate Gyrus	brain
4	chr10:6356000-6388200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr10:6356200-6377600	Weak transcription	Ovary	ovary
6	chr10:6357000-6369000	Weak transcription	Brain Substantia Nigra	brain
7	chr10:6357200-6397400	Weak transcription	Pancreas	Pancrea
8	chr10:6357400-6368400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr10:6358600-6373600	Weak transcription	Colon Smooth Muscle	Colon
10	chr10:6358800-6364200	Enhancers	Primary B cells from peripheral blood	blood
11	chr10:6360000-6363800	Enhancers	Primary B cells from cord blood	blood
12	chr10:6360600-6363000	Weak transcription	A549	lung
13	chr10:6361400-6375200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr10:6361600-6374600	Weak transcription	Dnd41	blood
15	chr10:6361800-6364000	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr10:6362400-6362800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr10:6362400-6363000	Genic enhancers	Aorta	Aorta
18	chr10:6362600-6362800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr10:6362600-6362800	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr10:6362600-6363000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr10:6362600-6363000	Bivalent Enhancer	GM12878-XiMat	blood
22	chr10:6362600-6370000	Weak transcription	Skeletal Muscle Male	skeletal muscle

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